Structure of Human Enterovirus 70 and Its Inhibition by Capsid-Binding Compounds

. 2022 Sep 14 ; 96 (17) : e0060422. [epub] 20220808

Jazyk angličtina Země Spojené státy americké Médium print-electronic

Typ dokumentu časopisecké články, práce podpořená grantem

Perzistentní odkaz   https://www.medvik.cz/link/pmid35939401

Enterovirus 70 (EV70) is a human pathogen belonging to the family Picornaviridae. EV70 is transmitted by eye secretions and causes acute hemorrhagic conjunctivitis, a serious eye disease. Despite the severity of the disease caused by EV70, its structure is unknown. Here, we present the structures of the EV70 virion, altered particle, and empty capsid determined by cryo-electron microscopy. The capsid of EV70 is composed of the subunits VP1, VP2, VP3, and VP4. The partially collapsed hydrophobic pocket located in VP1 of the EV70 virion is not occupied by a pocket factor, which is commonly present in other enteroviruses. Nevertheless, we show that the pocket can be targeted by the antiviral compounds WIN51711 and pleconaril, which block virus infection. The inhibitors prevent genome release by stabilizing EV70 particles. Knowledge of the structures of complexes of EV70 with inhibitors will enable the development of capsid-binding therapeutics against this virus. IMPORTANCE Globally distributed enterovirus 70 (EV70) causes local outbreaks of acute hemorrhagic conjunctivitis. The discharge from infected eyes enables the high-efficiency transmission of EV70 in overcrowded areas with low hygienic standards. Currently, only symptomatic treatments are available. We determined the structures of EV70 in its native form, the genome release intermediate, and the empty capsid resulting from genome release. Furthermore, we elucidated the structures of EV70 in complex with two inhibitors that block virus infection, and we describe the mechanism of their binding to the virus capsid. These results enable the development of therapeutics against EV70.

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Bruu A-L. 2002. Enteroviruses: polioviruses, coxsackieviruses, echoviruses and newer enteroviruses, p 44–45. In Haaheim LR, Pattison JR, Whitley RJ (ed), A practical guide to clinical virology, 2nd ed. John Wiley & Sons Ltd, Chichester, United Kingdom.

Mirkovic RR, Kono R, Yin-Murphy M, Sohier R, Schmidt NJ, Melnick JL. 1973. Enterovirus type 70: the etiologic agent of pandemic acute haemorrhagic conjunctivitis. Bull World Health Organ 49:341–346. PubMed PMC

Chatterjee S, Quarcoopome CO, Apenteng A. 1970. Unusual type of epidemic conjunctivitis in Ghana. Br J Ophthalmol 54:628–630. 10.1136/bjo.54.9.628. PubMed DOI PMC

Shulman LM, Manor Y, Azar R, Handsher R, Vonsover A, Mendelson E, Rothman S, Hassin D, Halmut T, Abramovitz B, Varsano N. 1997. Identification of a new strain of fastidious enterovirus 70 as the causative agent of an outbreak of hemorrhagic conjunctivitis. J Clin Microbiol 35:2145–2149. 10.1128/jcm.35.8.2145-2149.1997. PubMed DOI PMC

Maitreyi RS, Dar L, Muthukumar A, Vajpayee M, Xess I, Vajpayee RB, Seth P, Broor S. 1999. Acute hemorrhagic conjunctivitis due to enterovirus 70 in India. Emerg Infect Dis 5:267–269. 10.3201/eid0502.990212. PubMed DOI PMC

Hossain MM, Glass RI, Khan MU, Huq F, Hierholzer JC. 1983. Outbreak of enterovirus 70 conjunctivitis in Bangladesh—1981. Trans R Soc Trop Med Hyg 77:217–218. 10.1016/0035-9203(83)90075-5. PubMed DOI

Bern C, Pallansch MA, Gary HE, Alexander JP, Török TJ, Glass RI, Anderson LJ. 1992. Acute hemorrhagic conjunctivitis due to enterovirus 70 in American Samoa: serum-neutralizing antibodies and sex-specific protection. Am J Epidemiol 136:1502–1506. 10.1093/oxfordjournals.aje.a116471. PubMed DOI

Uchio E, Yamazaki K, Ishikawa H, Matsunaga I, Asato Y, Aoki K, Ohno S. 1999. An epidemic of acute haemorrhagic conjunctivitis caused by enterovirus 70 in Okinawa, Japan, in 1994. Graefes Arch Clin Exp Ophthalmol 237:568–572. 10.1007/s004170050280. PubMed DOI

Ramia S, Arif M. 1990. Isolation of enterovirus 70 (EV70) from patients with acute haemorrhagic conjunctivitis in two areas of Saudi Arabia. Trans R Soc Trop Med Hyg 84:139–140. 10.1016/0035-9203(90)90409-8. PubMed DOI

Katiyar BC, Misra S, Singh RB, Singh AK, Gupta S, Gulati AK, Christopher S, John TJ. 1983. Adult polio‐like syndrome following enterovirus 70 conjunctivitis (natural history of the disease). Acta Neurol Scand 67:263–274. 10.1111/j.1600-0404.1983.tb04575.x. PubMed DOI

Higgins PG. 1982. Enteroviral conjunctivitis and its neurological complications. Arch Virol 73:91–101. 10.1007/BF01314718. PubMed DOI

Chopra HC, Mason MM. 1970. A new virus in a spontaneous mammary tumor of a rhesus monkey. Cancer Res 30:2081–2086. PubMed

Chen D, Duggan C, Texada DE, Reden TB, Kooragayala LM, Langford MP. 2005. Immunogenicity of enterovirus 70 capsid protein VP1 and its non-overlapping N- and C-terminal fragments. Antiviral Res 66:111–117. 10.1016/j.antiviral.2005.02.004. PubMed DOI

Park K-B, Lim B-K, Ye MB, Chung S-Y, Nam J-H. 2012. A peptide vaccine based on a B-cell epitope on the VP1 protein of enterovirus 70 induces a strong antibody response. Acta Virol 56:337–342. 10.4149/av_2012_04_337. PubMed DOI

Ryan MD, Jenkins O, Hughes PJ, Brown A, Knowles NJ, Booth D, Minor PD, Almond JW. 1990. The complete nucleotide sequence of enterovirus type 70: relationships with other members of the Picornaviridae. J Gen Virol 71:2291–2299. 10.1099/0022-1317-71-10-2291. PubMed DOI

Rossmann MG, Arnold E, Erickson JW, Frankenberger EA, Griffith JP, Hecht HJ, Johnson JE, Kamer G, Luo M, Mosser AG, Rueckert RR, Sherry B, Vriend G. 1985. Structure of a human common cold virus and functional relationship to other picornaviruses. Nature 317:145–153. 10.1038/317145a0. PubMed DOI

Hogle JM, Chow M, Filman DJ. 1985. Three-dimensional structure of poliovirus at 2.9 Å resolution. Science 229:1358–1365. 10.1126/science.2994218. PubMed DOI

Tuthill TJ, Groppelli E, Hogle JM, Rowlands DJ. 2010. Picornaviruses. Curr Top Microbiol Immunol 343:43–89. 10.1007/82_2010_37. PubMed DOI PMC

Karnauchow TM, Dawe S, Lublin DM, Dimock K. 1998. Short consensus repeat domain 1 of decay-accelerating factor is required for enterovirus 70 binding. J Virol 72:9380–9383. 10.1128/JVI.72.11.9380-9383.1998. PubMed DOI PMC

Karnauchow TM, Tolson DL, Harrison BA, Altman E, Lublin DM, Dimock K. 1996. The HeLa cell receptor for enterovirus 70 is decay-accelerating factor (CD55). J Virol 70:5143–5152. 10.1128/JVI.70.8.5143-5152.1996. PubMed DOI PMC

Newcombe NG, Johansson ES, Au G, Lindberg AM, Barry RD, Shafren DR. 2004. Enterovirus capsid interactions with decay-accelerating factor mediate lytic cell infection. J Virol 78:1431–1439. 10.1128/jvi.78.3.1431-1439.2004. PubMed DOI PMC

Yoder JD, Cifuente JO, Pan J, Bergelson JM, Hafenstein S. 2012. The crystal structure of a coxsackievirus B3-RD variant and a refined 9-angstrom cryo-electron microscopy reconstruction of the virus complexed with decay-accelerating factor (DAF) provide a new footprint of DAF on the virus surface. J Virol 86:12571–12581. 10.1128/JVI.01592-12. PubMed DOI PMC

Plevka P, Hafenstein S, Harris KG, Cifuente JO, Zhang Y, Bowman VD, Chipman PR, Bator CM, Lin F, Medof ME, Rossmann MG. 2010. Interaction of decay-accelerating factor with echovirus 7. J Virol 84:12665–12674. 10.1128/JVI.00837-10. PubMed DOI PMC

He Y, Lin F, Chipman PR, Bator CM, Baker TS, Shoham M, Kuhn RJ, Medof ME, Rossmann MG. 2002. Structure of decay-accelerating factor bound to echovirus 7: a virus-receptor complex. Proc Natl Acad Sci USA 99:10325–10329. 10.1073/pnas.152161599. PubMed DOI PMC

Haddad A, Nokhbeh MR, Alexander DA, Dawe SJ, Grisé C, Gulzar N, Dimock K. 2004. Binding to decay-accelerating factor is not required for infection of human leukocyte cell lines by enterovirus 70. J Virol 78:2674–2681. 10.1128/jvi.78.6.2674-2681.2004. PubMed DOI PMC

Nokhbeh MR, Hazra S, Alexander DA, Khan A, McAllister M, Suuronen EJ, Griffith M, Dimock K. 2005. Enterovirus 70 binds to different glycoconjugates containing α2,3-linked sialic acid on different cell lines. J Virol 79:7087–7094. 10.1128/JVI.79.11.7087-7094.2005. PubMed DOI PMC

Alexander DA, Dimock K. 2002. Sialic acid functions in enterovirus 70 binding and infection. J Virol 76:11265–11272. 10.1128/jvi.76.22.11265-11272.2002. PubMed DOI PMC

Yamayoshi S, Fujii K, Koike S. 2014. Receptors for enterovirus 71. Emerg Microbes Infect 3:e53. 10.1038/emi.2014.49. PubMed DOI PMC

Rossmann MG, He Y, Kuhn RJ. 2002. Picornavirus-receptor interactions. Trends Microbiol 10:324–331. 10.1016/s0966-842x(02)02383-1. PubMed DOI

Hrebík D, Füzik T, Gondová M, Šmerdová L, Adamopoulos A, Šedo O, Zdráhal Z, Plevka P. 2021. ICAM-1 induced rearrangements of capsid and genome prime rhinovirus 14 for activation and uncoating. Proc Natl Acad Sci USA 118:e2024251118. 10.1073/pnas.2024251118. PubMed DOI PMC

Wang K, Zhu L, Sun Y, Li M, Zhao X, Cui L, Zhang L, Gao GF, Zhai W, Zhu F, Rao Z, Wang X. 2020. Structures of echovirus 30 in complex with its receptors inform a rational prediction for enterovirus receptor usage. Nat Commun 11:4421. 10.1038/s41467-020-18251-9. PubMed DOI PMC

Zhou D, Zhao Y, Kotecha A, Fry EE, Kelly JT, Wang X, Rao Z, Rowlands DJ, Ren J, Stuart DI. 2019. Unexpected mode of engagement between enterovirus 71 and its receptor SCARB2. Nat Microbiol 4:414–419. 10.1038/s41564-018-0319-z. PubMed DOI

He Y, Chipman PR, Howitt J, Bator CM, Whitt MA, Baker TS, Kuhn RJ, Anderson CW, Freimuth P, Rossmann MG. 2001. Interaction of coxsackievirus B3 with the full length coxsackievirus-adenovirus receptor. Nat Struct Biol 8:874–878. 10.1038/nsb1001-874. PubMed DOI PMC

Strauss M, Filman DJ, Belnap DM, Cheng N, Noel RT, Hogle JM. 2015. Nectin-like interactions between poliovirus and its receptor trigger conformational changes associated with cell entry. J Virol 89:4143–4157. 10.1128/JVI.03101-14. PubMed DOI PMC

Liu Y, Sheng J, Fokine A, Meng G, Shin W-H, Long F, Kuhn RJ, Kihara D, Rossmann MG. 2015. Structure and inhibition of EV-D68, a virus that causes respiratory illness in children. Science 347:71–74. 10.1126/science.1261962. PubMed DOI PMC

Oliveira MA, Zhao R, Lee W-M, Kremer MJ, Minor I, Rueckert RR, Diana GD, Pevear DC, Dutko FJ, McKinlay MA, Rossmann MG. 1993. The structure of human rhinovirus 16. Structure 1:51–68. 10.1016/0969-2126(93)90008-5. PubMed DOI

Verdaguer N, Blaas D, Fita I. 2000. Structure of human rhinovirus serotype 2 (HRV2). J Mol Biol 300:1179–1194. 10.1006/jmbi.2000.3943. PubMed DOI

Filman DJ, Syed R, Chow M, Macadam AJ, Minor PD, Hogle JM. 1989. Structural factors that control conformational transitions and serotype specificity in type 3 poliovirus. EMBO J 8:1567–1579. 10.1002/j.1460-2075.1989.tb03541.x. PubMed DOI PMC

Muckelbauer JK, Kremer M, Minor I, Diana G, Dutko FJ, Groarke J, Pevear DC, Rossmann MG. 1995. The structure of coxsackievirus B3 at 3.5 Å resolution. Structure 3:653–667. 10.1016/s0969-2126(01)00201-5. PubMed DOI

Plevka P, Perera R, Yap ML, Cardosa J, Kuhn RJ, Rossmann MG. 2013. Structure of human enterovirus 71 in complex with a capsid-binding inhibitor. Proc Natl Acad Sci USA 110:5463–5467. 10.1073/pnas.1222379110. PubMed DOI PMC

Smyth M, Pettitt T, Symonds A, Martin J. 2003. Identification of the pocket factors in a picornavirus. Arch Virol 148:1225–1233. 10.1007/s00705-002-0974-4. PubMed DOI

Ren J, Wang X, Hu Z, Gao Q, Sun Y, Li X, Porta C, Walter TS, Gilbert RJ, Zhao Y, Axford D, Williams M, McAuley K, Rowlands DJ, Yin W, Wang J, Stuart DI, Rao Z, Fry EE. 2013. Picornavirus uncoating intermediate captured in atomic detail. Nat Commun 4:1929. 10.1038/ncomms2889. PubMed DOI PMC

Buchta D, Füzik T, Hrebík D, Levdansky Y, Sukeník L, Mukhamedova L, Moravcová J, Vácha R, Plevka P. 2019. Enterovirus particles expel capsid pentamers to enable genome release. Nat Commun 10:1138. 10.1038/s41467-019-09132-x. PubMed DOI PMC

Levy HC, Bostina M, Filman DJ, Hogle JM. 2010. Catching a virus in the act of RNA release: a novel poliovirus uncoating intermediate characterized by cryo-electron microscopy. J Virol 84:4426–4441. 10.1128/JVI.02393-09. PubMed DOI PMC

Garriga D, Pickl-Herk A, Luque D, Wruss J, Castón JR, Blaas D, Verdaguer N. 2012. Insights into minor group rhinovirus uncoating: the X-ray structure of the HRV2 empty capsid. PLoS Pathog 8:e1002473. 10.1371/journal.ppat.1002473. PubMed DOI PMC

Wang X, Peng W, Ren J, Hu Z, Xu J, Lou Z, Li X, Yin W, Shen X, Porta C, Walter TS, Evans G, Axford D, Owen R, Rowlands DJ, Wang J, Stuart DI, Fry EE, Rao Z. 2012. A sensor-adaptor mechanism for enterovirus uncoating from structures of EV71. Nat Struct Mol Biol 19:424–429. 10.1038/nsmb.2255. PubMed DOI PMC

Shingler KL, Yoder JL, Carnegie MS, Ashley RE, Makhov AM, Conway JF, Hafenstein S. 2013. The enterovirus 71 A-particle forms a gateway to allow genome release: a cryoEM study of picornavirus uncoating. PLoS Pathog 9:e1003240. 10.1371/journal.ppat.1003240. PubMed DOI PMC

Hewat EA, Neumann E, Blaas D. 2002. The concerted conformational changes during human rhinovirus 2 uncoating. Mol Cell 10:317–326. 10.1016/s1097-2765(02)00603-2. PubMed DOI

De Palma AM, Vliegen I, De Clercq E, Neyts J. 2008. Selective inhibitors of picornavirus replication. Med Res Rev 28:823–884. 10.1002/med.20125. PubMed DOI

Otto MJ, Fox MP, Fancher MJ, Kuhrt MF, Diana GD, McKinlay MA. 1985. In vitro activity of WIN 51711, a new broad-spectrum antipicornavirus drug. Antimicrob Agents Chemother 27:883–886. 10.1128/AAC.27.6.883. PubMed DOI PMC

Zeichhardt H, Otto MJ, McKinlay MA, Willingmann P, Habermehl K-O. 1987. Inhibition of poliovirus uncoating by disoxaril (WIN 51711). Virology 160:281–285. 10.1016/0042-6822(87)90075-4. PubMed DOI

Hiremath CN, Grant RA, Filman DJ, Hogle JM. 1995. Binding of the antiviral drug WIN51711 to the Sabin strain of type 3 poliovirus: structural comparison with drug binding in rhinovirus 14. Acta Crystallogr D Biol Crystallogr 51:473–489. 10.1107/S090744499401084X. PubMed DOI

Pevear DC, Tull TM, Seipel ME, Groarke JM. 1999. Activity of pleconaril against enteroviruses. Antimicrob Agents Chemother 43:2109–2115. 10.1128/AAC.43.9.2109. PubMed DOI PMC

Smith TJ, Kremer MJ, Luo M, Vriend G, Arnold E, Kamer G, Rossmann MG, McKinlay MA, Diana GD, Otto MJ. 1986. The site of attachment in human rhinovirus 14 for antiviral agents that inhibit uncoating. Science 233:1286–1293. 10.1126/science.3018924. PubMed DOI

Thibaut HJ, De Palma AM, Neyts J. 2012. Combating enterovirus replication: state-of-the-art on antiviral research. Biochem Pharmacol 83:185–192. 10.1016/j.bcp.2011.08.016. PubMed DOI

Liu Y, Sheng J, van Vliet ALW, Buda G, van Kuppeveld FJM, Rossmann MG. 2018. Molecular basis for the acid-initiated uncoating of human enterovirus D68. Proc Natl Acad Sci USA 115:E12209–E12217. 10.1073/pnas.1803347115. PubMed DOI PMC

Reimann BY, Zell R, Kandolf R. 1991. Mapping of a neutralizing antigenic site of coxsackievirus B4 by construction of an antigen chimera. J Virol 65:3475–3480. 10.1128/JVI.65.7.3475-3480.1991. PubMed DOI PMC

Zheng H, Wang J, Li B, Guo L, Li H, Song J, Yang Z, Li H, Fan H, Huang X, Long H, Cheng C, Chu M, He Z, Yu W, Li J, Gao Y, Ning R, Li N, Yang J, Wu Q, Shi H, Sun M, Liu L. 2018. A novel neutralizing antibody specific to the DE loop of VP1 can inhibit EV-D68 infection in mice. J Immunol 201:2557–2569. 10.4049/jimmunol.1800655. PubMed DOI

McPhee F, Zell R, Reimann BY, Hofschneider PH, Kandolf R. 1994. Characterization of the N-terminal part of the neutralizing antigenic site I of coxsackievirus B4 by mutation analysis of antigen chimeras. Virus Res 34:139–151. 10.1016/0168-1702(94)90096-5. PubMed DOI

Imamura T, Okamoto M, Nakakita S, Suzuki A, Saito M, Tamaki R, Lupisan S, Roy CN, Hiramatsu H, Sugawara K, Mizuta K, Matsuzaki Y, Suzuki Y, Oshitani H, Perlman S. 2014. Antigenic and receptor binding properties of enterovirus 68. J Virol 88:2374–2384. 10.1128/JVI.03070-13. PubMed DOI PMC

Wang K, Zheng B, Zhang L, Cui L, Su X, Zhang Q, Guo Z, Guo Y, Zhang W, Zhu L, Zhu F, Rao Z, Wang X. 2020. Serotype specific epitopes identified by neutralizing antibodies underpin immunogenic differences in enterovirus B. Nat Commun 11:4419. 10.1038/s41467-020-18250-w. PubMed DOI PMC

Xu L, Zheng Q, Li S, He M, Wu Y, Li Y, Zhu R, Yu H, Hong Q, Jiang J, Li Z, Li S, Zhao H, Yang L, Hou W, Wang W, Ye X, Zhang J, Baker TS, Cheng T, Zhou ZH, Yan X, Xia N. 2017. Atomic structures of coxsackievirus A6 and its complex with a neutralizing antibody. Nat Commun 8:505. 10.1038/s41467-017-00477-9. PubMed DOI PMC

Zhao R, Pevear DC, Kremer MJ, Giranda VL, Kofron JA, Kuhn RJ, Rossmann MG. 1996. Human rhinovirus 3 at 3.0 Å resolution. Structure 4:1205–1220. 10.1016/s0969-2126(96)00128-1. PubMed DOI

Savolainen C, Blomqvist S, Mulders MN, Hovi T. 2002. Genetic clustering of all 102 human rhinovirus prototype strains: serotype 87 is close to human enterovirus 70. J Gen Virol 83:333–340. 10.1099/0022-1317-83-2-333. PubMed DOI

Oberste MS, Maher K, Schnurr D, Flemister MR, Lovchik JC, Peters H, Sessions W, Kirk C, Chatterjee N, Fuller S, Hanauer JM, Pallansch MA. 2004. Enterovirus 68 is associated with respiratory illness and shares biological features with both the enteroviruses and the rhinoviruses. J Gen Virol 85:2577–2584. 10.1099/vir.0.79925-0. PubMed DOI

Harutyunyan S, Kumar M, Sedivy A, Subirats X, Kowalski H, Köhler G, Blaas D. 2013. Viral uncoating is directional: exit of the genomic RNA in a common cold virus starts with the poly-(A) tail at the 3′-end. PLoS Pathog 9:e1003270. 10.1371/journal.ppat.1003270. PubMed DOI PMC

Zhao Y, Zhou D, Ni T, Karia D, Kotecha A, Wang X, Rao Z, Jones EY, Fry EE, Ren J, Stuart DI. 2020. Hand-foot-and-mouth disease virus receptor KREMEN1 binds the canyon of coxsackie virus A10. Nat Commun 11:38. 10.1038/s41467-019-13936-2. PubMed DOI PMC

He M, Xu L, Zheng Q, Zhu R, Yin Z, Zha Z, Lin Y, Yang L, Huang Y, Ye X, Li S, Hou W, Wu Y, Han J, Liu D, Li Z, Chen Z, Yu H, Que Y, Wang Y, Yan X, Zhang J, Gu Y, Zhou ZH, Cheng T, Li S, Xia N. 2020. Identification of antibodies with non-overlapping neutralization sites that target coxsackievirus A16. Cell Host Microbe 27:249–261.e5. 10.1016/j.chom.2020.01.003. PubMed DOI PMC

Fricks CE, Hogle JM. 1990. Cell-induced conformational change in poliovirus: externalization of the amino terminus of VP1 is responsible for liposome binding. J Virol 64:1934–1945. 10.1128/JVI.64.5.1934-1945.1990. PubMed DOI PMC

Lewis JK, Bothner B, Smith TJ, Siuzdak G. 1998. Antiviral agent blocks breathing of the common cold virus. Proc Natl Acad Sci USA 95:6774–6778. 10.1073/pnas.95.12.6774. PubMed DOI PMC

Zheng SQ, Palovcak E, Armache J, Verba KA, Cheng Y, Agard DA. 2017. MotionCor2—anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nat Methods 14:331–339. 10.1038/nmeth.4193. PubMed DOI PMC

Zhang K. 2016. Gctf: real-time CTF determination and correction. J Struct Biol 193:1–12. 10.1016/j.jsb.2015.11.003. PubMed DOI PMC

Wagner T, Merino F, Stabrin M, Moriya T, Antoni C, Apelbaum A, Hagel P, Sitsel O, Raisch T, Prumbaum D, Quentin D, Roderer D, Tacke S, Siebolds B, Schubert E, Shaikh TR, Lill P, Gatsogiannis C, Raunser S. 2019. SPHIRE-crYOLO is a fast and accurate fully automated particle picker for cryo-EM. Commun Biol 2:218. 10.1038/s42003-019-0437-z. PubMed DOI PMC

Punjani A, Rubinstein JL, Fleet DJ, Brubaker MA. 2017. CryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat Methods 14:290–296. 10.1038/nmeth.4169. PubMed DOI

Zivanov J, Nakane T, Forsberg BO, Kimanius D, Hagen WJH, Lindahl E, Scheres SHW. 2018. New tools for automated high-resolution cryo-EM structure determination in RELION-3. Elife 7:e42166. 10.7554/eLife.42166. PubMed DOI PMC

Zivanov J, Nakane T, Scheres SHW. 2020. Estimation of high-order aberrations and anisotropic magnification from cryo-EM data sets in RELION-3.1. IUCrJ 7:253–267. 10.1107/S2052252520000081. PubMed DOI PMC

Russo CJ, Henderson R. 2018. Ewald sphere correction using a single side-band image processing algorithm. Ultramicroscopy 187:26–33. 10.1016/j.ultramic.2017.11.001. PubMed DOI PMC

Chen S, McMullan G, Faruqi AR, Murshudov GN, Short JM, Scheres SHW, Henderson R. 2013. High-resolution noise substitution to measure overfitting and validate resolution in 3D structure determination by single particle electron cryomicroscopy. Ultramicroscopy 135:24–35. 10.1016/j.ultramic.2013.06.004. PubMed DOI PMC

Meng EC, Pettersen EF, Couch GS, Huang CC, Ferrin TE. 2006. Tools for integrated sequence-structure analysis with UCSF Chimera. BMC Bioinformatics 7:339. 10.1186/1471-2105-7-339. PubMed DOI PMC

Emsley P, Lohkamp B, Scott WG, Cowtan K. 2010. Features and development of Coot. Acta Crystallogr D Biol Crystallogr 66:486–501. 10.1107/S0907444910007493. PubMed DOI PMC

Liebschner D, Afonine PV, Baker ML, Bunkoczi G, Chen VB, Croll TI, Hintze B, Hung LW, Jain S, McCoy AJ, Moriarty NW, Oeffner RD, Poon BK, Prisant MG, Read RJ, Richardson JS, Richardson DC, Sammito MD, Sobolev OV, Stockwell DH, Terwilliger TC, Urzhumtsev AG, Videau LL, Williams CJ, Adams PD. 2019. Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Acta Crystallogr D Struct Biol 75:861–877. 10.1107/S2059798319011471. PubMed DOI PMC

Murshudov GN, Vagin AA, Dodson EJ. 1997. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr D Biol Crystallogr 53:240–255. 10.1107/S0907444996012255. PubMed DOI

Chen VB, Arendall WB, Headd JJ, Keedy DA, Immormino RM, Kapral GJ, Murray LW, Richardson JS, Richardson DC. 2010. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr D Biol Crystallogr 66:12–21. 10.1107/S0907444909042073. PubMed DOI PMC

Goddard TD, Huang CC, Meng EC, Pettersen EF, Couch GS, Morris JH, Ferrin TE. 2018. UCSF ChimeraX: meeting modern challenges in visualization and analysis. Protein Sci 27:14–25. 10.1002/pro.3235. PubMed DOI PMC

Landau M, Mayrose I, Rosenberg Y, Glaser F, Martz E, Pupko T, Ben-Tal N. 2005. ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures. Nucleic Acids Res 33:W299–W302. 10.1093/nar/gki370. PubMed DOI PMC

Taylor WR. 1986. The classification of amino acid conservation. J Theor Biol 119:205–218. 10.1016/s0022-5193(86)80075-3. PubMed DOI

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