Structure and replication of Pseudomonas aeruginosa phage JBD30

. 2024 Oct ; 43 (19) : 4384-4405. [epub] 20240814

Jazyk angličtina Země Velká Británie, Anglie Médium print-electronic

Typ dokumentu časopisecké články

Perzistentní odkaz   https://www.medvik.cz/link/pmid39143239

Grantová podpora
101043452 EC | European Research Council (ERC)
LX22NPO5103 EC | HORIZON EUROPE Framework Programme (Horizon Europe)
LM2023050 Ministerstvo Školství, Mládeže a Tělovýchovy (MŠMT)
LM2023042 Ministerstvo Školství, Mládeže a Tělovýchovy (MŠMT)
90254 Ministerstvo Školství, Mládeže a Tělovýchovy (MŠMT)
N/A Brno city municipality

Odkazy

PubMed 39143239
PubMed Central PMC11445458
DOI 10.1038/s44318-024-00195-1
PII: 10.1038/s44318-024-00195-1
Knihovny.cz E-zdroje

Bacteriophages are the most abundant biological entities on Earth, but our understanding of many aspects of their lifecycles is still incomplete. Here, we have structurally analysed the infection cycle of the siphophage Casadabanvirus JBD30. Using its baseplate, JBD30 attaches to Pseudomonas aeruginosa via the bacterial type IV pilus, whose subsequent retraction brings the phage to the bacterial cell surface. Cryo-electron microscopy structures of the baseplate-pilus complex show that the tripod of baseplate receptor-binding proteins attaches to the outer bacterial membrane. The tripod and baseplate then open to release three copies of the tape-measure protein, an event that is followed by DNA ejection. JBD30 major capsid proteins assemble into procapsids, which expand by 7% in diameter upon filling with phage dsDNA. The DNA-filled heads are finally joined with 180-nm-long tails, which bend easily because flexible loops mediate contacts between the successive discs of major tail proteins. It is likely that the structural features and replication mechanisms described here are conserved among siphophages that utilize the type IV pili for initial cell attachment.

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Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Crystallogr Sect Struct Biol 74:531–544 PubMed PMC

Aksyuk AA, Rossmann MG (2011) Bacteriophage assembly. Viruses 3:172–203 PubMed PMC

Arnaud C-A, Effantin G, Vivès C, Engilberge S, Bacia M, Boulanger P, Girard E, Schoehn G, Breyton C (2017) Bacteriophage T5 tail tube structure suggests a trigger mechanism for Siphoviridae DNA ejection. Nat Commun 8:1953 PubMed PMC

Augustyniak D, Olszak T, Drulis-Kawa Z (2022) Outer membrane vesicles (OMVs) of Pseudomonas aeruginosa provide passive resistance but not sensitization to LPS-specific phages. Viruses 14:121 PubMed PMC

Bae H-W, Cho Y-H (2013) Complete genome sequence of Pseudomonas aeruginosa podophage MPK7, which requires type IV pili for infection. Genome Announc 1:e00744–13 PubMed PMC

Bárdy P, Füzik T, Hrebík D, Pantůček R, Thomas Beatty J, Plevka P (2020) Structure and mechanism of DNA delivery of a gene transfer agent. Nat Commun 11:3034 PubMed PMC

Bayfield OW, Klimuk E, Winkler DC, Hesketh EL, Chechik M, Cheng N, Dykeman EC, Minakhin L, Ranson NA, Severinov K et al (2019) Cryo-EM structure and in vitro DNA packaging of a thermophilic virus with supersized T=7 capsids. Proc Natl Acad Sci USA 116:3556–3561 PubMed PMC

Bebeacua C, Lai L, Vegge CS, Brøndsted L, Van Heel M, Veesler D, Cambillau C (2013) Visualizing a complete siphoviridae member by single-particle electron microscopy: the structure of lactococcal phage TP901-1. J Virol 87:1061–1068 PubMed PMC

Berg HC (1993) Random walks in biology. Princeton University Press, Princeton, N.J

Bondy-Denomy J, Garcia B, Strum S, Du M, Rollins MF, Hidalgo-Reyes Y, Wiedenheft B, Maxwell KL, Davidson AR (2015) Multiple mechanisms for CRISPR–Cas inhibition by anti-CRISPR proteins. Nature 526:136–139 PubMed PMC

Bondy-Denomy J, Pawluk A, Maxwell KL, Davidson AR (2013) Bacteriophage genes that inactivate the CRISPR/Cas bacterial immune system. Nature 493:429–432 PubMed PMC

Bondy-Denomy J, Qian J, Westra ER, Buckling A, Guttman DS, Davidson AR, Maxwell KL (2016) Prophages mediate defense against phage infection through diverse mechanisms. ISME J 10:2854–2866 PubMed PMC

Boulanger P, Jacquot P, Plançon L, Chami M, Engel A, Parquet C, Herbeuval C, Letellier L (2008) Phage T5 straight tail fiber is a multifunctional protein acting as a tape measure and carrying fusogenic and muralytic activities. J Biol Chem 283:13556–13564 PubMed

Bradley DE (1972) Shortening of Pseudomonas aeruginosa pili after RNA-phage adsorption. J Gen Microbiol 72:303–319 PubMed

Bradley DE, Pitt TL (1974) Pilus-dependence of four Pseudomonas aeruginosa bacteriophages with non-contractile tails. J Gen Virol 24:1–15 PubMed

Burrows LL (2012) Pseudomonas aeruginosa twitching motility: type IV pili in action. Annu Rev Microbiol 66:493–520 PubMed

Campbell PL, Duda RL, Nassur J, Conway JF, Huet A (2020) Mobile loops and electrostatic interactions maintain the flexible tail tube of bacteriophage lambda. J Mol Biol 432:384–395 PubMed PMC

Chen D-H, Baker ML, Hryc CF, DiMaio F, Jakana J, Wu W, Dougherty M, Haase-Pettingell C, Schmid MF, Jiang W et al (2011) Structural basis for scaffolding-mediated assembly and maturation of a dsDNA virus. Proc Natl Acad Sci USA 108:1355–1360 PubMed PMC

Chiang P, Habash M, Burrows LL (2005) Disparate subcellular localization patterns of Pseudomonas aeruginosa Type IV pilus ATPases involved in twitching motility. J Bacteriol 187:829–839 PubMed PMC

Chibeu A, Ceyssens P-J, Hertveldt K, Volckaert G, Cornelis P, Matthijs S, Lavigne R (2009) The adsorption of Pseudomonas aeruginosa bacteriophage φKMV is dependent on expression regulation of type IV pili genes. FEMS Microbiol Lett 296:210–218 PubMed

Chowdhury S, Carter J, Rollins MF, Golden SM, Jackson RN, Hoffmann C, Nosaka L, Bondy-Denomy J, Maxwell KL, Davidson AR et al (2017) Structure reveals mechanisms of viral suppressors that intercept a CRISPR RNA-guided surveillance complex. Cell 169:47–57.e11 PubMed PMC

Clarke K, Gray GW, Reaveley DA (1967) The cell walls of Pseudomonas aeruginosa. General composition. Biochem J 105:749–754 PubMed PMC

Craig L, Forest KT, Maier B (2019) Type IV pili: dynamics, biophysics and functional consequences. Nat Rev Microbiol 17:429–440 PubMed

Cuervo A, Fàbrega-Ferrer M, Machón C, Conesa JJ, Fernández FJ, Pérez-Luque R, Pérez-Ruiz M, Pous J, Vega MC, Carrascosa JL et al (2019) Structures of T7 bacteriophage portal and tail suggest a viral DNA retention and ejection mechanism. Nat Commun 10:3746 PubMed PMC

Dedeo CL, Teschke CM, Alexandrescu AT (2020) Keeping it together: structures, functions, and applications of viral decoration proteins. Viruses 12:1163 PubMed PMC

Dion MB, Oechslin F, Moineau S (2020) Phage diversity, genomics and phylogeny. Nat Rev Microbiol 18:125–138 PubMed

Duda RL, Teschke CM (2019) The amazing HK97 fold: versatile results of modest differences. Curr Opin Virol 36:9–16 PubMed PMC

Edmonds L, Liu A, Kwan JJ, Avanessy A, Caracoglia M, Yang I, Maxwell KL, Rubenstein J, Davidson AR, Donaldson LW (2007) The NMR structure of the gpU tail-terminator protein from bacteriophage lambda: identification of sites contributing to Mg(II)-mediated oligomerization and biological function. J Mol Biol 365:175–186 PubMed

Ellison CK, Dalia TN, Dalia AB, Brun YV (2019) Real-time microscopy and physical perturbation of bacterial pili using maleimide-conjugated molecules. Nat Protoc 14:1803–1819 PubMed PMC

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

Evans R, O’Neill M, Pritzel A, Antropova N, Senior A, Green T, Žídek A, Bates R, Blackwell S, Yim J et al (2021) Protein complex prediction with AlphaFold-Multimer. Bioinformatics, 10.1101/2021.10.04.463034v1

Fang Q, Tang W-C, Fokine A, Mahalingam M, Shao Q, Rossmann MG, Rao VB (2022) Structures of a large prolate virus capsid in unexpanded and expanded states generate insights into the icosahedral virus assembly. Proc Natl Acad Sci USA 119:e2203272119 PubMed PMC

Fang Q, Tang W-C, Tao P, Mahalingam M, Fokine A, Rossmann MG, Rao VB (2020) Structural morphing in a symmetry-mismatched viral vertex. Nat Commun 11:1713 PubMed PMC

George M, Bukhari AI (1981) Heterogeneous host DNA attached to the left end of mature bacteriophage Mu DNA. Nature 292:175–176 PubMed

Goulet A, Spinelli S, Mahony J, Cambillau C (2020) Conserved and diverse traits of adhesion devices from siphoviridae recognizing proteinaceous or saccharidic receptors. Viruses 12:512 PubMed PMC

Guo F, Liu Z, Fang P-A, Zhang Q, Wright ET, Wu W, Zhang C, Vago F, Ren Y, Jakana J et al (2014) Capsid expansion mechanism of bacteriophage T7 revealed by multistate atomic models derived from cryo-EM reconstructions. Proc Natl Acad Sci USA 111:E4606–4614 PubMed PMC

Hagen WJH, Wan W, Briggs JAG (2017) Implementation of a cryo-electron tomography tilt-scheme optimized for high resolution subtomogram averaging. J Struct Biol 197:191–198 PubMed PMC

Hardy JM, Dunstan RA, Grinter R, Belousoff MJ, Wang J, Pickard D, Venugopal H, Dougan G, Lithgow T, Coulibaly F (2020) The architecture and stabilisation of flagellotropic tailed bacteriophages. Nat Commun 11:3748 PubMed PMC

Harvey H, Bondy-Denomy J, Marquis H, Sztanko KM, Davidson AR, Burrows LL (2017) Pseudomonas aeruginosa defends against phages through type IV pilus glycosylation. Nat Microbiol 3:47–52 PubMed

Holm L (2022) Dali server: structural unification of protein families. Nucleic Acids Res 50:W210–W215 PubMed PMC

Hrebík D, Štveráková D, Škubník K, Füzik T, Pantůček R, Plevka P (2019) Structure and genome ejection mechanism of Staphylococcus aureus phage P68. Sci Adv 5:eaaw7414 PubMed PMC

Huet A, Duda RL, Boulanger P, Conway JF (2019) Capsid expansion of bacteriophage T5 revealed by high resolution cryoelectron microscopy. Proc Natl Acad Sci USA 116:21037–21046 PubMed PMC

Ilca SL, Kotecha A, Sun X, Poranen MM, Stuart DI, Huiskonen JT (2015) Localized reconstruction of subunits from electron cryomicroscopy images of macromolecular complexes. Nat Commun 6:8843 PubMed PMC

Ishii T, Yanagida M (1977) The two dispensable structural proteins (soc and hoc) of the T4 phage capsid; their purification and properties, isolation and characterization of the defective mutants, and their binding with the defective heads in vitro. J Mol Biol 109:487–514 PubMed

Juhas M, Eberl L, Tümmler B (2005) Quorum sensing: the power of cooperation in the world of Pseudomonas. Environ Microbiol 7:459–471 PubMed

Kiewitz C, Tümmler B (2000) Sequence diversity of Pseudomonas aeruginosa: impact on population structure and genome evolution. J Bacteriol 182:3125–3135 PubMed PMC

Kim S, Rahman M, Seol SY, Yoon SS, Kim J (2012) Pseudomonas aeruginosa bacteriophage PA1Ø requires Type IV pili for infection and shows broad bactericidal and biofilm removal activities. Appl Environ Microbiol 78:6380–6385 PubMed PMC

Kizziah JL, Manning KA, Dearborn AD, Dokland T (2020) Structure of the host cell recognition and penetration machinery of a Staphylococcus aureus bacteriophage. PLoS Pathog 16:e1008314 PubMed PMC

Klockgether J, Cramer N, Wiehlmann L, Davenport C, Tümmler B (2011) Pseudomonas aeruginosa Genomic Structure and Diversity. Front Microbiol 2:150 PubMed PMC

Koch MD, Fei C, Wingreen NS, Shaevitz JW, Gitai Z (2021) Competitive binding of independent extension and retraction motors explains the quantitative dynamics of type IV pili. Proc Natl Acad Sci USA 118:e2014926118 PubMed PMC

Kremer JR, Mastronarde DN, McIntosh JR (1996) Computer visualization of three-dimensional image data using IMOD. J Struct Biol 116:71–76 PubMed

Kropinski AM (2018) Practical advice on the one-step growth curve. In: Clokie MRJ, Kropinski AM, Lavigne R (eds). Bacteriophages: methods and protocols, Vol. 3. Springer, New York, pp 41–47 PubMed

Kucukelbir A, Sigworth FJ, Tagare HD (2014) Quantifying the local resolution of cryo-EM density maps. Nat Methods 11:63–65 PubMed PMC

Lander GC, Evilevitch A, Jeembaeva M, Potter CS, Carragher B, Johnson JE (2008) Bacteriophage lambda stabilization by auxiliary protein gpD: timing, location, and mechanism of attachment determined by cryoEM. Struct Lond Engl 16:1399–1406 PubMed PMC

Lhuillier S, Gallopin M, Gilquin B, Brasilès S, Lancelot N, Letellier G, Gilles M, Dethan G, Orlova EV, Couprie J et al (2009) Structure of bacteriophage SPP1 head-to-tail connection reveals mechanism for viral DNA gating. Proc Natl Acad Sci USA 106:8507–8512 PubMed PMC

Linares R, Arnaud CA, Effantin G, Darnault C, Epalle NH, Boeri Erba E, Schoehn G, Breyton C (2023) Structural basis of bacteriophage T5 infection trigger and E. coli cell wall perforation. Sci Adv 9:eade9674 PubMed PMC

Mahony J, Alqarni M, Stockdale S, Spinelli S, Feyereisen M, Cambillau C, Sinderen Dvan (2016) Functional and structural dissection of the tape measure protein of lactococcal phage TP901-1. Sci Rep 6:36667 PubMed PMC

Mastronarde DN (2005) Automated electron microscope tomography using robust prediction of specimen movements. J Struct Biol 152:36–51 PubMed

Maxwell KL, Yee AA, Arrowsmith CH, Gold M, Davidson AR (2002) The solution structure of the bacteriophage λ head–tail joining protein, gpFII. J Mol Biol 318:1395–1404 PubMed

Maxwell KL, Yee AA, Booth V, Arrowsmith CH, Gold M, Davidson AR (2001) The solution structure of bacteriophage λ protein W, a small morphogenetic protein possessing a novel fold. J Mol Biol 308:9–14 PubMed

McCutcheon J, Peters D, Dennis J (2018) Identification and characterization of type IV pili as the cellular receptor of broad host range Stenotrophomonas maltophilia bacteriophages DLP1 and DLP2. Viruses 10:338 PubMed PMC

Mistry J, Chuguransky S, Williams L, Qureshi M, Salazar GA, Sonnhammer ELL, Tosatto SCE, Paladin L, Raj S, Richardson LJ et al (2021) Pfam: The protein families database in 2021. Nucleic Acids Res 49:D412–D419 PubMed PMC

Orlov I, Roche S, Brasilès S, Lukoyanova N, Vaney M-C, Tavares P, Orlova EV (2022) CryoEM structure and assembly mechanism of a bacterial virus genome gatekeeper. Nat Commun 13:7283 PubMed PMC

Paysan-Lafosse T, Blum M, Chuguransky S, Grego T, Pinto BL, Salazar GA, Bileschi ML, Bork P, Bridge A, Colwell L et al (2023) InterPro in 2022. Nucleic Acids Res 51:D418–D427 PubMed PMC

Pell LG, Gasmi-Seabrook GMC, Morais M, Neudecker P, Kanelis V, Bona D, Donaldson LW, Edwards AM, Howell PL, Davidson AR et al (2010) The solution structure of the C-terminal Ig-like domain of the bacteriophage λ tail tube protein. J Mol Biol 403:468–479 PubMed

Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE (2004) UCSF Chimera-a visualization system for exploratory research and analysis. J Comput Chem 25:1605–1612 PubMed

Pintilie GD, Zhang J, Goddard TD, Chiu W, Gossard DC (2010) Quantitative analysis of cryo-EM density map segmentation by watershed and scale-space filtering, and fitting of structures by alignment to regions. J Struct Biol 170:427–438 PubMed PMC

Plattner M, Shneider MM, Arbatsky NP, Shashkov AS, Chizhov AO, Nazarov S, Prokhorov NS, Taylor NMI, Buth SA, Gambino M et al (2019) Structure and function of the branched receptor-binding complex of bacteriophage CBA120. J Mol Biol 431:3718–3739 PubMed

Plisson C, White HE, Auzat I, Zafarani A, São-José C, Lhuillier S, Tavares P, Orlova EV (2007) Structure of bacteriophage SPP1 tail reveals trigger for DNA ejection. EMBO J 26:3720–3728 PubMed PMC

Punjani A, Rubinstein JL, Fleet DJ, Brubaker MA (2017) cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat Methods 14:290–296 PubMed

Punjani A, Zhang H, Fleet DJ (2020) Non-uniform refinement: adaptive regularization improves single-particle cryo-EM reconstruction. Nat Methods 17:1214–1221 PubMed

Qin L, Fokine A, O’Donnell E, Rao VB, Rossmann MG (2010) Structure of the small outer capsid protein, soc: a clamp for stabilizing capsids of T4-like phages. J Mol Biol 395:728 PubMed PMC

Ross PD, Black LW, Bisher ME, Steven AC (1985) Assembly-dependent conformational changes in a viral capsid protein: Calorimetric comparison of successive conformational states of the gp23 surface lattice of bacteriophage T4. J Mol Biol 183:353–364 PubMed

Sainz-Polo MA, González B, Menéndez M, Pastor FIJ, Sanz-Aparicio J (2015) Exploring multimodularity in plant cell wall deconstruction. J Biol Chem 290:17116–17130 PubMed PMC

Sathaliyawala T, Islam MZ, Li Q, Fokine A, Rossmann MG, Rao VB (2010) Functional analysis of the highly antigenic outer capsid protein, Hoc, a virus decoration protein from T4-like bacteriophages. Mol Microbiol 77:444–455 PubMed PMC

Scheres SHW (2012) RELION: Implementation of a Bayesian approach to cryo-EM structure determination. J Struct Biol 180:519–530 PubMed PMC

Schindelin J, Arganda-Carreras I, Frise E, Kaynig V, Longair M, Pietzsch T, Preibisch S, Rueden C, Saalfeld S, Schmid B et al (2012) Fiji: an open-source platform for biological-image analysis. Nat Methods 9:676–682 PubMed PMC

Schneider WR, Doetsch RN (1977) Temperature effects on bacterial movement. Appl Environ Microbiol 34:695–700 PubMed PMC

Sciara G, Bebeacua C, Bron P, Tremblay D, Ortiz-Lombardia M, Lichière J, van Heel M, Campanacci V, Moineau S, Cambillau C (2010) Structure of lactococcal phage p2 baseplate and its mechanism of activation. Proc Natl Acad Sci 107:6852–6857 PubMed PMC

Selivanovitch E, LaFrance B, Douglas T (2021) Molecular exclusion limits for diffusion across a porous capsid. Nat Commun 12:2903 PubMed PMC

Shah M, Taylor VL, Bona D, Tsao Y, Stanley SY, Pimentel-Elardo SM, McCallum M, Bondy-Denomy J, Howell PL, Nodwell JR et al (2021) A phage-encoded anti-activator inhibits quorum sensing in Pseudomonas aeruginosa. Mol Cell 81:571–583.e6 PubMed

Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Söding J et al (2011) Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol 7:539 PubMed PMC

Spinelli S, Tremblay D, Moineau S, Cambillau C, Goulet A (2020) Structural Insights into Lactococcal Siphophage p2 Baseplate Activation Mechanism. Viruses 12:878 PubMed PMC

Suhanovsky MM, Teschke CM (2015) Nature׳s favorite building block: deciphering folding and capsid assembly of proteins with the HK97-fold. Virology 479–480:487–497 PubMed PMC

Tam W, Pell LG, Bona D, Tsai A, Dai XX, Edwards AM, Hendrix RW, Maxwell KL, Davidson AR (2013) Tail tip proteins related to bacteriophage λ gpL coordinate an iron-sulfur cluster. J Mol Biol 425:2450–2462 PubMed PMC

Tang G, Peng L, Baldwin PR, Mann DS, Jiang W, Rees I, Ludtke SJ (2007) EMAN2: An extensible image processing suite for electron microscopy. J Struct Biol 157:38–46 PubMed

Tsao Y-F, Taylor VL, Kala S, Bondy-Denomy J, Khan AN, Bona D, Cattoir V, Lory S, Davidson AR, Maxwell KL (2018) Phage morons play an important role in Pseudomonas aeruginosa phenotypes. J Bacteriol 200:e00189–18 PubMed PMC

Tsuji A, Kaneko Y, Takahashi K, Ogawa M, Goto S (1982) The effects of temperature and pH on the growth of eight enteric and nine glucose non-fermenting species of gram-negative rods. Microbiol Immunol 26:15–24 PubMed

van der Wielen PWJJ, Dignum M, Donocik A, Prest EI (2023) Influence of temperature on growth of four different opportunistic pathogens in drinking water biofilms. Microorganisms 11:1574 PubMed PMC

van Kempen M, Kim SS, Tumescheit C, Mirdita M, Lee J, Gilchrist CLM, Söding J, Steinegger M (2024) Fast and accurate protein structure search with Foldseek. Nat Biotechnol 42:243–246 PubMed PMC

Vernhes E, Renouard M, Gilquin B, Cuniasse P, Durand D, England P, Hoos S, Huet A, Conway JF, Glukhov A et al (2017) High affinity anchoring of the decoration protein pb10 onto the bacteriophage T5 capsid. Sci Rep 7:41662 PubMed PMC

Vollmer W, Bertsche U (2008) Murein (peptidoglycan) structure, architecture and biosynthesis in Escherichia coli. Biochim Biophys Acta BBA - Biomembr 1778:1714–1734 PubMed

Wagner T, Merino F, Stabrin M, Moriya T, Antoni C, Apelbaum A, Hagel P, Sitsel O, Raisch T, Prumbaum D et al (2019) SPHIRE-crYOLO is a fast and accurate fully automated particle picker for cryo-EM. Commun Biol 2:1–13 PubMed PMC

Wang F, Coureuil M, Osinski T, Orlova A, Altindal T, Gesbert G, Nassif X, Egelman EH, Craig L (2017) Cryoelectron microscopy reconstructions of the Pseudomonas aeruginosa and Neisseria gonorrhoeae type IV Pili at sub-nanometer resolution. Structure 25:1423–1435.e4 PubMed PMC

Wikoff WR, Liljas L, Duda RL, Tsuruta H, Hendrix RW, Johnson JE (2000) Topologically linked protein rings in the bacteriophage HK97 capsid. Science 289:2129–2133 PubMed

Williams CJ, Headd JJ, Moriarty NW, Prisant MG, Videau LL, Deis LN, Verma V, Keedy DA, Hintze BJ, Chen VB et al (2018) MolProbity: more and better reference data for improved all-atom structure validation. Protein Sci Publ Protein Soc 27:293–315 PubMed PMC

Zhang K (2016) Gctf: Real-time CTF determination and correction. J Struct Biol 193:1–12 PubMed PMC

Zheng SQ, Palovcak E, Armache J-P, Verba KA, Cheng Y, Agard DA (2017) MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nat Methods 14:331–332 PubMed PMC

Zimmermann L, Stephens A, Nam S-Z, Rau D, Kübler J, Lozajic M, Gabler F, Söding J, Lupas AN, Alva V (2018) A completely reimplemented MPI bioinformatics toolkit with a new HHpred server at its core. J Mol Biol 430:2237–2243 PubMed

Zinke M, Sachowsky KAA, Öster C, Zinn-Justin S, Ravelli R, Schröder GF, Habeck M, Lange A (2020) Architecture of the flexible tail tube of bacteriophage SPP1. Nat Commun 11:5759 PubMed PMC

Zivanov J, Nakane T, Forsberg BO, Kimanius D, Hagen WJ, Lindahl E, Scheres SH (2018) New tools for automated high-resolution cryo-EM structure determination in RELION-3. eLife 7:e42166 PubMed PMC

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