5IV5

Cryo-electron microscopy structure of the hexagonal pre-attachment T4 baseplate-tail tube complex

PDB DOI: https://doi.org/10.2210/pdb5IV5/pdb
EM Map EMD-3374: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Tequatrovirus T4
Mutation(s): No

Deposited: 2016-03-19 Released: 2016-05-18
Deposition Author(s): Taylor, N.M.I., Guerrero-Ferreira, R.C., Goldie, K.N., Stahlberg, H., Leiman, P.G.

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.11 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Structure of the T4 baseplate and its function in triggering sheath contraction.

Taylor, N.M., Prokhorov, N.S., Guerrero-Ferreira, R.C., Shneider, M.M., Browning, C., Goldie, K.N., Stahlberg, H., Leiman, P.G.

(2016) Nature 533: 346-352

PubMed: 27193680 Search on PubMed
DOI: https://doi.org/10.1038/nature17971

PubMed Abstract:
Several systems, including contractile tail bacteriophages, the type VI secretion system and R-type pyocins, use a multiprotein tubular apparatus to attach to and penetrate host cell membranes. This macromolecular machine resembles a stretched, coiled spring (or sheath) wound around a rigid tube with a spike-shaped protein at its tip. A baseplate structure, which is arguably the most complex part of this assembly, relays the contraction signal to the sheath. Here we present the atomic structure of the approximately 6-megadalton bacteriophage T4 baseplate in its pre- and post-host attachment states and explain the events that lead to sheath contraction in atomic detail. We establish the identity and function of a minimal set of components that is conserved in all contractile injection systems and show that the triggering mechanism is universally conserved.

Organizational Affiliation

École Polytechnique Fédérale de Lausanne (EPFL), BSP-415, 1015 Lausanne, Switzerland.

Macromolecule Content

Total Structure Weight: 6,490.1 kDa
Atom Count: 549,576
Modelled Residue Count: 56,082
Deposited Residue Count: 58,591
Unique protein chains: 15

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Baseplate wedge protein gp6	A B LD [auth GD] MD [auth GE] OC [auth EA] A, B, LD [auth GD], MD [auth GE], OC [auth EA], PC [auth EB], RB [auth BH], SB [auth BI], UA [auth u], VA [auth v], X, Y	660	Tequatrovirus T4	Mutation(s): 0
UniProt
Find proteins for P19060 (Enterobacteria phage T4) Explore P19060 Go to UniProtKB: P19060
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P19060
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Baseplate wedge protein gp7	C ND [auth GF] QC [auth EC] TB [auth BJ] WA [auth w] C, ND [auth GF], QC [auth EC], TB [auth BJ], WA [auth w], Z	1,032	Tequatrovirus T4	Mutation(s): 0
UniProt
Find proteins for P19061 (Enterobacteria phage T4) Explore P19061 Go to UniProtKB: P19061
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P19061
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Baseplate wedge protein gp8	AA [auth a] BA [auth b] D E OD [auth GG] AA [auth a], BA [auth b], D, E, OD [auth GG], PD [auth GH], RC [auth ED], SC [auth EE], UB [auth CA], VB [auth CB], XA [auth x], YA [auth y]	334	Tequatrovirus T4	Mutation(s): 0
UniProt
Find proteins for P19062 (Enterobacteria phage T4) Explore P19062 Go to UniProtKB: P19062
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P19062
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Baseplate wedge protein gp9	AB [auth AA] BB [auth AB] CA [auth c] DA [auth d] EA [auth e] AB [auth AA], BB [auth AB], CA [auth c], DA [auth d], EA [auth e], F, G, H, QD [auth GI], RD [auth GJ], SD [auth HA], TC [auth EF], UC [auth EG], VC [auth EH], WB [auth CC], XB [auth CD], YB [auth CE], ZA [auth z]	288	Tequatrovirus T4	Mutation(s): 0
UniProt
Find proteins for P10927 (Enterobacteria phage T4) Explore P10927 Go to UniProtKB: P10927
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P10927
Sequence Annotations Expand
Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Baseplate wedge protein gp10	AC [auth CG] BC [auth CH] CB [auth AC] DB [auth AD] EB [auth AE] AC [auth CG], BC [auth CH], CB [auth AC], DB [auth AD], EB [auth AE], FA [auth f], GA [auth g], HA [auth h], I, J, K, TD [auth HB], UD [auth HC], VD [auth HD], WC [auth EI], XC [auth EJ], YC [auth FA], ZB [auth CF]	602	Tequatrovirus T4	Mutation(s): 0
UniProt
Find proteins for P10928 (Enterobacteria phage T4) Explore P10928 Go to UniProtKB: P10928
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P10928
Sequence Annotations Expand
Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Baseplate wedge protein gp11	AD [auth FC] BD [auth FD] CC [auth CI] DC [auth CJ] EC [auth DA] AD [auth FC], BD [auth FD], CC [auth CI], DC [auth CJ], EC [auth DA], FB [auth AF], GB [auth AG], HB [auth AH], IA [auth i], JA [auth j], KA [auth k], L, M, N, WD [auth HE], XD [auth HF], YD [auth HG], ZC [auth FB]	219	Tequatrovirus T4	Mutation(s): 0
UniProt
Find proteins for P10929 (Enterobacteria phage T4) Explore P10929 Go to UniProtKB: P10929
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P10929
Sequence Annotations Expand
Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Short tail fiber protein gp12	AE [auth HI] BE [auth HJ] CD [auth FE] DD [auth FF] ED [auth FG] AE [auth HI], BE [auth HJ], CD [auth FE], DD [auth FF], ED [auth FG], FC [auth DB], GC [auth DC], HC [auth DD], IB [auth AI], JB [auth AJ], KB [auth BA], LA [auth l], MA [auth m], NA [auth n], O, P, Q, ZD [auth HH]	527	Tequatrovirus T4	Mutation(s): 0
UniProt
Find proteins for P10930 (Enterobacteria phage T4) Explore P10930 Go to UniProtKB: P10930
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P10930
Sequence Annotations Expand
Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Tail tube protein gp19	CE [auth IA] DE [auth IB] FD [auth FH] GD [auth FI] IC [auth DE] CE [auth IA], DE [auth IB], FD [auth FH], GD [auth FI], IC [auth DE], JC [auth DF], LB [auth BB], MB [auth BC], OA [auth o], PA [auth p], R, S	163	Tequatrovirus T4	Mutation(s): 0
UniProt
Find proteins for P13333 (Enterobacteria phage T4) Explore P13333 Go to UniProtKB: P13333
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P13333
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Baseplate wedge protein gp25	EE [auth IC] HD [auth FJ] KC [auth DG] NB [auth BD] QA [auth q] EE [auth IC], HD [auth FJ], KC [auth DG], NB [auth BD], QA [auth q], T	132	Tequatrovirus T4	Mutation(s): 0
UniProt
Find proteins for P09425 (Enterobacteria phage T4) Explore P09425 Go to UniProtKB: P09425
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P09425
Sequence Annotations Expand
Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Baseplate tail-tube protein gp48	FE [auth ID] ID [auth GA] LC [auth DH] OB [auth BE] RA [auth r] FE [auth ID], ID [auth GA], LC [auth DH], OB [auth BE], RA [auth r], U	364	Tequatrovirus T4	Mutation(s): 0
UniProt
Find proteins for P13339 (Enterobacteria phage T4) Explore P13339 Go to UniProtKB: P13339
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P13339
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Baseplate wedge protein gp53	GE [auth IE] JD [auth GB] MC [auth DI] PB [auth BF] SA [auth s] GE [auth IE], JD [auth GB], MC [auth DI], PB [auth BF], SA [auth s], V	196	Tequatrovirus T4	Mutation(s): 0
UniProt
Find proteins for P16011 (Enterobacteria phage T4) Explore P16011 Go to UniProtKB: P16011
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P16011
Sequence Annotations Expand
Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Baseplate tail-tube protein gp54	HE [auth IF] KD [auth GC] NC [auth DJ] QB [auth BG] TA [auth t] HE [auth IF], KD [auth GC], NC [auth DJ], QB [auth BG], TA [auth t], W	320	Tequatrovirus T4	Mutation(s): 0
UniProt
Find proteins for P13341 (Enterobacteria phage T4) Explore P13341 Go to UniProtKB: P13341
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P13341
Sequence Annotations Expand
Reference Sequence

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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidoglycan hydrolase gp5	IE [auth YA], JE [auth YB], KE [auth YC]	575	Tequatrovirus T4	Mutation(s): 0 EC: 3.2.1.17
UniProt
Find proteins for P16009 (Enterobacteria phage T4) Explore P16009 Go to UniProtKB: P16009
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P16009
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Baseplate hub protein gp27	LE [auth YD], ME [auth YE], NE [auth YF]	391	Tequatrovirus T4	Mutation(s): 0
UniProt
Find proteins for P17172 (Enterobacteria phage T4) Explore P17172 Go to UniProtKB: P17172
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P17172
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized 10.2 kDa protein in segC-Gp6 intergenic region	OE [auth ZA]	97	Tequatrovirus T4	Mutation(s): 0
UniProt
Find proteins for P39234 (Enterobacteria phage T4) Explore P39234 Go to UniProtKB: P39234
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P39234
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain PE [auth O] SDF format, chain QE [auth l] SDF format, chain RE [auth AI] SDF format, chain SE [auth DB] SDF format, chain TE [auth FE] SDF format, chain UE [auth HH] MOL2 format, chain PE [auth O] MOL2 format, chain QE [auth l] MOL2 format, chain RE [auth AI] MOL2 format, chain SE [auth DB] MOL2 format, chain TE [auth FE] MOL2 format, chain UE [auth HH] mmCIF format, chain PE [auth O] mmCIF format, chain QE [auth l] mmCIF format, chain RE [auth AI] mmCIF format, chain SE [auth DB] mmCIF format, chain TE [auth FE] mmCIF format, chain UE [auth HH]	PE [auth O] QE [auth l] RE [auth AI] SE [auth DB] TE [auth FE] PE [auth O], QE [auth l], RE [auth AI], SE [auth DB], TE [auth FE], UE [auth HH]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain PE [auth O] Focus chain QE [auth l] Focus chain RE [auth AI] Focus chain SE [auth DB] Focus chain TE [auth FE] Focus chain UE [auth HH] Interactions & Density Focus chain PE [auth O] Focus chain QE [auth l] Focus chain RE [auth AI] Focus chain SE [auth DB] Focus chain TE [auth FE] Focus chain UE [auth HH]
FE Query on FE Download Ideal Coordinates CCD File SDF format, chain VE [auth ZA] MOL2 format, chain VE [auth ZA] mmCIF format, chain VE [auth ZA]	VE [auth ZA]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain VE [auth ZA] Interactions & Density Focus chain VE [auth ZA]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 4.11 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	1.4
MODEL REFINEMENT	PHENIX	1.10.1-2155

Structure Validation

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Entry History

Deposition Data

Released Date: 2016-05-18

Deposition Author(s):

Taylor, N.M.I.

Guerrero-Ferreira, R.C.

Goldie, K.N.

Stahlberg, H.

Leiman, P.G.

Revision History (Full details and data files)

Version 1.0: 2016-05-18
Type: Initial release
Version 1.1: 2016-05-25
Changes: Database references
Version 1.2: 2016-06-08
Changes: Database references
Version 1.3: 2017-08-30
Changes: Advisory, Data collection
Version 1.4: 2018-02-07
Changes: Data collection
Version 1.5: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.

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Help and Resources

5IV5

Cryo-electron microscopy structure of the hexagonal pre-attachment T4 baseplate-tail tube complex

Structure of the T4 baseplate and its function in triggering sheath contraction.

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)