5IW9 | pdb_00005iw9

Structure of bacteriophage T4 gp25, sheath polymerization initiator

• PDB DOI: https://doi.org/10.2210/pdb5IW9/pdb
• Entry: 5IW9 supersedes: 4HRZ

• Classification: VIRAL PROTEIN
• Organism(s): Tequatrovirus T4
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-03-22 Released: 2016-05-11 
• Deposition Author(s): Leiman, P.G., Browning, C., Shneider, M.M.
• Funding Organization(s): EPFL

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.47 Å
• R-Value Free: 
  0.217 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

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 
• DOI: https://doi.org/10.1038/nature17971
• Primary Citation Related Structures: 
  5IV5, 5IV7, 5IW9


• 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.

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Organizational Affiliation: 
• École Polytechnique Fédérale de Lausanne (EPFL), BSP-415, 1015 Lausanne, Switzerland.
Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, pr. 60-letiya Oktyabrya, 7 build. 2, 117312, Moscow, Russia.
Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Laboratory of Molecular Bioengineering, 16/10 Miklukho-Maklaya St., 117997 Moscow, Russia.
Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, Mattenstrasse 26, 4058 Basel, Switzerland.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 30.24 kDa 
• Atom Count: 2,135 
• Modeled Residue Count: 251 
• Deposited Residue Count: 262 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Baseplate wedge protein gp25	A, B	131	Tequatrovirus T4	Mutation(s): 0  Gene Names: 25
UniProt
Find proteins for P09425 (Enterobacteria phage T4) Explore P09425  Go to UniProtKB:  P09425

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.47 Å
• R-Value Free:  0.217 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.859	α = 90
b = 69.859	β = 90
c = 222.179	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
SHELXCD	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-05-11 
Deposition Author(s): Leiman, P.G., Browning, C., Shneider, M.M.
• This entry supersedes: 4HRZ

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Funding Organization	Location	Grant Number
EPFL	Switzerland	577

Revision History  

• Version 1.0: 2016-05-11
  Type: Initial release
  
• Version 1.1: 2016-05-25
  Changes: Database references
• Version 1.2: 2016-06-08
  Changes: Database references
• Version 1.3: 2024-11-20
  Changes: Data collection, Database references, Structure summary