5NXH | pdb_00005nxh

Crystal structure of the carboxy-terminal region of the bacteriophage T4 proximal long tail fibre protein gp34, residues 744-1289 at 2.9 Angstrom resolution

• PDB DOI: https://doi.org/10.2210/pdb5NXH/pdb

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


• Deposited: 2017-05-10 Released: 2017-07-12 
• Deposition Author(s): Namura, M., van Raaij, M.J., Kanamaru, S.
• Funding Organization(s): Japan Society for the Promotion of Science

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.89 Å
• R-Value Free: 
  0.263 (Depositor), 0.263 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.206 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of the Carboxy-Terminal Region of the Bacteriophage T4 Proximal Long Tail Fiber Protein Gp34.

Granell, M., Namura, M., Alvira, S., Kanamaru, S., van Raaij, M.J.

(2017) Viruses 9

• PubMed: 28665339 
• DOI: https://doi.org/10.3390/v9070168
• Primary Citation Related Structures: 
  4UXE, 4UXF, 4UXG, 5NXF, 5NXH


• PubMed Abstract: 
  

  Long tail fibers of bacteriophage T4 are formed by proteins gp34, gp35, gp36, and gp37, with gp34 located at the phage-proximal end and gp37 at the phage-distal, receptor-binding end. We have solved the structure of the carboxy-terminal region of gp34, consisting of amino acids 894-1289, by single-wavelength anomalous diffraction and extended the structure to amino acids 744-1289 using data collected from crystals containing longer gp34-fragments. The structure reveals three repeats of a mixed α-β fibrous domain in residues 744 to 877. A triple-helical neck connects to an extended triple β-helix domain (amino acids 900-1127) punctuated by two β-prism domains. Next, a β-prism domain decorated with short helices and extended β-helices is present (residues 1146-1238), while the C -terminal end is capped with another short β-helical region and three β-hairpins. The structure provides insight into the stability of the fibrous gp34 protein.

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Organizational Affiliation: 
• Departmento de Estructura de Macromoleculas, Centro Nacional de Biotecnologia (CNB-CSIC), Calle Darwin 3, E-28049 Madrid, Spain.
Department of Life Science and Technology, Tokyo Institute of Technology, M6-11 2-12-1 Ookayama, Meguro-ku Tokyo 152-8550, Japan. [e-mail].
Departmento Bioquimica y Biologia Molecular, Facultad de Farmacia, Universidad de Santiago de Compostela, E-15782 Santiago de Compostela, Spain.
Department of Life Science and Technology, Tokyo Institute of Technology, M6-11 2-12-1 Ookayama, Meguro-ku Tokyo 152-8550, Japan. [e-mail].
Departmento de Estructura de Macromoleculas, Centro Nacional de Biotecnologia (CNB-CSIC), Calle Darwin 3, E-28049 Madrid, Spain. [e-mail].
Departmento Bioquimica y Biologia Molecular, Facultad de Farmacia, Universidad de Santiago de Compostela, E-15782 Santiago de Compostela, Spain. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 3-mer - A3 

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

Biological Assembly Evidence: equilibrium centrifugation, native gel electrophoresis

Macromolecule Content 

• Total Structure Weight: 182.54 kDa 
• Atom Count: 12,797 
• Modeled Residue Count: 1,638 
• Deposited Residue Count: 1,692 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Long-tail fiber proximal subunit	A, B, C	564	Tequatrovirus T4	Mutation(s): 0  Gene Names: 34
UniProt
Find proteins for P18771 (Enterobacteria phage T4) Explore P18771  Go to UniProtKB:  P18771

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.89 Å
• R-Value Free:  0.263 (Depositor), 0.263 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.206 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.297	α = 90
b = 76.133	β = 97.62
c = 139.868	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-07-12 
Deposition Author(s): Namura, M., van Raaij, M.J., Kanamaru, S.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science	Japan	JP25440066

Revision History  

• Version 1.0: 2017-07-12
  Type: Initial release
  
• Version 1.1: 2017-07-19
  Changes: Database references
• Version 1.2: 2017-09-13
  Changes: Author supporting evidence
• Version 1.3: 2024-01-17
  Changes: Data collection, Database references, Refinement description