5NXF | pdb_00005nxf

Crystal structure of the carboxy-terminal region of the bacteriophage T4 proximal long tail fibre protein gp34, residues 795 to 1289, at 1.9 Angstrom.

• PDB DOI: https://doi.org/10.2210/pdb5NXF/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): Spanish Ministry of Economy and Competitiveness, European Commission, Japan Society for the Promotion of Science

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.208 (Depositor), 0.212 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.172 (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.

---

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: 167.51 kDa 
• Atom Count: 13,250 
• Modeled Residue Count: 1,483 
• Deposited Residue Count: 1,527 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Long-tail fiber proximal subunit	A, B, C	509	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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	G [auth A], P [auth B], Z [auth C]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	D [auth A], E [auth A], F [auth A], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B], Q [auth C], R [auth C], S [auth C], T [auth C], U [auth C], V [auth C], W [auth C], X [auth C], Y [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
URE	AA [auth C]	UREA C H4 N2 O XSQUKJJJFZCRTK-UHFFFAOYSA-N
ACT	H [auth A], I [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
NA	J [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.208 (Depositor), 0.212 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.107	α = 90
b = 75.943	β = 90.21
c = 149.128	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.

---

Funding Organization	Location	Grant Number
Spanish Ministry of Economy and Competitiveness	Spain	BFU2008-01588
Spanish Ministry of Economy and Competitiveness		BFU2011-24843
Spanish Ministry of Economy and Competitiveness		BFU2014-53425-P
Spanish Ministry of Economy and Competitiveness	Spain	BFU2014-61367-EXP
European Commission	Spain	NMP4-CT-2006-033256
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 2.0: 2017-09-13
  Changes: Atomic model, Author supporting evidence, Derived calculations, Structure summary
• Version 2.1: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 2.2: 2024-11-13
  Changes: Structure summary