7REJ | pdb_00007rej

Tailspike protein 4 (TSP4) from phage CBA120, residues 1-335, obtained in the presence of NaK-Tartrate

• PDB DOI: https://doi.org/10.2210/pdb7REJ/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Kuttervirus CBA120
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-07-13 Released: 2022-02-23 
• Deposition Author(s): Chao, K., Shang, X., Grenfield, J., Linden, S.B., Nelson, D.C., Herzberg, O.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.229 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.206 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Starting Model: experimental

Literature

Structure of Escherichia coli O157:H7 bacteriophage CBA120 tailspike protein 4 baseplate anchor and tailspike assembly domains (TSP4-N).

Chao, K.L., Shang, X., Greenfield, J., Linden, S.B., Alreja, A.B., Nelson, D.C., Herzberg, O.

(2022) Sci Rep 12: 2061-2061

• PubMed: 35136138 
• DOI: https://doi.org/10.1038/s41598-022-06073-2
• Primary Citation Related Structures: 
  7REJ, 7RFO, 7RFV


• PubMed Abstract: 
  

  Four tailspike proteins (TSP1-4) of Escherichia coli O157:H7 bacteriophage CBA120 enable infection of multiple hosts. They form a branched complex that attaches to the tail baseplate. Each TSP recognizes a different lipopolysaccharide on the membrane of a different bacterial host. The 335 N-terminal residues of TSP4 promote the assembly of the TSP complex and anchor it to the tail baseplate. The crystal structure of TSP4-N ₃₃₅ reveals a trimeric protein comprising four domains. The baseplate anchor domain (AD) contains an intertwined triple-stranded β-helix. The ensuing XD1, XD2 and XD3 β-sheet containing domains mediate the binding of TSP1-3 to TSP4. Each of the XD domains adopts the same fold as the respective XD domains of bacteriophage T4 gp10 baseplate protein, known to engage in protein-protein interactions via its XD2 and XD3 domains. The structural similarity suggests that XD2 and XD3 of TSP4 also function in protein-protein interactions. Analytical ultracentrifugation analyses of TSP4-N ₃₃₅ and of domain deletion proteins showed how TSP4-N ₃₃₅ promotes the formation of the TSP quaternary complex. TSP1 and TSP2 bind directly to TSP4 whereas TSP3 binding requires a pre-formed TSP4-N ₃₃₅ :TSP2 complex. A 3-dimensional model of the bacteriophage CBA120 TSP complex has been developed based on the structural and ultracentrifuge information.

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Organizational Affiliation: 
• Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD, 20850, USA.
Department of Chemistry and Biochemistry, University of Maryland, Chemistry Building, 8051 Regents Drive, College Park, MD, 20742, USA.
Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD, 20850, USA. [e-mail].
Department of Veterinary Medicine, University of Maryland, 8075 Greenmead Drive, College Park, MD, 20742, USA. [e-mail].
Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD, 20850, USA. [e-mail].
Department of Chemistry and Biochemistry, University of Maryland, Chemistry Building, 8051 Regents Drive, College Park, MD, 20742, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 72.78 kDa 
• Atom Count: 4,322 
• Modeled Residue Count: 576 
• Deposited Residue Count: 682 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tailspike protein	A, B	341	Kuttervirus CBA120	Mutation(s): 0  Gene Names: orf213
UniProt
Find proteins for G3M192 (Escherichia phage Cba120) Explore G3M192  Go to UniProtKB:  G3M192

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IMD	C [auth A], D [auth B]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.229 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.206 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.03	α = 90
b = 78.03	β = 90
c = 326.87	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-02-23 
Deposition Author(s): Chao, K., Shang, X., Grenfield, J., Linden, S.B., Nelson, D.C., Herzberg, O.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	RO1GM110202

Revision History  

• Version 1.0: 2022-02-23
  Type: Initial release
  
• Version 1.1: 2024-04-03
  Changes: Data collection, Refinement description