6XNJ | pdb_00006xnj

Crystal structure of the PDZ domain of human GOPC in complex with a peptide of E. coli O157:H7 str. Sakai effector NleG8

• PDB DOI: https://doi.org/10.2210/pdb6XNJ/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens, Escherichia coli O157:H7 str. Sakai
• Expression System: Escherichia coli BL21(DE3), Escherichia coli
• Mutation(s): No 


• Deposited: 2020-07-03 Released: 2020-08-12 
• Deposition Author(s): Stogios, P.J., Skarina, T., Popov, G., Chang, C., Savchenko, A., Joachimiak, A., Satchell, K.J.F., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): Canadian Institutes of Health Research (CIHR), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.195 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.163 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the PDZ domain of human GOPC in complex with a peptide of E. coli O157:H7 str. Sakai effector NleG8

Popov, G.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 11.05 kDa 
• Atom Count: 920 
• Modeled Residue Count: 95 
• Deposited Residue Count: 101 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Golgi-associated PDZ and coiled-coil motif-containing protein	A	91	Homo sapiens	Mutation(s): 0  Gene Names: GOPC, CAL, FIG
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HD26 (Homo sapiens) Explore Q9HD26  Go to UniProtKB:  Q9HD26
PHAROS:  Q9HD26 GTEx:  ENSG00000047932

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NleG8 peptide	B	10	Escherichia coli O157:H7 str. Sakai	Mutation(s): 0  Gene Names: NleG8 EC: 2.3.2.27
UniProt
Find proteins for Q8XAN6 (Escherichia coli O157:H7) Explore Q8XAN6  Go to UniProtKB:  Q8XAN6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.195 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.163 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.759	α = 90
b = 68.759	β = 90
c = 59.941	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing
PHENIX	model building
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-08-12 
Deposition Author(s): Stogios, P.J., Skarina, T., Popov, G., Chang, C., Savchenko, A., Joachimiak, A., Satchell, K.J.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	--
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History  

• Version 1.0: 2020-08-12
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-06
  Changes: Structure summary