4AM9

CRYSTAL STRUCTURE OF THE YERSINIA ENTEROCOLITICA TYPE III SECRETION CHAPERONE SYCD IN COMPLEX WITH A PEPTIDE OF THE TRANSLOCATOR YOPD

• PDB DOI: https://doi.org/10.2210/pdb4AM9/pdb

• Classification: CHAPERONE
• Organism(s): Yersinia enterocolitica
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-03-08 Released: 2012-05-30 
• Deposition Author(s): Schreiner, M., Niemann, H.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.238 
• R-Value Work: 0.190 
• R-Value Observed: 0.192 

Literature

Crystal Structure of the Yersinia Enterocolitica Type III Secretion Chaperone Sycd in Complex with a Peptide of the Minor Translocator Yopd

Schreiner, M., Niemann, H.H.

(2012) BMC Struct Biol 12: 12

• PubMed: 22708907 
• DOI: https://doi.org/10.1186/1472-6807-12-13
• Primary Citation of Related Structures:  
  4AM9


• PubMed Abstract: 
  

  Type III secretion systems are used by Gram-negative bacteria as "macromolecular syringes" to inject effector proteins into eukaryotic cells. Two hydrophobic proteins called translocators form the necessary pore in the host cell membrane. Both translocators depend on binding to a single chaperone in the bacterial cytoplasm to ensure their stability and efficient transport through the secretion needle. It was suggested that the conserved chaperones bind the more divergent translocators via a hexapeptide motif that is found in both translocators and conserved between species.

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Organizational Affiliation: 

Department of Chemistry, Bielefeld University, PO Box 10 01 31, 33501 Bielefeld, Germany.

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: 18.2 kDa 
• Atom Count: 1,179 
• Modelled Residue Count: 141 
• Deposited Residue Count: 159 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CHAPERONE SYCD	A	148	Yersinia enterocolitica	Mutation(s): 0
UniProt
Find proteins for O87496 (Yersinia enterocolitica W22703) Explore O87496  Go to UniProtKB:  O87496

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
YOP EFFECTOR YOPD	B	11	Yersinia enterocolitica	Mutation(s): 0
UniProt
Find proteins for P37132 (Yersinia enterocolitica) Explore P37132  Go to UniProtKB:  P37132

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
BU3	D [auth A], E [auth A], F [auth A], G [auth A], H [auth B]	(R,R)-2,3-BUTANEDIOL C4 H10 O2 OWBTYPJTUOEWEK-QWWZWVQMSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.238 
• R-Value Work: 0.190 
• R-Value Observed: 0.192 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.369	α = 90
b = 106.369	β = 90
c = 51.998	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-05-30 
Deposition Author(s): Schreiner, M., Niemann, H.H.

Revision History  

• Version 1.0: 2012-05-30
  Type: Initial release
  
• Version 1.1: 2012-06-27
  Changes: Other
• Version 1.2: 2019-03-06
  Changes: Data collection, Derived calculations, Experimental preparation, Other
• Version 1.3: 2019-09-25
  Changes: Data collection, Experimental preparation, Other
• Version 1.4: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Refinement description