6RMU

Crystal structure of disulphide-linked human C3d dimer in complex with Staphylococcus aureus complement subversion protein Sbi-IV

• PDB DOI: https://doi.org/10.2210/pdb6RMU/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Staphylococcus aureus subsp. aureus Mu50
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-05-07 Released: 2020-11-18 
• Deposition Author(s): Wahid, A.A., van den Elsen, J.M.H., Crennell, S.J.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.211 
• R-Value Work: 0.156 
• R-Value Observed: 0.159 

Starting Model: experimental

Literature

Staphylococcal Complement Evasion Protein Sbi Stabilises C3d Dimers by Inducing an N-Terminal Helix Swap

Dunphy, R.W., Wahid, A.A., Back, C.R., Martin, R.L., Watts, A.G., Dodson, C.A., Crennell, S.J., van den Elsen, J.M.H.

(2022) Front Immunol 13

• DOI: https://doi.org/10.3389/fimmu.2022.892234

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Macromolecule Content

• Total Structure Weight: 88.26 kDa 
• Atom Count: 6,120 
• Modelled Residue Count: 727 
• Deposited Residue Count: 782 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Complement C3	A, C [auth B]	310	Homo sapiens	Mutation(s): 0  Gene Names: C3, CPAMD1
UniProt & NIH Common Fund Data Resources
Find proteins for P01024 (Homo sapiens) Explore P01024  Go to UniProtKB:  P01024
GTEx:  ENSG00000125730

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Immunoglobulin-binding protein Sbi	B [auth C], D	81	Staphylococcus aureus subsp. aureus Mu50	Mutation(s): 0  Gene Names: sbi, SAV2418
UniProt
Find proteins for Q2FVK5 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2FVK5  Go to UniProtKB:  Q2FVK5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	E [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO	F [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.211 
• R-Value Work: 0.156 
• R-Value Observed: 0.159 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.518	α = 90
b = 115.169	β = 90
c = 118.925	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
Aimless	data scaling
BALBES	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-11-18 
Deposition Author(s): Wahid, A.A., van den Elsen, J.M.H., Crennell, S.J.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/N022165/1

Revision History  

• Version 1.0: 2020-11-18
  Type: Initial release
  
• Version 1.1: 2021-12-01
  Changes: Database references
• Version 1.2: 2022-03-16
  Changes: Database references
• Version 1.3: 2022-06-01
  Changes: Database references
• Version 1.4: 2024-01-24
  Changes: Data collection, Refinement description