6RMU | pdb_00006rmu

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.211 (Depositor), 0.211 (DCC)
R-Value Work:
0.156 (Depositor), 0.156 (DCC)
R-Value Observed:
0.159 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6RMU

This is version 1.5 of the entry. See complete history.

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

Macromolecule Content

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

Macromolecules

Find similar proteins by:

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
PHAROS: P01024 GTEx: ENSG00000125730
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01024
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2FVK5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B] mmCIF format, chain F [auth B]	F [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.211 (Depositor), 0.211 (DCC)
R-Value Work: 0.156 (Depositor), 0.156 (DCC)
R-Value Observed: 0.159 (Depositor)

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-11-18

Deposition Author(s):

van den Elsen, J.M.H.

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

Revision History (Full details and data files)

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
Version 1.5: 2024-11-20
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.