Download MendeleyStaphylococcal 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
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
- 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), 0.210 (DCC)
- R-Value Work: 0.156 (Depositor), 0.160 (DCC)
- R-Value Observed: 0.159 (Depositor)
Starting Model: experimental
View more details
wwPDB Validation 3D Report Full Report
This is version 1.5 of the entry. See complete history.
Literature
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P01024 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q2FVK5 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| PEG Query on PEG | E [auth A] | DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N |  | ||
| EDO Query on 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 (Depositor), 0.210 (DCC)
- R-Value Work: 0.156 (Depositor), 0.160 (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 Name | Purpose |
|---|---|
| PHENIX | refinement |
| DIALS | data reduction |
| Aimless | data scaling |
| BALBES | phasing |
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.
| 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
