Experimental Data Snapshot
(2010) J Mol Biology 402: 17-29
The human complement system plays an essential role in innate and adaptive immunity by marking and eliminating microbial intruders. Activation of complement on foreign surfaces results in proteolytic cleavage of complement component 3 (C3) into the potent opsonin C3b, which triggers a variety of immune responses and participates in a self-amplification loop mediated by a multi-protein assembly known as the C3 convertase. The human pathogen Staphylococcus aureus has evolved a sophisticated and potent complement evasion strategy, which is predicated upon an arsenal of potent inhibitory proteins. One of these, the staphylococcal complement inhibitor (SCIN), acts at the level of the C3 convertase (C3bBb) and impairs downstream complement function by trapping the convertase in a stable but inactive state. Previously, we have shown that SCIN binds C3b directly and competitively inhibits binding of human factor H and, to a lesser degree, that of factor B to C3b. Here, we report the co-crystal structures of SCIN bound to C3b and C3c at 7.5 and 3.5 A limiting resolution, respectively, and show that SCIN binds a critical functional area on C3b. Most significantly, the SCIN binding site sterically occludes the binding sites of both factor H and factor B. Our results give insight into SCIN binding to activated derivatives of C3, explain how SCIN can recognize C3b in the absence of other complement components, and provide a structural basis for the competitive C3b-binding properties of SCIN. In the future, this may suggest templates for the design of novel complement inhibitors based upon the SCIN structure.
 Explore in 3D: Structure |Sequence Annotations |Electron Density |Validation Report |Ligand Interaction (NAG)
Biological assembly 1 assigned by authors.
Macromolecule Content 
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Complement C3 | 645 | Homo sapiens | Mutation(s): 0  | ![]() | |
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 | |||||
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Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Complement C3 | B [auth C] | 343 | Homo sapiens | Mutation(s): 0  | ![]() |
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 | |||||
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Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Staphylococcal complement inhibitor | C [auth M] | 88 | Staphylococcus aureus subsp. aureus Mu50 | Mutation(s): 0  Gene Names: SAV1942, scn | ![]() |
UniProt | |||||
Find proteins for Q931M7 (Staphylococcus aureus (strain Mu50 / ATCC 700699)) Explore Q931M7  Go to UniProtKB:  Q931M7 | |||||
Entity Groups  | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q931M7 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 4 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Complement C3 | D [auth B] | 206 | Homo sapiens | Mutation(s): 0  | ![]() |
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 | |||||
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| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| NAG Query on NAG Download Ideal Coordinates CCD File  | E [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 214.067 | α = 90 |
| b = 68.434 | β = 90 |
| c = 114.928 | γ = 90 |
| Software Name | Purpose |
|---|---|
| DENZO | data reduction |
| SCALEPACK | data scaling |
| PHASER | phasing |
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
| HKL-2000 | data collection |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
RCSB PDB Core Operations are funded by theU.S. National Science Foundation (DBI-2321666), theUS Department of Energy (DE-SC0019749), and theNational Cancer Institute,National Institute of Allergy and Infectious Diseases, andNational Institute of General Medical Sciences of theNational 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.