2WY7: Complement C3D fragment

Staphylococcus aureus complement subversion protein Sbi-IV in complex with complement fragment C3d revealing an alternative binding mode. Determined by X-ray diffraction at 1.7 Å resolution. Released 1 Dec 2010.

Method: X-ray diffraction
Resolution: 1.7 Å
Organisms: HOMO SAPIENS, STAPHYLOCOCCUS AUREUS
Chains: 2
Atoms: 3,226
Mol. weight: 44.28 kDa
Released: 1 Dec 2010

Explore 2WY7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2WY7 contains 19 α-helices and 6 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 16 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	15-17	3
α-helix	27-45	19
α-helix	48-51	4
α-helix	55-71	17
β-strand	74	1	1
β-strand	80	1	1
α-helix	87-89	3
α-helix	90-103	14
α-helix	111-125	15
β-strand	126	1	2
β-strand	132	1	2
α-helix	141-147	7
α-helix	153-172	20
α-helix	179-193	15
α-helix	194-196	3
α-helix	200-212	13
α-helix	218-227	10
β-strand	229	1	3
β-strand	233	1	3
α-helix	240-257	18
α-helix	263-272	10
α-helix	283-299	17

Chain Q: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	13-37	25
α-helix	41-52	12
α-helix	56-76	21

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Complement C3D fragment	A	protein	310	HOMO SAPIENS	P01024 (AlphaFold model)
IgG-binding protein	Q	protein	80	STAPHYLOCOCCUS AUREUS	C8LN82

Sequence of entity 1 (A), FASTA

>2WY7_1 COMPLEMENT C3D FRAGMENT (chains A)
MLDAERLKHLIVTPSGAGEQNMIGMTPTVIAVHYLDETEQWEKFGLEKRQGALELIKKGY
TQQLAFRQPSSAFAAFVKRAPSTWLTAYVVKVFSLAVNLIAIDSQVLCGAVKWLILEKQK
PDGVFQEDAPVIHQEMIGGLRNNNEKDMALTAFVLISLQEAKDICEEQVNSLPGSITKAG
DFLEANYMNLQRSYTVAIAGYALAQMGRLKGPLLNKFLTTAKDKNRWEDPGKQLYNVEAT
SYALLALLQLKDFDFVPPVVRWLNEQRYYGGGYGSTQATFMVFQALAQYQKDAPDHQELN
LDVSLQLPSR

Sequence of entity 2 (Q), FASTA

>2WY7_2 IGG-BINDING PROTEIN (chains Q)
MRGSHHHHHHMVSIEKAIVRHDERVKSANDAISKLNEKDSIENRRLAQREVNKAPMDVKE
HLQKQLDALVAQKDAEKKVA

Primary citation

A Structural Basis for Staphylococcal Complement Subversion: X-Ray Structure of the Complement- Binding Domain of Staphylococcus Aureus Protein Sbi in Complex with Ligand C3D. Clark, E.A., Crennell, S., Upadhyay, A. et al. Mol Immunol (2011) 48:452. DOI 10.1016/J.MOLIMM.2010.09.017 · PubMed

Other PDB entries of the same protein (UniProt P01024 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2WY8 1.7 Å, Staphylococcus aureus complement subversion protein Sbi-IV in complex with complement…
7UE9 1.75 Å, Structure of anti-C3d Fab(3d8b) in complex with C3d
1C3D 1.8 Å, X-ray crystal structure of C3D: a C3 fragment and ligand for complement receptor 2
6RMT 2.0 Å, Crystal structure of disulphide-linked human C3d dimer
7BAG 2.0 Å, C3b in complex with CP40
1GHQ 2.04 Å, CR2-C3D complex structure
3D5R 2.1 Å, Crystal Structure of Efb-C (N138A) / C3d Complex
3OXU 2.1 Å, Complement components factor H CCP19-20 and C3d in complex
4I6O 2.14 Å, Crystal structure of chemically synthesized human anaphylatoxin C3a
4ONT 2.15 Å, Ternary host recognition complex of complement factor H, C3d, and sialic acid
2GOX 2.2 Å, Crystal structure of Efb-C / C3d Complex
4ZH1 2.24 Å, Complement factor H in complex with the GM1 glycan

Browse structure collections

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