4WWI: C domain of staphylococcal protein A

Crystal structure of the C domain of staphylococcal protein A in complex with the Fc fragment of human IgG at 2.3 Angstrom resolution. Determined by X-ray diffraction at 2.31 Å resolution. Released 15 Jul 2015.

Method: X-ray diffraction
Resolution: 2.31 Å
Organisms: Staphylococcus aureus, Homo sapiens
Chains: 6
Atoms: 6,419
Mol. weight: 95.29 kDa
Released: 15 Jul 2015

Explore 4WWI in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4WWI contains 43 α-helices and 58 β-strands across 6 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.

Chains A and B: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	7-18	12
α-helix	24-36	13
α-helix	38-40	3
α-helix	41-54	14

Chain C: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	7-17	11
α-helix	24-36	13
α-helix	38-40	3
α-helix	41-54	14

Chain D: 11 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	239-243	5	1
α-helix	244-246	3
α-helix	247-251	5
β-strand	258-264	7	1
β-strand	274-279	6	2
β-strand	282-283	2	2
β-strand	287-289	3	1
α-helix	290-292	3
β-strand	302-307	6	1
α-helix	310-314	5
β-strand	319-324	6	2
β-strand	332-336	5	2
α-helix	338-340	3
β-strand	344	1	3
α-helix	345-346	2
β-strand	347-351	5	4
α-helix	352-354	3
α-helix	355-359	5
β-strand	362-372	11	4
β-strand	373	1	3
β-strand	378-383	6	5
β-strand	386-387	2	5
β-strand	391-393	3	4
α-helix	394-396	3
β-strand	397-398	2	4
β-strand	404-413	10	4
α-helix	414-418	5
β-strand	423-428	6	5
α-helix	433-435	3
β-strand	437-441	5	5

Chain E: 10 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	241-243	3	6
α-helix	244-246	3
α-helix	247-251	5
β-strand	258-262	5	6
β-strand	277-279	3	7
β-strand	283-284	2	7
β-strand	288-289	2	6
β-strand	303-307	5	6
α-helix	310-314	5
β-strand	319-321	3	7
β-strand	334-336	3	7
α-helix	338-340	3
β-strand	344	1	8
α-helix	345-346	2
β-strand	347-351	5	9
α-helix	352-354	3
α-helix	355-357	3
β-strand	362-372	11	9
β-strand	373	1	8
β-strand	378-383	6	10
β-strand	386-388	3	10
β-strand	391-393	3	9
α-helix	394-396	3
β-strand	397-398	2	9
β-strand	404-413	10	9
α-helix	414-418	5
β-strand	423-428	6	10
α-helix	433-435	3
β-strand	437-441	5	10

Chain F: 10 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	239-243	5	11
α-helix	244-246	3
α-helix	247-251	5
β-strand	258-267	10	11
β-strand	273-279	7	12
β-strand	283-284	2	12
β-strand	288-289	2	11
β-strand	293-294	2	11
β-strand	299-307	9	11
α-helix	310-314	5
β-strand	319-325	7	12
β-strand	333-336	4	12
α-helix	338-340	3
β-strand	344	1	13
α-helix	345-346	2
β-strand	347-351	5	14
α-helix	352-354	3
α-helix	357-359	3
β-strand	362-372	11	14
β-strand	373	1	13
β-strand	378-383	6	15
β-strand	386-388	3	15
β-strand	391-393	3	14
α-helix	394-396	3
β-strand	397-398	2	14
β-strand	404-413	10	14
α-helix	414-418	5
β-strand	423-428	6	15
α-helix	433-435	3
β-strand	437-441	5	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Immunoglobulin G-binding protein A	A, B, C	protein	58	Staphylococcus aureus	P38507 (AlphaFold model)
Ig gamma-3 chain C region	D, E, F	protein	220	Homo sapiens	P01860 (AlphaFold model)

Sequence of entity 1 (A, B, C), FASTA

>4WWI_1 Immunoglobulin G-binding protein A (chains A, B, C)
ADNKFNKEQQNAFYEILHLPNLTEEQRNGFIQSLKDDPSVSKEILAEAKKLNDAQAPK

Sequence of entity 2 (D, E, F), FASTA

>4WWI_2 Ig gamma-3 chain C region (chains D, E, F)
PSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVQFKWYVDGVEVHNAKTKPREEQFN
STFRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKTKGQPREPQVYTLPPSREE
MTKNQVSLTCLVKGFYPSDIAVEWESSGQPENNYNTTPPMLDSDGSFFLYSKLTVDKSRW
QQGNIFSCSVMHEALHNHYTQKSLSLSPGKGSLEHHHHHH

Primary citation

Suppression of conformational heterogeneity at a protein-protein interface. Deis, L.N., Wu, Q., Wang, Y. et al. Proc Natl Acad Sci U S A (2015) 112:9028-9033. DOI 10.1073/pnas.1424724112 · PubMed

Other PDB entries of the same protein (UniProt P38507 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4NPD 0.9 Å, High-resolution structure of C domain of staphylococcal protein A at cryogenic temperature
4NPE 1.42 Å, High-resolution structure of C domain of staphylococcal protein A at room temperature
4NPF 1.49 Å, High-resolution structure of two tandem B domains of staphylococcal protein A connected…
8CPL 1.6 Å, YZw2 a scaffold for cryo-EM of small proteins of interest
4ZMD 1.87 Å, C domain of staphylococcal protein A mutant - Q9W
4ZNC 2.28 Å, Fc fragment of human IgG in complex with the C domain of staphylococcal protein A mutant…
1LP1 2.3 Å, Protein Z in complex with an in vitro selected affibody
5CBN 2.3 Å, Fusion protein of mbp3-16 and B4 domain of protein A from staphylococcal aureus with…
5H7D 2.57 Å, Crystal structure of the YgjG-protein A-Zpa963-calmodulin complex
5EWX 2.6 Å, Fusion protein of T4 lysozyme and B4 domain of protein A from staphylococcal aureus with…
5H76 2.6 Å, Crystal structure of the DARPin-Protein A fusion protein
5H79 2.7 Å, Crystal structure of a repeat protein with three Protein A repeat module

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