9N20: C3d

Structure of C3d Bound to a Fragment of FHR-2 and S. aureus Efb-C. Determined by X-ray diffraction at 3.3 Å resolution. Released 10 Dec 2025.

Method: X-ray diffraction
Resolution: 3.3 Å
Organisms: Homo sapiens, Staphylococcus aureus subsp. aureus Mu50
Chains: 3
Atoms: 3,808
Mol. weight: 56.4 kDa
Released: 10 Dec 2025

Explore 9N20 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9N20 contains 27 α-helices and 24 β-strands across 3 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: 17 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	999-1003	5
α-helix	1013-1031	19
α-helix	1034-1037	4
α-helix	1040-1056	17
α-helix	1057-1059	3
β-strand	1060	1	1
β-strand	1066	1	1
α-helix	1073-1075	3
α-helix	1076-1089	14
α-helix	1097-1109	13
β-strand	1112	1	2
β-strand	1118	1	2
α-helix	1131-1134	4
α-helix	1139-1153	15
α-helix	1155-1158	4
α-helix	1165-1178	14
α-helix	1186-1199	14
α-helix	1205-1212	8
β-strand	1215	1	3
β-strand	1219	1	3
α-helix	1226-1243	18
α-helix	1249-1258	10
α-helix	1269-1284	16

Chain B: 6 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	149	1	4
α-helix	151-155	5
β-strand	158-160	3	5
α-helix	163-165	3
β-strand	168	1	4
β-strand	174-175	2	6
β-strand	176-178	3	5
α-helix	182	1
β-strand	183-185	3	7
β-strand	189-190	2	6
α-helix	197-198	2
β-strand	202-204	3	7
β-strand	207-208	2	8
α-helix	211-217	7
β-strand	219-221	3	9
β-strand	230-231	2	8
β-strand	237-238	2	10
β-strand	239-241	3	9
β-strand	246-247	2	11
β-strand	254-255	2	10
β-strand	258	1	12
β-strand	261	1	12
α-helix	263-265	3
β-strand	267-268	2	11

Chain C: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	102-123	22
α-helix	127-138	12
α-helix	142-144	3
α-helix	145-161	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Complement C3dg fragment	A	protein	297	Homo sapiens	P01024 (AlphaFold model)
Fibrinogen-binding protein	C	protein	75	Staphylococcus aureus subsp. aureus Mu50	P68799 (AlphaFold model)
Complement factor H-related protein 2	B	protein	131	Homo sapiens	P36980 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9N20_1 Complement C3dg fragment (chains A)
GSRSTDAERLKHLIVTPSGAGEQNMIGMTPTVIAVHYLDETEQWEKFGLEKRQGALELIK
KGYTQQLAFRQPSSAFAAFVKRAPSTWLTAYVVKVFSLAVNLIAIDSQVLCGAVKWLILE
KQKPDGVFQEDAPVIHQEMIGGLRNNNEKDMALTAFVLISLQEAKDICEEQVNSLPGSIT
KAGDFLEANYMNLQRSYTVAIAGYALAQMGRLKGPLLNKFLTTAKDKNRWEDPGKQLYNV
EATSYALLALLQLKDFDFVPPVVRWLNEQRYYGGGYGSTQATFMVFQALAQYQKDAP

Sequence of entity 2 (C), FASTA

>9N20_2 Fibrinogen-binding protein (chains C)
GSTFNKPAAKTDATIKKEQKLIQAQNLVREFEKTHTVSAHRKAQKAVNLVSFEYKVKKMV
LQERIDNVLKQGLVR

Sequence of entity 3 (B), FASTA

>9N20_3 Complement factor H-related protein 2 (chains B)
GSTGSSAEKCGPPPPIDNGDITSFLLSVYAPGSSVEYQCQNLYQLEGNNQITCRNGQWSE
PPKCLDPCVISQEIMEKYNIKLKWTNQQKLYSRTGDIVEFVCKSGYHPTKSHSFRAMCQN
GKLVYPSCEEK

Primary citation

The C-terminal domain of Staphylococcus aureus Efb recruits FHR-2 to C3b, synergistically inhibiting the terminal complement pathway. Duan, H., Kortvely, E., Mary, J.L. et al. J Immunol (2026) 215. DOI 10.1093/jimmun/vkaf316 · PubMed

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

2WY7 1.7 Å, Staphylococcus aureus complement subversion protein Sbi-IV in complex with complement…
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

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