9N1Z: C3d

Structure of C3d Bound to a Fragment of FHR-2. Determined by X-ray diffraction at 2.31 Å resolution. Released 10 Dec 2025.

Method: X-ray diffraction
Resolution: 2.31 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,876
Mol. weight: 96 kDa
Released: 10 Dec 2025

Explore 9N1Z in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9N1Z contains 49 α-helices and 52 β-strands across 4 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: 18 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	994-996	3
α-helix	998-1003	6
α-helix	1013-1031	19
α-helix	1034-1037	4
α-helix	1039-1057	19
β-strand	1060	1	1
β-strand	1066	1	1
α-helix	1073-1075	3
α-helix	1076-1089	14
α-helix	1097-1110	14
β-strand	1112	1	2
β-strand	1118	1	2
α-helix	1127-1129	3
α-helix	1131-1134	4
α-helix	1139-1153	15
α-helix	1155-1158	4
α-helix	1165-1179	15
α-helix	1186-1197	12
α-helix	1205-1212	8
β-strand	1215	1	3
β-strand	1219	1	3
α-helix	1226-1243	18
α-helix	1249-1259	11
α-helix	1269-1284	16

Chain B: 7 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	147-148	2
β-strand	149	1	4
α-helix	152-154	3
β-strand	158-160	3	5
β-strand	168	1	4
β-strand	173-175	3	6
β-strand	176-178	3	5
α-helix	179	1
α-helix	182	1
β-strand	183-185	3	7
β-strand	189-191	3	6
β-strand	192-193	2	8
β-strand	196-197	2	8
α-helix	198-201	4
β-strand	202-204	3	7
β-strand	207-209	3	9
α-helix	211-217	7
β-strand	219-221	3	10
β-strand	229-231	3	9
β-strand	236-238	3	11
β-strand	239-241	3	10
α-helix	242	1
β-strand	246-247	2	12
β-strand	254-256	3	11
β-strand	258	1	13
β-strand	261	1	13
β-strand	267-268	2	12

Chain C: 16 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	1013-1031	19
α-helix	1034-1037	4
α-helix	1043-1057	15
β-strand	1060	1	14
β-strand	1066	1	14
α-helix	1073-1075	3
α-helix	1076-1089	14
α-helix	1094-1096	3
α-helix	1097-1110	14
β-strand	1112	1	15
β-strand	1118	1	15
α-helix	1127-1129	3
α-helix	1139-1153	15
α-helix	1165-1179	15
α-helix	1180-1182	3
α-helix	1186-1198	13
α-helix	1205-1212	8
β-strand	1215	1	16
β-strand	1219	1	16
α-helix	1229-1242	14
α-helix	1249-1257	9
α-helix	1269-1284	16

Chain D: 8 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	149	1	17
α-helix	152-154	3
β-strand	158-160	3	18
α-helix	163-165	3
β-strand	168	1	17
β-strand	173-175	3	19
β-strand	176-178	3	18
α-helix	179	1
α-helix	182	1
β-strand	183-185	3	20
β-strand	189-191	3	19
β-strand	192-193	2	21
β-strand	196-197	2	21
α-helix	198-201	4
β-strand	202-204	3	20
β-strand	207-208	2	22
α-helix	211-216	6
β-strand	219-221	3	23
β-strand	230-231	2	22
β-strand	236-238	3	24
β-strand	239-241	3	23
α-helix	242	1
β-strand	246-247	2	25
β-strand	254-256	3	24
α-helix	257	1
β-strand	258	1	26
β-strand	261	1	26
β-strand	267-268	2	25

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Complement C3dg fragment	A, C	protein	297	Homo sapiens	P01024 (AlphaFold model)
Complement factor H-related protein 2	B, D	protein	131	Homo sapiens	P36980 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>9N1Z_1 Complement C3dg fragment (chains A, C)
GSRSTDAERLKHLIVTPSGAGEQNMIGMTPTVIAVHYLDETEQWEKFGLEKRQGALELIK
KGYTQQLAFRQPSSAFAAFVKRAPSTWLTAYVVKVFSLAVNLIAIDSQVLCGAVKWLILE
KQKPDGVFQEDAPVIHQEMIGGLRNNNEKDMALTAFVLISLQEAKDICEEQVNSLPGSIT
KAGDFLEANYMNLQRSYTVAIAGYALAQMGRLKGPLLNKFLTTAKDKNRWEDPGKQLYNV
EATSYALLALLQLKDFDFVPPVVRWLNEQRYYGGGYGSTQATFMVFQALAQYQKDAP

Sequence of entity 2 (B, D), FASTA

>9N1Z_2 Complement factor H-related protein 2 (chains B, D)
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

Browse structure collections

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