3RJ3: Complement C3d fragment

Complement components factor H CCP19-20 (S1191L mutant) and C3D in complex. Determined by X-ray diffraction at 2.35 Å resolution. Released 14 Mar 2012.

Method: X-ray diffraction
Resolution: 2.35 Å
Organism: Homo sapiens
Chains: 6
Atoms: 10,236
Mol. weight: 151.1 kDa
Released: 14 Mar 2012

Explore 3RJ3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3RJ3 contains 75 α-helices and 75 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.

Chain A: 18 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	4-10	7
α-helix	20-37	18
α-helix	41-44	4
α-helix	46-63	18
α-helix	64-66	3
β-strand	67	1	1
β-strand	73	1	1
α-helix	80-82	3
α-helix	83-96	14
α-helix	104-117	14
β-strand	119	1	2
β-strand	125	1	2
α-helix	134-140	7
α-helix	146-160	15
α-helix	162-165	4
α-helix	172-186	15
α-helix	187-189	3
α-helix	193-206	14
α-helix	211-219	9
β-strand	222	1	3
β-strand	226	1	3
α-helix	233-250	18
α-helix	256-265	10
α-helix	276-292	17

Chain B: 18 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	17-37	21
α-helix	46-48	3
α-helix	49-63	15
α-helix	64-66	3
β-strand	67	1	4
β-strand	73	1	4
α-helix	80-82	3
α-helix	83-94	12
α-helix	104-117	14
β-strand	119	1	5
β-strand	125	1	5
α-helix	134-141	8
α-helix	146-165	20
α-helix	172-186	15
α-helix	187-189	3
α-helix	193-205	13
α-helix	212-219	8
β-strand	222	1	6
β-strand	226	1	6
α-helix	233-250	18
α-helix	256-265	10
α-helix	276-292	17
α-helix	296-299	4
α-helix	304-306	3

Chain C: 21 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	4-10	7
α-helix	12-14	3
α-helix	20-34	15
α-helix	41-44	4
α-helix	46-63	18
α-helix	64-66	3
β-strand	67	1	7
β-strand	73	1	7
α-helix	80-81	2
β-strand	82	1	7
α-helix	83-96	14
α-helix	104-113	10
α-helix	114-118	5
β-strand	119	1	8
β-strand	125	1	8
α-helix	134-136	3
α-helix	138-140	3
α-helix	146-165	20
α-helix	166-168	3
α-helix	172-186	15
α-helix	187-189	3
α-helix	193-205	13
α-helix	211-219	9
α-helix	233-250	18
α-helix	256-265	10
α-helix	276-292	17

Chain D: 6 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	1109	1	9
α-helix	1111-1114	4
β-strand	1118-1120	3	10
β-strand	1128	1	9
β-strand	1133-1135	3	11
β-strand	1136-1138	3	10
α-helix	1139	1
β-strand	1143-1145	3	12
β-strand	1149-1151	3	11
β-strand	1152-1153	2	13
β-strand	1156-1157	2	13
α-helix	1158-1160	3
β-strand	1162-1164	3	12
α-helix	1165-1166	2
β-strand	1167-1168	2	14
α-helix	1171-1176	6
β-strand	1179-1181	3	15
β-strand	1190-1191	2	14
β-strand	1196-1198	3	16
β-strand	1199-1201	3	15
α-helix	1202	1
β-strand	1205-1207	3	17
β-strand	1215-1217	3	16
β-strand	1219	1	18
β-strand	1222	1	18
β-strand	1228-1230	3	17

Chain E: 9 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	1109	1	19
α-helix	1112-1114	3
β-strand	1118-1120	3	20
β-strand	1128	1	19
β-strand	1133-1135	3	21
β-strand	1136-1138	3	20
α-helix	1139	1
α-helix	1142	1
β-strand	1143-1145	3	22
β-strand	1149-1151	3	21
β-strand	1152	1	23
β-strand	1157	1	23
α-helix	1158-1160	3
β-strand	1162-1164	3	22
β-strand	1167-1168	2	24
α-helix	1171-1177	7
β-strand	1179-1181	3	25
β-strand	1190-1191	2	24
β-strand	1196-1198	3	26
β-strand	1199-1201	3	25
α-helix	1202	1
β-strand	1205-1207	3	27
α-helix	1208	1
α-helix	1211-1213	3
β-strand	1215-1217	3	26
β-strand	1219	1	28
β-strand	1222	1	28
α-helix	1224-1226	3
β-strand	1228-1230	3	27

Chain F: 3 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	1109	1	29
α-helix	1112-1114	3
β-strand	1118-1120	3	30
β-strand	1128	1	29
β-strand	1133-1135	3	31
β-strand	1136-1138	3	30
β-strand	1143-1145	3	32
β-strand	1149-1151	3	31
β-strand	1152-1153	2	33
β-strand	1156-1157	2	33
α-helix	1158-1160	3
β-strand	1162-1164	3	32
β-strand	1167-1169	3	34
β-strand	1180-1181	2	35
β-strand	1189-1191	3	34
β-strand	1196-1198	3	36
β-strand	1199-1200	2	35
β-strand	1215-1217	3	36
β-strand	1219	1	37
β-strand	1222	1	37
α-helix	1225-1227	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Complement C3d fragment	A, B, C	protein	317	Homo sapiens	P01024 (AlphaFold model)
Complement Factor H-related protein 1	D, E, F	protein	129	Homo sapiens	P08603 (AlphaFold model)

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

>3RJ3_1 Complement C3d fragment (chains A, B, C)
GPLGSPEFRDAERLKHLIVTPSGAGEQNMIGMTPTVIAVHYLDETEQWEKFGLEKRQGAL
ELIKKGYTQQLAFRQPSSAFAAFVKRAPSTWLTAYVVKVFSLAVNLIAIDSQVLCGAVKW
LILEKQKPDGVFQEDAPVIHQEMIGGLRNNNEKDMALTAFVLISLQEAKDICEEQVNSLP
GSITKAGDFLEANYMNLQRSYTVAIAGYALAQMGRLKGPLLNKFLTTAKDKNRWEDPGKQ
LYNVEATSYALLALLQLKDFDFVPPVVRWLNEQRYYGGGYGSTQATFMVFQALAQYQKDA
PDHQELNLDVSLQLPSR

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

>3RJ3_2 Complement Factor H-related protein 1 (chains D, E, F)
EAEFGKCGPPPPIDNGDITSFPLSVYAPASSVEYQCQNLYQLEGNKRITCRNGQWSEPPK
CLHPCVISREIMENYNIALRWTAKQKLYLRTGESVEFVCKRGYRLSSRSHTLRTTCWDGK
LEYPTCAKR

Primary citation

Structural and functional characterization of the product of disease-related factor h gene conversion. Herbert, A.P., Kavanagh, D., Johansson, C. et al. Biochemistry (2012) 51:1874-1884. DOI 10.1021/bi201689j · 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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