4ONT: Complement factor H

Ternary host recognition complex of complement factor H, C3d, and sialic acid. Determined by X-ray diffraction at 2.15 Å resolution. Released 26 Nov 2014.

Method: X-ray diffraction
Resolution: 2.15 Å
Organism: Homo sapiens
Chains: 6
Atoms: 10,510
Mol. weight: 153.2 kDa
Released: 26 Nov 2014

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

Secondary structure: helices and β-sheets

4ONT contains 75 α-helices and 78 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: 21 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	1-3	3
α-helix	4-10	7
α-helix	20-37	18
α-helix	41-44	4
α-helix	47-64	18
β-strand	67	1	11
β-strand	73	1	11
α-helix	80-82	3
α-helix	83-95	13
α-helix	96-98	3
α-helix	101-103	3
α-helix	104-113	10
α-helix	114-118	5
β-strand	119	1	12
β-strand	125	1	12
α-helix	134-140	7
α-helix	146-160	15
α-helix	162-165	4
α-helix	171-186	16
α-helix	187-189	3
α-helix	193-204	12
α-helix	211-220	10
β-strand	222	1	13
β-strand	226	1	13
α-helix	233-249	17
α-helix	256-264	9
α-helix	276-291	16

Chain B: 17 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	17-37	21
α-helix	41-44	4
α-helix	46-48	3
α-helix	49-64	16
β-strand	67	1	24
β-strand	73	1	24
α-helix	80-82	3
α-helix	83-95	13
α-helix	104-113	10
α-helix	114-118	5
β-strand	119	1	25
β-strand	125	1	25
α-helix	134-141	8
α-helix	146-165	20
α-helix	172-186	15
α-helix	193-205	13
α-helix	211-220	10
β-strand	222	1	26
β-strand	226	1	26
α-helix	234-249	16
α-helix	256-264	9
α-helix	276-292	17
α-helix	296-298	3

Chain C: 17 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3
α-helix	20-37	18
α-helix	41-44	4
α-helix	49-63	15
α-helix	64-66	3
β-strand	67	1	37
β-strand	73	1	37
α-helix	80-82	3
α-helix	83-95	13
α-helix	104-117	14
β-strand	119	1	38
β-strand	125	1	38
α-helix	134-140	7
α-helix	146-165	20
α-helix	172-186	15
α-helix	187-189	3
α-helix	193-205	13
α-helix	211-220	10
β-strand	222	1	39
β-strand	226	1	39
α-helix	233-250	18
α-helix	256-265	10
α-helix	276-291	16

Chain D: 6 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	1109	1	14
α-helix	1112-1114	3
β-strand	1118-1120	3	15
β-strand	1128	1	14
β-strand	1133-1135	3	16
β-strand	1136-1138	3	15
α-helix	1139	1
β-strand	1143-1145	3	17
β-strand	1149-1151	3	16
β-strand	1152-1153	2	18
β-strand	1156-1157	2	18
α-helix	1158-1160	3
β-strand	1162-1164	3	17
α-helix	1165-1166	2
β-strand	1167-1168	2	19
α-helix	1171-1177	7
β-strand	1179-1181	3	20
β-strand	1190-1191	2	19
β-strand	1196-1198	3	21
β-strand	1199-1201	3	20
α-helix	1202	1
β-strand	1205-1207	3	22
β-strand	1215-1217	3	21
β-strand	1219	1	23
β-strand	1222	1	23
β-strand	1228-1230	3	22

Chain E: 9 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	1109	1	27
α-helix	1112-1114	3
β-strand	1118-1120	3	28
α-helix	1123-1125	3
β-strand	1128	1	27
β-strand	1133-1135	3	29
β-strand	1136-1138	3	28
α-helix	1139	1
α-helix	1142	1
β-strand	1143-1145	3	30
β-strand	1149-1151	3	29
β-strand	1152-1153	2	31
β-strand	1156-1157	2	31
α-helix	1158-1160	3
β-strand	1162-1164	3	30
β-strand	1167-1168	2	32
α-helix	1171-1177	7
β-strand	1179-1181	3	33
β-strand	1190-1191	2	32
β-strand	1196-1198	3	34
β-strand	1199-1201	3	33
α-helix	1202	1
β-strand	1205-1207	3	35
α-helix	1211-1213	3
β-strand	1215-1217	3	34
β-strand	1218-1219	2	36
β-strand	1222-1223	2	36
α-helix	1224-1226	3
β-strand	1228-1230	3	35

Chain F: 5 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	1109	1	1
α-helix	1112-1114	3
β-strand	1118-1120	3	2
β-strand	1128	1	1
β-strand	1133-1135	3	3
β-strand	1136-1138	3	2
α-helix	1139	1
β-strand	1143-1145	3	4
β-strand	1149-1151	3	3
β-strand	1152	1	5
β-strand	1157	1	5
α-helix	1158-1161	4
β-strand	1162-1164	3	4
β-strand	1167-1169	3	6
α-helix	1171-1177	7
β-strand	1179-1181	3	7
β-strand	1189-1191	3	6
β-strand	1195-1198	4	8
β-strand	1199-1201	3	7
β-strand	1206-1207	2	9
β-strand	1215-1218	4	8
β-strand	1219	1	10
β-strand	1222	1	10
α-helix	1224-1227	4
β-strand	1228-1229	2	9

Molecules and chains

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

Sequence of entity 1 (D, E, F), FASTA

>4ONT_1 Complement factor H (chains D, E, F)
EAEFGKCGPPPPIDNGDITSFPLSVYAPASSVEYQCQNLYQLEGNKRITCRNGQWSEPPK
CLHPCVISREIMENYNIALRWTAKQKLYSRTGESVEFVCKRGYRLSSRSHTLRTTCWDGK
LEYPTCAKR

Sequence of entity 2 (A, B, C), FASTA

>4ONT_2 Complement C3d fragment (chains A, B, C)
GPLGSPEFRDAERLKHLIVTPSGAGEQNMIGMTPTVIAVHYLDETEQWEKFGLEKRQGAL
ELIKKGYTQQLAFRQPSSAFAAFVKRAPSTWLTAYVVKVFSLAVNLIAIDSQVLCGAVKW
LILEKQKPDGVFQEDAPVIHQEMIGGLRNNNEKDMALTAFVLISLQEAKDICEEQVNSLP
GSITKAGDFLEANYMNLQRSYTVAIAGYALAQMGRLKGPLLNKFLTTAKDKNRWEDPGKQ
LYNVEATSYALLALLQLKDFDFVPPVVRWLNEQRYYGGGYGSTQATFMVFQALAQYQKDA
PDHQELNLDVSLQLPSR

Primary citation

Structural basis for sialic acid-mediated self-recognition by complement factor H. Blaum, B.S., Hannan, J.P., Herbert, A.P. et al. Nat Chem Biol (2015) 11:77-82. DOI 10.1038/nchembio.1696 · PubMed

Other PDB entries of the same protein (UniProt P08603 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4K12 1.08 Å, Structural Basis for Host Specificity of Factor H Binding by Streptococcus pneumoniae
3R62 1.52 Å, Structure of complement regulator Factor H mutant, T1184R.
3KZJ 1.65 Å, Structure of complement Factor H variant R1203A
2G7I 1.75 Å, Structure of Human Complement Factor H Carboxyl Terminal Domains 19-20: a Basis for…
3SW0 1.8 Å, Structure of the C-terminal region (modules 18-20) of complement regulator Factor H
6ATG 1.8 Å, Insights to complement factor H recruitment by the borrelial CspZ protein as revealed by…
9MLU 1.82 Å, FbaA with Factor H 6-7 domain
9MMX 1.9 Å, M6 protein with Factor H 6-7 domain
3KXV 2.0 Å, Structure of complement Factor H variant Q1139A
3OXU 2.1 Å, Complement components factor H CCP19-20 and C3d in complex
6ZH1 2.2 Å, Crystal structure of complex between FH19-20 and FhbA protein from Borrelia hermsii
4ZH1 2.24 Å, Complement factor H in complex with the GM1 glycan

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