4AYD: Complement factor H

Structure of a complex between CCPs 6 and 7 of Human Complement Factor H and Neisseria meningitidis FHbp Variant 1 R106A mutant. Determined by X-ray diffraction at 2.4 Å resolution. Released 7 Nov 2012.

Method: X-ray diffraction
Resolution: 2.4 Å
Organisms: HOMO SAPIENS, NEISSERIA MENINGITIDIS
Chains: 6
Atoms: 9,233
Mol. weight: 126.32 kDa
Released: 7 Nov 2012

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

Secondary structure: helices and β-sheets

4AYD contains 43 α-helices and 104 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: 6 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	322-324	3
β-strand	325	1	1
α-helix	326-328	3
β-strand	333-335	3	2
α-helix	338-341	4
α-helix	342-344	3
β-strand	347	1	1
β-strand	352-357	6	2
β-strand	361-362	2	3
β-strand	369-375	7	2
β-strand	378-380	3	2
β-strand	386-387	2	3
β-strand	388-390	3	4
α-helix	391-393	3
β-strand	397	1	5
β-strand	404	1	6
β-strand	405-407	3	4
β-strand	411-413	3	7
β-strand	416	1	5
α-helix	417	1
β-strand	428-432	5	7
β-strand	435-437	3	7

Chain B: 5 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	325	1	8
α-helix	326-328	3
β-strand	333-335	3	9
α-helix	338-341	4
α-helix	342-344	3
β-strand	347	1	8
β-strand	352-357	6	9
β-strand	361-362	2	10
β-strand	369-375	7	9
β-strand	378-380	3	9
β-strand	386-387	2	10
β-strand	388-390	3	11
α-helix	391-393	3
β-strand	397	1	12
β-strand	405-407	3	11
β-strand	411-413	3	13
β-strand	416	1	12
α-helix	417	1
β-strand	428-432	5	13
β-strand	435-437	3	13

Chain C: 8 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	81-86	6
α-helix	94	1
β-strand	99-100	2	14
β-strand	110-115	6	15
β-strand	118-122	5	15
α-helix	126	1
β-strand	127-128	2	14
α-helix	130-132	3
α-helix	134	1
β-strand	138-146	9	15
β-strand	155-165	11	15
β-strand	169-180	12	15
β-strand	188-201	14	15
β-strand	203	1	16
α-helix	204	1
β-strand	205	1	17
α-helix	206-208	3
β-strand	214-223	10	16
β-strand	226-236	11	16
β-strand	241-247	7	16
α-helix	252-254	3
β-strand	257-265	9	16
β-strand	270	1	17
β-strand	271-279	9	16
β-strand	282-292	11	16
β-strand	298-307	10	16
β-strand	310-320	11	16

Chain D: 9 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	81-86	6
α-helix	88-89	2
α-helix	94	1
β-strand	99-100	2	18
β-strand	109-115	7	19
β-strand	118-122	5	19
α-helix	126	1
β-strand	127-128	2	18
α-helix	130-132	3
α-helix	134	1
β-strand	138-149	12	19
β-strand	152-165	14	19
β-strand	169-180	12	19
β-strand	184	1	6
β-strand	187-201	15	19
β-strand	203	1	20
α-helix	204	1
β-strand	205	1	21
α-helix	206-208	3
β-strand	214-223	10	20
β-strand	226-236	11	20
β-strand	241-247	7	20
α-helix	252-254	3
β-strand	257-265	9	20
β-strand	270	1	21
β-strand	271-279	9	20
β-strand	282-292	11	20
β-strand	298-307	10	20
β-strand	310-320	11	20

Chain E: 7 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	324	1
β-strand	325	1	22
α-helix	326-328	3
β-strand	333-335	3	23
α-helix	338-341	4
α-helix	342-344	3
β-strand	347	1	22
β-strand	352-357	6	23
β-strand	361-362	2	24
β-strand	369-375	7	23
β-strand	378-380	3	23
β-strand	386-387	2	24
β-strand	388-390	3	25
α-helix	391-393	3
β-strand	397	1	26
β-strand	405-407	3	25
β-strand	411-413	3	27
β-strand	416	1	26
α-helix	417	1
α-helix	423-425	3
β-strand	428-432	5	27
β-strand	435-437	3	27

Chain F: 8 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	81-86	6
α-helix	88-89	2
β-strand	99-100	2	28
β-strand	109-115	7	19
β-strand	118-122	5	19
α-helix	126	1
β-strand	127-128	2	28
α-helix	130-132	3
α-helix	134	1
β-strand	138-149	12	19
β-strand	152-165	14	19
β-strand	169-180	12	19
β-strand	188-201	14	19
β-strand	203	1	29
α-helix	204	1
β-strand	205	1	30
α-helix	206-208	3
β-strand	214-223	10	29
β-strand	226-236	11	29
β-strand	241-247	7	29
α-helix	252-254	3
β-strand	257-265	9	29
β-strand	270	1	30
β-strand	271-279	9	29
β-strand	282-292	11	29
β-strand	298-307	10	29
β-strand	310-320	11	29

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Complement factor H	A, B, E	protein	125	HOMO SAPIENS	P08603 (AlphaFold model)
Factor H binding protein	C, D, F	protein	257	NEISSERIA MENINGITIDIS	Q9JXV4 (AlphaFold model)

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

>4AYD_1 COMPLEMENT FACTOR H (chains A, B, E)
MGTLKPCDYPDIKHGGLYHENMRRPYFPVAVGKYYSYYCDEHFETPSGSYWDHIHCTQDG
WSPAVPCLRKCYFPYLENGYNQNHGRKFVQGKSIDVACHPGYALPKAQTTVTCMENGWSP
TPRCI

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

>4AYD_2 FACTOR H BINDING PROTEIN (chains C, D, F)
MVAADIGAGLADALTAPLDHKDKGLQSLTLDQSVAKNEKLKLAAQGAEKTYGNGDSLNTG
KLKNDKVSRFDFIRQIEVDGQLITLESGEFQVYKQSHSALTAFQTEQIQDSEHSGKMVAK
RQFRIGDIAGEHTSFDKLPEGGRATYRGTAFGSDDAGGKLTYTIDFAAKQGNGKIEHLKS
PELNVDLAAADIKPDGKRHAVISGSVLYNQAEKGSYSLGIFGGKAQEVAGSAEVKTVNGI
RHIGLAAKQELHHHHHH

Primary citation

Design and Evaluation of Meningococcal Vaccines Through Structure-Based Modification of Host and Pathogen Molecules. Johnson, S., Tan, L., Van Der Veen, S. et al. PLoS Pathog (2012) 8:2981. DOI 10.1371/JOURNAL.PPAT.1002981 · 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
4ONT 2.15 Å, Ternary host recognition complex of complement factor H, C3d, and sialic acid
6ZH1 2.2 Å, Crystal structure of complex between FH19-20 and FhbA protein from Borrelia hermsii

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