5O14: Factor H binding protein variant 1.1

Co-crystal structure of a cross-reactive bactericidal human antibody targeting meningococcal vaccine antigen factor H binding protein. Determined by X-ray diffraction at 2.19 Å resolution. Released 14 Feb 2018.

Method: X-ray diffraction
Resolution: 2.19 Å
Organisms: Neisseria meningitidis serogroup B (strain MC58), Homo sapiens
Chains: 6
Atoms: 10,853
Mol. weight: 153.92 kDa
Released: 14 Feb 2018

Explore 5O14 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5O14 contains 59 α-helices and 124 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: 9 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	16-21	6
α-helix	23-24	2
α-helix	29	1
α-helix	31	1
β-strand	34-35	2	1
β-strand	45-50	6	2
β-strand	53-57	5	2
β-strand	62-63	2	1
α-helix	65-67	3
α-helix	69	1
β-strand	73-81	9	2
β-strand	90-100	11	2
β-strand	104-114	11	2
β-strand	124-136	13	2
β-strand	138	1	3
α-helix	139	1
β-strand	140	1	4
α-helix	141-143	3
β-strand	149-158	10	3
β-strand	161-171	11	3
β-strand	176-182	7	3
α-helix	187-189	3
β-strand	192-200	9	3
β-strand	205	1	4
β-strand	206-214	9	3
β-strand	217-227	11	3
β-strand	233-242	10	3
β-strand	245-254	10	3

Chain B: 8 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	16-21	6
α-helix	23-24	2
α-helix	29	1
β-strand	34-35	2	5
β-strand	45-50	6	6
β-strand	53-57	5	6
β-strand	62-63	2	5
α-helix	65-67	3
α-helix	69	1
β-strand	73-81	9	6
β-strand	90-100	11	6
β-strand	104-114	11	6
β-strand	124-136	13	6
β-strand	138	1	7
α-helix	139	1
β-strand	140	1	8
α-helix	141-143	3
β-strand	149-158	10	7
β-strand	161-171	11	7
β-strand	176-182	7	7
α-helix	187-189	3
β-strand	192-200	9	7
β-strand	205	1	8
β-strand	206-214	9	7
β-strand	217-227	11	7
β-strand	233-242	10	7
β-strand	245-254	10	7

Chain C: 13 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	9
α-helix	7-9	3
β-strand	10-12	3	10
β-strand	18-25	8	9
α-helix	29-31	3
β-strand	34-39	6	10
β-strand	46-52	7	10
β-strand	57-60	4	10
α-helix	62-64	3
β-strand	68-73	6	9
α-helix	74-76	3
β-strand	78-83	6	9
α-helix	88-90	3
β-strand	92-100	9	10
β-strand	108-112	5	10
β-strand	116-120	5	10
α-helix	124-125	2
β-strand	126	1	11
α-helix	127-128	2
β-strand	129-133	5	12
α-helix	134-136	3
α-helix	139-140	2
β-strand	144-154	11	12
β-strand	155	1	11
β-strand	160-163	4	13
α-helix	164-166	3
β-strand	168	1	13
β-strand	172-174	3	12
α-helix	175-177	3
β-strand	178-179	2	12
β-strand	185-194	10	12
α-helix	195-197	3
β-strand	204-209	6	13
α-helix	210-212	3
β-strand	214-219	6	13

Chain D: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	14
β-strand	10-14	5	15
β-strand	19-25	7	14
β-strand	33-38	6	15
β-strand	45-49	5	15
β-strand	53-54	2	15
α-helix	55	1
β-strand	62-67	6	14
β-strand	70-75	6	14
α-helix	80-82	3
β-strand	84-90	7	15
α-helix	98	1
β-strand	99	1	15
α-helix	100	1
β-strand	103-108	6	15
β-strand	112	1	16
α-helix	113-114	2
β-strand	115-119	5	17
α-helix	120-122	3
α-helix	123-128	6
β-strand	130-140	11	17
β-strand	141	1	16
β-strand	146-151	6	18
β-strand	154-155	2	18
β-strand	160-164	5	17
α-helix	165-168	4
β-strand	174-183	10	17
α-helix	184-188	5
β-strand	192-198	7	18
β-strand	206-211	6	18

Chain H: 11 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	24
α-helix	7-9	3
β-strand	10-12	3	25
β-strand	18-25	8	24
α-helix	29-31	3
β-strand	34-39	6	25
β-strand	46-52	7	25
β-strand	57-60	4	25
β-strand	68-73	6	24
α-helix	74-76	3
β-strand	78-83	6	24
α-helix	88-90	3
β-strand	92-100	9	25
β-strand	108-112	5	25
β-strand	116-120	5	25
α-helix	124-125	2
β-strand	126	1	26
α-helix	127-128	2
β-strand	129-133	5	27
α-helix	134-136	3
β-strand	144-154	11	27
β-strand	155	1	26
β-strand	160-163	4	28
α-helix	164-166	3
β-strand	168	1	28
β-strand	172-174	3	27
α-helix	175-177	3
β-strand	178-179	2	27
β-strand	185-194	10	27
α-helix	195-197	3
β-strand	204-209	6	28
α-helix	210-212	3
β-strand	214-219	6	28

Chain L: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	19
β-strand	10-14	5	20
β-strand	19-25	7	19
β-strand	33-38	6	20
β-strand	45-49	5	20
β-strand	53-54	2	20
α-helix	55	1
β-strand	62-67	6	19
β-strand	70-75	6	19
α-helix	80-82	3
β-strand	84-90	7	20
α-helix	98	1
β-strand	99	1	20
α-helix	100	1
β-strand	103-108	6	20
β-strand	112	1	21
α-helix	113-114	2
β-strand	115-119	5	22
α-helix	120-122	3
α-helix	123-127	5
β-strand	130-140	11	22
β-strand	141	1	21
β-strand	146-151	6	23
β-strand	154-155	2	23
β-strand	160-164	5	22
α-helix	165-168	4
β-strand	174-183	10	22
α-helix	184-188	5
β-strand	192-198	7	23
β-strand	206-211	6	23

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Factor H binding protein variant 1.1	A, B	protein	257	Neisseria meningitidis serogroup B (strain MC58)	Q9JXV4 (AlphaFold model)
Fab 1A12 Heavy Chain	C, H	protein	235	Homo sapiens
Fab 1A12 Light Chain	D, L	protein	217	Homo sapiens

Sequence of entity 1 (A, B), FASTA

>5O14_1 Factor H binding protein variant 1.1 (chains A, B)
MVAADIGAGLADALTAPLDHKDKGLQSLTLDQSVRKNEKLKLAAQGAEKTYGNGDSLNTG
KLKNDKVSRFDFIRQIEVDGQLITLESGEFQVYKQSHSALTAFQTEQIQDSEHSGKMVAK
RQFRIGDIAGEHTSFDKLPEGGRATYRGTAFGSDDAGGKLTYTIDFAAKQGNGKIEHLKS
PELNVDLAAADIKPDGKRHAVISGSVLYNQAEKGSYSLGIFGGKAQEVAGSAEVKTVNGI
RHIGLAAKQLEHHHHHH

Sequence of entity 2 (C, H), FASTA

>5O14_2 Fab 1A12 Heavy Chain (chains C, H)
EVQLVQSGAELKKPGESLKISCKASGYTFTNYWVVWVRQMPGEGLEWMGSIHPRDSDARY
SLSFEGRVTFSVDKSTTTAYLQWSSLKVSDSAIYYCARLSQVSGWSPWVGPWGQGTLVTV
SSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQ
SSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKLEHHHHHH

Sequence of entity 3 (D, L), FASTA

>5O14_3 Fab 1A12 Light Chain (chains D, L)
ADIVMTQSPSSLSASVGDRVTITCRASQSISVSLNWYQQKPGKAPKVLIYAASRLQSGIP
SRFSGSGSGSHFTLTISSLQPEDFATYYCQETYSDLMYTFGQGTKVEIKRTVAAPSVFIF
PPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSST
LTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGECS

Primary citation

Crystal structure reveals vaccine elicited bactericidal human antibody targeting a conserved epitope on meningococcal fHbp. Lopez-Sagaseta, J., Beernink, P.T., Bianchi, F. et al. Nat Commun (2018) 9:528-528. DOI 10.1038/s41467-018-02827-7 · PubMed

Other PDB entries of the same protein (UniProt Q9JXV4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8UP2 1.6 Å, Murine Fab JAR 4 bound to meningococcal Factor H binding protein
5NQZ 1.63 Å, Structure of a fHbp(V1.1):PorA(P1.16) chimera. Fusion at fHbp position 309.
7LCV 1.7 Å, Factor H enhancing human antibody fragment (Fab) to meningococcal Factor H binding protein
2YPV 1.8 Å, Crystal structure of the Meningococcal vaccine antigen factor H binding protein in…
2Y7S 1.9 Å, Structure of a designed meningococcal antigen (factor H binding protein, mutant G1)…
7KET 2.0 Å, Factor H enhancing human antibody fragment (Fab) to meningococcal Factor H binding protein
2W80 2.35 Å, Structure of a complex between Neisseria meningitidis factor H binding protein and CCPs…
2W81 2.35 Å, Structure of a complex between Neisseria meningitidis factor H binding protein and CCPs…
4AYD 2.4 Å, Structure of a complex between CCPs 6 and 7 of Human Complement Factor H and Neisseria…
6XZW 2.4 Å, Crystal structure of the meningococcal vaccine antigen fHbp in complex with a…
4AYE 2.8 Å, Structure of a complex between CCPs 6 and 7 of Human Complement Factor H and Neisseria…
7SBZ 2.9 Å, JAR5 Fab bound to fHbp v1.1 crystallized in space group I422

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