6XZW: Meningococcal vaccine antigen fHbp

Crystal structure of the meningococcal vaccine antigen fHbp in complex with a cross-reactive human Fab. Determined by X-ray diffraction at 2.4 Å resolution. Released 14 Oct 2020.

Method: X-ray diffraction
Resolution: 2.4 Å
Organisms: Neisseria meningitidis serogroup B (strain MC58), Homo sapiens
Chains: 3
Atoms: 5,117
Mol. weight: 74.51 kDa
Released: 14 Oct 2020

Explore 6XZW in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6XZW contains 25 α-helices and 62 β-strands across 3 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 D: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	16-21	6
α-helix	23-24	2
β-strand	34-35	2	1
β-strand	45-50	6	2
β-strand	53-57	5	2
α-helix	61	1
β-strand	62-63	2	1
α-helix	65-67	3
β-strand	73-83	11	2
β-strand	88-100	13	2
β-strand	104-114	11	2
β-strand	115	1	3
β-strand	123	1	3
β-strand	129-136	8	2
β-strand	138	1	4
α-helix	139	1
β-strand	140	1	5
α-helix	141-143	3
β-strand	149-158	10	4
β-strand	161-171	11	4
β-strand	176-182	7	4
α-helix	187-189	3
β-strand	192-200	9	4
β-strand	205	1	5
β-strand	206-214	9	4
β-strand	217-227	11	4
β-strand	233-242	10	4
β-strand	245-255	11	4

Chain H: 7 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	3-8	6	11
β-strand	10-12	3	12
β-strand	18-25	8	11
α-helix	29-31	3
β-strand	34-39	6	12
β-strand	45-51	7	12
β-strand	58-60	3	12
β-strand	68-73	6	11
β-strand	78-83	6	11
α-helix	88-90	3
β-strand	92-98	7	12
β-strand	106	1	12
β-strand	110-114	5	12
α-helix	121-122	2
β-strand	123-127	5	13
β-strand	138-148	11	13
β-strand	154-157	4	14
α-helix	158-160	3
β-strand	162	1	14
β-strand	166-168	3	13
α-helix	169-171	3
β-strand	172-173	2	13
β-strand	179-188	10	13
α-helix	189-191	3
β-strand	198-203	6	14
α-helix	204-206	3
β-strand	208-213	6	14

Chain L: 11 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	6
β-strand	10-13	4	7
β-strand	19-25	7	6
α-helix	31-33	3
β-strand	34-39	6	7
β-strand	46-50	5	7
β-strand	54-55	2	7
α-helix	56	1
β-strand	63-68	6	6
β-strand	71-76	6	6
α-helix	81-83	3
β-strand	86-91	6	7
α-helix	98	1
β-strand	99	1	7
α-helix	100	1
β-strand	103-107	5	7
β-strand	112	1	8
α-helix	113-114	2
β-strand	115-119	5	9
α-helix	120-122	3
α-helix	123-127	5
β-strand	130-140	11	9
β-strand	141	1	8
β-strand	146-151	6	10
β-strand	154-155	2	10
α-helix	156	1
β-strand	160-164	5	9
α-helix	165-168	4
β-strand	174-183	10	9
α-helix	184-187	4
β-strand	192-198	7	10
β-strand	206-211	6	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Lipoprot_C domain-containing protein	D	protein	251	Neisseria meningitidis serogroup B (strain MC58)	Q9JXV4 (AlphaFold model)
Fab 4B3 (light chain)	L	protein	215	Homo sapiens
Fab 4B3 (heavy chain)	H	protein	221	Homo sapiens

Sequence of entity 1 (D), FASTA

>6XZW_1 Lipoprot_C domain-containing protein (chains D)
MVAADIGAGLADALTAPLDHKDKGLQSLTLDQSVRKNEKLKLAAQGAEKTYGNGDSLNTG
KLKNDKVSRFDFIRQIEVDGQLITLESGEFQVYKQSHSALTAFQTEQIQDSEHSGKMVAK
RQFRIGDIAGEHTSFDKLPEGGRATYRGTAFGSDDAGGKLTYTIDFAAKQGNGKIEHLKS
PELNVDLAAADIKPDGKRHAVISGSVLYNQAEKGSYSLGIFGGKAQEVAGSAEVKTVNGI
RHIGLAAKQEH

Sequence of entity 2 (L), FASTA

>6XZW_2 Fab 4B3 (light chain) (chains L)
EIVMTQSPGTLSLSPGETATLSCRASQMISSPFLAWYQQRRGQAPRLLIYGASTRATDTP
DRFRGSGSGTDFILTISRLEPEDFAVYYCQYYDDSPFTFGQGTKLEIKRTVAAPSVFIFP
PSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (H), FASTA

>6XZW_3 Fab 4B3 (heavy chain) (chains H)
QVQLVQSGGGLVKPGGSLRLSCAASGFPFSSYYMSWIRQAPGKGLEWVSDINNSGNVKEY
ADFVKGRLTISRDNVKNSMYLHMNSLRVEDTAVYYCARNRGRFDVWGQGTLVTVSAASTK
GPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYS
LSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDK

Primary citation

4CMenB vaccine induces elite cross-protective human antibodies that compete with human factor H for binding to meningococcal fHbp. Veggi, D., Bianchi, F., Santini, L. et al. PLoS Pathog (2020) 16:e1008882-e1008882. DOI 10.1371/journal.ppat.1008882 · 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
5O14 2.19 Å, Co-crystal structure of a cross-reactive bactericidal human antibody targeting…
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…
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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