2YPV: Lipoprotein

Crystal structure of the Meningococcal vaccine antigen factor H binding protein in complex with a bactericidal antibody. Determined by X-ray diffraction at 1.8 Å resolution. Released 20 Feb 2013.

Method: X-ray diffraction
Resolution: 1.8 Å
Organisms: NEISSERIA MENINGITIDIS MC58, MUS MUSCULUS
Chains: 3
Atoms: 5,533
Mol. weight: 74.64 kDa
Released: 20 Feb 2013

Explore 2YPV in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2YPV contains 27 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 A: 10 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
α-helix	61	1
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	104-113	10	2
β-strand	125-136	12	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	245-255	11	3

Chain H: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	5
β-strand	10-12	3	6
β-strand	18-24	7	5
α-helix	29-31	3
β-strand	34-40	7	6
β-strand	44-51	8	6
β-strand	58-60	3	6
α-helix	62-64	3
β-strand	68-73	6	5
β-strand	78-83	6	5
α-helix	88-90	3
β-strand	92-98	7	6
β-strand	108-109	2	6
β-strand	113-117	5	6
α-helix	120-122	3
β-strand	123	1	7
α-helix	124-125	2
β-strand	126-130	5	8
β-strand	141-151	11	8
β-strand	152	1	7
β-strand	157-160	4	9
α-helix	161-163	3
β-strand	165	1	9
β-strand	169-171	3	8
α-helix	172-174	3
β-strand	175-176	2	8
β-strand	181-190	10	8
β-strand	199-205	7	9
α-helix	206-208	3
β-strand	210-216	7	9

Chain L: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	10
β-strand	10-13	4	11
β-strand	19-25	7	10
β-strand	33-38	6	11
β-strand	45-49	5	11
β-strand	53-54	2	11
α-helix	55	1
β-strand	62-67	6	10
β-strand	70-75	6	10
α-helix	80-82	3
β-strand	84-90	7	11
α-helix	96	1
β-strand	97-98	2	11
β-strand	102-106	5	11
β-strand	111	1	12
α-helix	112-113	2
β-strand	114-118	5	13
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	13
β-strand	140	1	12
β-strand	145-150	6	14
β-strand	153-155	3	14
β-strand	159-163	5	13
α-helix	164-167	4
β-strand	173-182	10	13
α-helix	183-187	5
β-strand	191-197	7	14
α-helix	204	1
β-strand	205-210	6	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Lipoprotein	A	protein	253	NEISSERIA MENINGITIDIS MC58	Q9JXV4 (AlphaFold model)
FAB 12C1	H	protein	218	MUS MUSCULUS
FAB 12C1	L	protein	214	MUS MUSCULUS

Sequence of entity 1 (A), FASTA

>2YPV_1 LIPOPROTEIN (chains A)
GGGGVAADIGAGLADALTAPLDHKDKGLQSLTLDQSVRKNEKLKLAAQGAEKTYGNGDSL
NTGKLKNDKVSRFDFIRQIEVDGQLITLESGEFQVYKQSHSALTAFQTEQIQDSEHSGKM
VAKRQFRIGDIAGEHTSFDKLPEGGRATYRGTAFGSDDAGGKLTYTIDFAAKQGNGKIEH
LKSPELNVDLAAADIKPDGKRHAVISGSVLYNQAEKGSYSLGIFGGKAQEVAGSAEVKTV
NGIRHIGLAAKQL

Sequence of entity 2 (H), FASTA

>2YPV_2 FAB 12C1 (chains H)
QVQLQESGPELVKPGASVKISCKASGYSFSDYNMSWVKQSNGKSLEWIGIIDPKYGTINY
NQKFKGKATLTVDQASSTAYMQLNSLTSEDSAVYYCVRDYYGSSYFDYWGQGTTLTVSSA
KTTPPSVYPLAPGCGDTTGSSVTLGCLVKGYFPESVTVTWNSGSLSSSVHTFPALLQSGL
YTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKLCR

Sequence of entity 3 (L), FASTA

>2YPV_3 FAB 12C1 (chains L)
DIVLTQSPSSIYASLGERVTLTCKASQDIHNYLNWFQQKPGKSPKTLIYRANRLVDGVPS
RFSGGGSGQDYSLTISSLEFEDIGIYYCLQYDEFPPTFGGGTRLEIKRADAAPTVSIFPP
SSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLT
LTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Primary citation

Defining a Protective Epitope on Factor H Binding Protein, a Key Meningococcal Virulence Factor and Vaccine Antigen. Malito, E., Faleri, A., Lo Surdo, P. et al. Proc Natl Acad Sci U S A (2013) 110:3304. DOI 10.1073/PNAS.1222845110 · 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
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…
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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