7LCV: Immunoglobulin heavy chain Fd fragment

Factor H enhancing human antibody fragment (Fab) to meningococcal Factor H binding protein. Determined by X-ray diffraction at 1.7 Å resolution. Released 9 Jun 2021.

Method: X-ray diffraction
Resolution: 1.7 Å
Organisms: Homo sapiens, Neisseria meningitidis
Chains: 3
Atoms: 5,032
Mol. weight: 75.69 kDa
Released: 9 Jun 2021

Explore 7LCV in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7LCV contains 15 α-helices and 59 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: 4 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	11-12	2	2
β-strand	18-25	8	1
α-helix	29-31	3
β-strand	34-39	6	3
β-strand	45-51	7	3
β-strand	57	1	4
β-strand	58-60	3	3
α-helix	62-64	3
β-strand	68-73	6	1
β-strand	78-83	6	1
α-helix	88-90	3
β-strand	92-99	8	3
β-strand	109-112	4	3
β-strand	116-118	3	3
β-strand	119-120	2	2
β-strand	129-133	5	5
β-strand	147-154	8	5
β-strand	172-174	3	5
α-helix	175-177	3
β-strand	178-179	2	5
β-strand	185-191	7	5

Chain B: 6 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	6
β-strand	11-14	4	7
β-strand	20-30	11	6
α-helix	32-34	3
β-strand	35-40	6	7
β-strand	47-51	5	7
β-strand	55-56	2	7
α-helix	57	1
β-strand	64-77	14	6
α-helix	82-84	3
β-strand	87-92	6	7
β-strand	99-100	2	7
β-strand	104-108	5	7
β-strand	113	1	8
β-strand	116-120	5	9
α-helix	121-123	3
β-strand	131-141	11	9
β-strand	142	1	8
β-strand	147-152	6	10
β-strand	155-156	2	10
β-strand	161-165	5	9
α-helix	166-169	4
β-strand	175-184	10	9
α-helix	185-189	5
β-strand	193-199	7	10
β-strand	207-212	6	10

Chain C: 5 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	34-35	2	11
β-strand	45-50	6	12
β-strand	51	1	4
β-strand	53-57	5	12
α-helix	61	1
β-strand	62-63	2	11
α-helix	69	1
β-strand	73-84	12	12
β-strand	87-100	14	12
β-strand	104-115	12	12
β-strand	123-125	3	12
β-strand	129-136	8	12
β-strand	138	1	13
α-helix	139	1
β-strand	140	1	14
α-helix	141-143	3
β-strand	149-158	10	13
β-strand	161-171	11	13
β-strand	176-182	7	13
α-helix	187-189	3
β-strand	192-200	9	13
β-strand	205	1	14
β-strand	206-214	9	13
β-strand	217-227	11	13
β-strand	233-240	8	13
β-strand	247-254	8	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Immunoglobulin heavy chain Fd fragment	A	protein	227	Homo sapiens
Immunoglobulin kappa light chain	B	protein	217	Homo sapiens
Factor H binding protein	C	protein	263	Neisseria meningitidis	Q9JXV4 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7LCV_1 Immunoglobulin heavy chain Fd fragment (chains A)
EVQLVESGGGLVQPGGSLRLSCAASGFTFSSYAMSWVRQAPGKGLEWVSAISGSGGSSHY
TDSVKGRFTISRDNSKNTLWLQMNSLRAEDTAIYYCAKTSGSYYYHYEIDVWGQGTTVTV
SSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQ
SSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDK

Sequence of entity 2 (B), FASTA

>7LCV_2 Immunoglobulin kappa light chain (chains B)
AEIVLTQSPGTLSLSPGERATLSCRASQSVSSSYLAWYQQKPGQAPRLLIYGTSNRATGI
PDRFSGSGSGTDFTLTVSRLEPEDFAVYYCQQYGSSPCSFGQGTKLELKRTVAAPSVFIF
PPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSST
LTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGECS

Sequence of entity 3 (C), FASTA

>7LCV_3 Factor H binding protein (chains C)
CSSGGGGVAADIGAGLADALTAPLDHKDKGLQSLTLDQSVRKNEKLKLAAQGAEKTYGNG
DSLNTGKLKNDKVSRFDFIRQIEVDGQLITLESGEFQVYKQSHSALTAFQTEQIQDSEHS
GKMVAKRQFRIGDIAGEHTSFDKLPEGGRATYRGTAFGSDDAGGKLTYTIDFAAKQGNGK
IEHLKSPELNVDLAAADIKPDGKRHAVISGSVLYNQAEKGSYSLGIFGGKAQEVAGSAEV
KTVNGIRHIGLAAKQLEHHHHHH

Primary citation

Two human antibodies to a meningococcal serogroup B vaccine antigen enhance binding of complement Factor H by stabilizing the Factor H binding site. Sands, N.A., Beernink, P.T. PLoS Pathog (2021) 17:e1009655-e1009655. DOI 10.1371/journal.ppat.1009655 · 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.
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…
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

Browse structure collections

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