8UP2: Murine Fab JAR 4

Murine Fab JAR 4 bound to meningococcal Factor H binding protein. Determined by X-ray diffraction at 1.6 Å resolution. Released 16 Oct 2024.

Method: X-ray diffraction
Resolution: 1.6 Å
Organisms: Mus musculus, Neisseria meningitidis
Chains: 6
Atoms: 11,203
Mol. weight: 151.88 kDa
Released: 16 Oct 2024

Explore 8UP2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8UP2 contains 58 α-helices and 128 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: 11 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	1
α-helix	7-9	3
β-strand	10-12	3	2
β-strand	18-25	8	1
α-helix	29-31	3
β-strand	34-39	6	2
β-strand	45-51	7	2
β-strand	58-60	3	2
α-helix	62-64	3
β-strand	68-73	6	1
α-helix	74-76	3
β-strand	78-83	6	1
α-helix	88-90	3
β-strand	92-98	7	2
β-strand	108	1	2
β-strand	112-116	5	2
α-helix	120-121	2
β-strand	122	1	3
α-helix	123-124	2
β-strand	125-129	5	4
β-strand	142-150	9	4
β-strand	151	1	3
β-strand	156-159	4	5
α-helix	160-162	3
β-strand	164	1	5
β-strand	168-170	3	4
α-helix	171-173	3
β-strand	174-175	2	4
β-strand	181-188	8	4
α-helix	191-194	4
β-strand	200-205	6	5
α-helix	206-208	3
β-strand	210-215	6	5

Chains B and E: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	6
β-strand	10-14	5	7
β-strand	19-25	7	6
β-strand	30-32	3	8
β-strand	35-36	2	8
β-strand	38-43	6	7
β-strand	50-54	5	7
β-strand	58-59	2	7
α-helix	60	1
β-strand	67-72	6	6
β-strand	75-80	6	6
α-helix	85-87	3
β-strand	89-95	7	7
α-helix	101	1
β-strand	102-103	2	7
β-strand	107-112	6	7
β-strand	116	1	9
α-helix	117-118	2
β-strand	119-123	5	10
α-helix	124-126	3
α-helix	127-131	5
β-strand	134-144	11	10
β-strand	145	1	9
β-strand	150-155	6	11
β-strand	158-159	2	11
α-helix	160	1
β-strand	164-168	5	10
α-helix	169-172	4
β-strand	178-187	10	10
α-helix	188-193	6
β-strand	196-202	7	11
β-strand	210-215	6	11

Chain C: 9 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	16-21	6
α-helix	23-24	2
α-helix	31	1
β-strand	34-35	2	12
β-strand	45-50	6	13
β-strand	53-57	5	13
α-helix	61	1
β-strand	62-63	2	12
α-helix	65-67	3
α-helix	69	1
β-strand	73-84	12	13
β-strand	87-100	14	13
β-strand	104-116	13	13
β-strand	122-136	15	13
β-strand	138	1	14
α-helix	139	1
β-strand	140	1	15
α-helix	141-143	3
β-strand	149-158	10	14
β-strand	161-171	11	14
β-strand	176-182	7	14
α-helix	187-189	3
β-strand	192-200	9	14
β-strand	205	1	15
β-strand	206-214	9	14
β-strand	217-227	11	14
β-strand	233-242	10	14
β-strand	245-254	10	14

Chain D: 11 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	16
α-helix	7-9	3
β-strand	10-12	3	17
β-strand	18-25	8	16
α-helix	29-31	3
β-strand	34-39	6	17
β-strand	45-51	7	17
β-strand	58-60	3	17
α-helix	62-64	3
β-strand	68-73	6	16
α-helix	74-76	3
β-strand	78-83	6	16
α-helix	88-90	3
β-strand	92-98	7	17
β-strand	108	1	17
β-strand	112-116	5	17
α-helix	120-121	2
β-strand	122	1	18
α-helix	123-124	2
β-strand	125-129	5	19
β-strand	142-150	9	19
β-strand	151	1	18
β-strand	156-159	4	20
α-helix	160-162	3
β-strand	164	1	20
β-strand	168-170	3	19
α-helix	171-173	3
β-strand	174-175	2	19
β-strand	181-188	8	19
α-helix	191-193	3
β-strand	199-205	7	20
α-helix	206-208	3
β-strand	210-216	7	20

Chain F: 9 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	16-21	6
α-helix	23-24	2
α-helix	31	1
β-strand	34-35	2	27
β-strand	45-50	6	28
β-strand	53-57	5	28
α-helix	61	1
β-strand	62-63	2	27
α-helix	65-67	3
α-helix	69	1
β-strand	73-84	12	28
β-strand	87-100	14	28
β-strand	104-115	12	28
β-strand	123-136	14	28
β-strand	138	1	29
α-helix	139	1
β-strand	140	1	30
α-helix	141-143	3
β-strand	149-158	10	29
β-strand	161-171	11	29
β-strand	176-182	7	29
α-helix	187-189	3
β-strand	192-200	9	29
β-strand	205	1	30
β-strand	206-214	9	29
β-strand	217-227	11	29
β-strand	233-242	10	29
β-strand	245-254	10	29

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Human-mouse chimeric immunoglobulin heavy chain, Fd fragment	A, D	protein	223	Mus musculus
Human-mouse chimeric immunoglobulin, kappa light chain	B, E	protein	220	Mus musculus
Factor H binding protein, sequence variant ID 1	C, F	protein	257	Neisseria meningitidis	Q9JXV4 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>8UP2_1 Human-mouse chimeric immunoglobulin heavy chain, Fd fragment (chains A, D)
EVQLQQSGPVLVKPGASVKMSCKASGYTFTDYYMNWVKQSHGKSLEWIGRVNPSNGATTY
NQKFKGKATVTVDKSLSTSYMQLNSLTSEDSAVYFCARDWEGPWFAYWGQGTLVTVSSAS
TKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGL
YSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDK

Sequence of entity 2 (B, E), FASTA

>8UP2_2 Human-mouse chimeric immunoglobulin, kappa light chain (chains B, E)
DVVMTQTPLTLSVTIGQPASISCKSSQTLFYSKGKTYLNWLFQRPGQSPKRLIYLVSKLD
SGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCLQSTHFPYTFGGGTKLEIKRTVAAPSV
FIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSL
SSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGECS

Sequence of entity 3 (C, F), FASTA

>8UP2_3 Factor H binding protein, sequence variant ID 1 (chains C, F)
MVAADIGAGLADALTAPLDHKDKGLQSLTLDQSVRKNEKLKLAAQGAEKTYGNGDSLNTG
KLKNDKVSRFDFIRQIEVDGQLITLESGEFQVYKQSHSALTAFQTEQIQDSEHSGKMVAK
RQFRIGDIAGEHTSFDKLPEGGRATYRGTAFGSDDAGGKLTYTIDFAAKQGNGKIEHLKS
PELNVDLAAADIKPDGKRHAVISGSVLYNQAEKGSYSLGIFGGKAQEVAGSAEVKTVNGI
RHIGLAAKQLEHHHHHH

Primary citation

Structure of murine Fab JAR 4 bound to FHbp at 1.60-Angstroms resolution. Beernink, P.T., Beernink, B.P. To be published.

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

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…
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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