7SBZ: JAR5 Fab

JAR5 Fab bound to fHbp v1.1 crystallized in space group I422. Determined by X-ray diffraction at 2.9 Å resolution. Released 5 Oct 2022.

Method: X-ray diffraction
Resolution: 2.9 Å
Organisms: Mus musculus, Neisseria meningitidis serogroup B
Chains: 6
Atoms: 10,211
Mol. weight: 161.07 kDa
Ligands: CD
Released: 5 Oct 2022

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

Secondary structure: helices and β-sheets

7SBZ contains 37 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: 6 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	1
β-strand	9-12	4	2
β-strand	18-25	8	1
α-helix	29-31	3
β-strand	32-39	8	2
β-strand	45-51	7	2
β-strand	59-60	2	2
β-strand	68-73	6	1
β-strand	78-83	6	1
α-helix	88-90	3
β-strand	92-100	9	2
β-strand	108-112	5	2
β-strand	116-120	5	2
α-helix	123-125	3
β-strand	126	1	3
α-helix	127-128	2
β-strand	129-133	5	4
β-strand	144-154	11	4
β-strand	155	1	3
β-strand	160-163	4	5
β-strand	172-174	3	4
α-helix	175-177	3
β-strand	178-180	3	4
β-strand	183-193	11	4
β-strand	203-208	6	5
β-strand	213-218	6	5
α-helix	221-223	3

Chain B: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3
β-strand	5-6	2	6
β-strand	10-13	4	7
β-strand	19-24	6	6
β-strand	30	1	8
β-strand	36	1	8
β-strand	38-43	6	7
β-strand	50-54	5	7
β-strand	58-59	2	7
β-strand	67-71	5	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	107-111	5	7
α-helix	113-115	3
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	151-155	5	11
β-strand	158-160	3	11
β-strand	164-168	5	10
β-strand	178-187	10	10
α-helix	188-191	4
β-strand	196-201	6	11
β-strand	210-215	6	11

Chain C: 7 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	15-19	5
β-strand	33-35	3	23
β-strand	45-50	6	24
β-strand	53-57	5	24
α-helix	61	1
β-strand	62-64	3	23
α-helix	65-67	3
α-helix	69	1
β-strand	73-84	12	24
β-strand	87-100	14	24
β-strand	104-115	12	24
β-strand	123-124	2	24
β-strand	129-136	8	24
β-strand	138	1	25
α-helix	139	1
β-strand	140	1	26
α-helix	141-143	3
β-strand	149-158	10	25
β-strand	161-171	11	25
β-strand	176-182	7	25
α-helix	187-189	3
β-strand	192-200	9	25
β-strand	205	1	26
β-strand	206-213	8	25
β-strand	218-227	10	25
β-strand	233-241	9	25
β-strand	246-254	9	25

Chain D: 4 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	35	1	27
β-strand	45-50	6	28
β-strand	53-57	5	28
β-strand	62	1	27
α-helix	69	1
β-strand	73-83	11	28
β-strand	88-100	13	28
β-strand	104-115	12	28
β-strand	123-124	2	28
β-strand	128-136	9	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	206-213	8	29
β-strand	218-227	10	29
β-strand	233-242	10	29
β-strand	245-254	10	29

Chain H: 5 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	12
β-strand	9-12	4	13
β-strand	18-25	8	12
α-helix	29-31	3
β-strand	32-39	8	13
β-strand	45-51	7	13
β-strand	58-60	3	13
β-strand	68-73	6	12
β-strand	78-83	6	12
α-helix	88-90	3
β-strand	92-100	9	13
β-strand	108-112	5	13
β-strand	116-120	5	13
β-strand	126	1	14
α-helix	127-128	2
β-strand	129-133	5	15
α-helix	139-140	2
β-strand	144-154	11	15
β-strand	155	1	14
β-strand	160-163	4	16
β-strand	172-174	3	15
α-helix	175-177	3
β-strand	178-180	3	15
β-strand	183-193	11	15
β-strand	203-208	6	16
β-strand	213-218	6	16

Chain L: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	17
β-strand	10-13	4	18
β-strand	19-25	7	17
β-strand	30	1	19
β-strand	36	1	19
β-strand	38-43	6	18
β-strand	50-54	5	18
β-strand	58-59	2	18
α-helix	60	1
β-strand	67-71	5	17
β-strand	75-80	6	17
β-strand	89-95	7	18
α-helix	102	1
β-strand	103	1	18
α-helix	104	1
β-strand	107-111	5	18
β-strand	116	1	20
α-helix	117-118	2
β-strand	119-123	5	21
α-helix	124-126	3
α-helix	127-130	4
β-strand	134-144	11	21
β-strand	145	1	20
β-strand	152-155	4	22
β-strand	158-159	2	22
β-strand	164-168	5	21
β-strand	178-187	10	21
α-helix	188-192	5
β-strand	196-200	5	22
β-strand	211-215	5	22

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
JAR5 Heavy Chain	A, H	protein	253	Mus musculus
JAR5 Light Chain	B, L	protein	216	Mus musculus
Factor H-binding protein	C, D	protein	257	Neisseria meningitidis serogroup B	Q9JXV4 (AlphaFold model)

Sequence of entity 1 (A, H), FASTA

>7SBZ_1 JAR5 Heavy Chain (chains A, H)
MEFGLSWVFLVAILEGVHCQVQMQQPGAELVKPGASVKLSCKASGYTFISYWMHWVKQRP
GRGLEWIGRIAPDTGIIYYNEKFKNKATLTVDTPSSTAYMQLNSLTSEDSAVYYCARYLK
YDGSTYRFDYWGQGTTLTVSSAKTTPPSVYPLAPGCGDTTGSSVTLGCLVKGYFPEPVTV
TWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSPWPSETVTCNVAHPASSTKVDKKLVP
RDCGGSENLYFQG

Sequence of entity 2 (B, L), FASTA

>7SBZ_2 JAR5 Light Chain (chains B, L)
DIVMTQAAPSVPVTPGESVSISCRSSKSLLHSNGNTYLFWFLQRPGQSPQLLIYRMSNLA
SGVPDRFSGSGSGTSFTLRISRVEAEDVGVYYCMQHLEYPYTFGGGTKLEIKRADAAPTV
SIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSM
SSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR

Sequence of entity 3 (C, D), FASTA

>7SBZ_3 Factor H-binding protein (chains C, D)
MVAADIGAGLADALTAPLDHKDKGLQSLTLDQSVRKNEKLKLAAQGAEKTYGNGDSLNTG
KLKNDKVSRFDFIRQIEVDGQLITLESGEFQVYKQSHSALTAFQTEQIQDSEHSGKMVAK
RQFRIGDIAGEHTSFDKLPEGGRATYRGTAFGSDDAGGKLTYTIDFAAKQGNGKIEHLKS
PELNVDLAAADIKPDGKRHAVISGSVLYNQAEKGSYSLGIFGGKAQEVAGSAEVKTVNGI
RHIGLAAKQLEHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
CD	Cadmium ion	Cd	25

Primary citation

Active Learning for Rapid Design: An iterative AI approach for accelerated vaccine design that combines active machine learning and high-throughput experimental evaluation. Chesterman, C., Desautels, T., Sierra, L.J. et al. To be published.

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…
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…

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