8QYA: J22.9-FNY Fab antibody light chain

J22.9-FNY, fully humanized, CDR optimized Fab Fragment based on chimeric J22.9-xi IgG against BCMA; with VH CDR2 glycosylation. Determined by X-ray diffraction at 2.72 Å resolution. Released 17 Jan 2024.

Method: X-ray diffraction
Resolution: 2.72 Å
Organisms: Mus musculus, Homo sapiens
Chains: 3
Atoms: 3,649
Mol. weight: 51.04 kDa
Ligands: CU
Released: 17 Jan 2024

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

Secondary structure: helices and β-sheets

8QYA contains 15 α-helices and 45 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: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
β-strand	12-15	4	11
β-strand	20-23	4	11
α-helix	25-28	4

Chain H: 6 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	6
β-strand	10-12	3	7
β-strand	18-25	8	6
α-helix	29-31	3
β-strand	34-39	6	7
β-strand	45-51	7	7
β-strand	60	1	7
α-helix	62-64	3
β-strand	68-73	6	6
β-strand	78-83	6	6
β-strand	92-102	11	7
β-strand	105-110	6	7
β-strand	114-118	5	7
β-strand	124	1	8
α-helix	125-126	2
β-strand	127-131	5	9
β-strand	142-152	11	9
β-strand	153	1	8
β-strand	158-161	4	10
β-strand	166	1	10
β-strand	170-172	3	9
α-helix	173-175	3
β-strand	176-177	2	9
β-strand	183-192	10	9
α-helix	194-196	3
β-strand	201-207	7	10
α-helix	208-210	3
β-strand	212-218	7	10

Chain L: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-13	4	2
β-strand	19-25	7	1
β-strand	33-38	6	2
α-helix	43-44	2
β-strand	45-49	5	2
β-strand	53-54	2	2
β-strand	62-67	6	1
β-strand	70-75	6	1
α-helix	80-82	3
β-strand	85-90	6	2
α-helix	96	1
β-strand	97-98	2	2
β-strand	102-106	5	2
β-strand	111	1	3
α-helix	112-113	2
β-strand	114-118	5	4
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	4
β-strand	140	1	3
β-strand	145-150	6	5
β-strand	153-154	2	5
β-strand	159-163	5	4
α-helix	164-167	4
β-strand	173-182	10	4
α-helix	183-186	4
β-strand	191-197	7	5
β-strand	205-210	6	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
J22.9-FNY Fab antibody light chain	L	protein	214	Mus musculus
J22.9-FNY Fab antibody heavy chain	H	protein	216	Mus musculus
Tumor necrosis factor receptor superfamily member 17	A	protein	36	Homo sapiens	Q02223 (AlphaFold model)

Sequence of entity 1 (L), FASTA

>8QYA_1 J22.9-FNY Fab antibody light chain (chains L)
EIVMTQSPATLSVSPGERATLSCKASQSVESNVAWYQQKPGQSPRALIYSASLRFSGIPA
RFSGSGSGTEFTLTISSLQSEDFAVYYCQQYNNYPLTFGAGTKLELKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEA

Sequence of entity 2 (H), FASTA

>8QYA_2 J22.9-FNY Fab antibody heavy chain (chains H)
EVQLVESGGGLVQPGGSLRLSCAASGFTFSRYWMSWVRQAPGKGLVWVGEINPNSSTINY
APSLKDKFTISRDNAKNTLYLQMNSLRAEDTAVYYCASLYYDYGDAYDYWGQGTLVTVSS
ASTKGPSVFPLAPSSGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSL
SSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPA

Sequence of entity 3 (A), FASTA

>8QYA_3 Tumor necrosis factor receptor superfamily member 17 (chains A)
GQCSQNEYFDSLLHACIPCQLRCSSNTPPLTCQRYC

Ligands and cofactors

ID	Name	Formula	Copies
CU	Copper (II) ion	Cu	1

Primary citation

Structure-based humanization of a therapeutic antibody for multiple myeloma. Marino, S.F., Daumke, O. J Mol Med (Berl) (2024) 102:1151-1161. DOI 10.1007/s00109-024-02470-4 · PubMed

Other PDB entries of the same protein (UniProt Q02223 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4ZFO 1.9 Å, J22.9-xi: chimeric mouse/human antibody against human BCMA (CD269)
1XU2 2.35 Å, The crystal structure of APRIL bound to BCMA
8HXQ 2.4 Å, Nanobody1 in complex with human BCMA ECD
1OQD 2.6 Å, Crystal structure of sTALL-1 and BCMA
6J7W 2.6 Å, Crystal Structure of Human BCMA in complex with UniAb(TM) VH
8HXR 2.7 Å, Nanobody2 in complex with human BCMA ECD
12ER 2.99 Å, Cryo-EM structure of BCMA in complex with the BCMA-targeted Fab arm of teclistamab and…
8QYB 3.09 Å, J22.9-ISY, fully humanized and CDR optimized Fab Fragment based on chimeric J22.9-xi IgG…
8QY9 3.1 Å, J22.9-H, fully humanized Fab Fragment based on chimeric J22.9-xi IgG against BCMA
9MQO 3.18 Å, Crystal structure of BCMA in complex with CA10v2 Fab
12ES 3.43 Å, Cryo-EM structure of BCMA in complex with the BCMA-targeted Fab arm of linvoseltamab and…
2KN1 Solution NMR Structure of BCMA

Browse structure collections

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