8QY9: Fab light chain of J22.9-H

J22.9-H, fully humanized Fab Fragment based on chimeric J22.9-xi IgG against BCMA. Determined by X-ray diffraction at 3.1 Å resolution. Released 17 Jan 2024.

Method: X-ray diffraction
Resolution: 3.1 Å
Organisms: Mus musculus, Homo sapiens
Chains: 3
Atoms: 3,504
Mol. weight: 50.48 kDa
Ligands: CU
Released: 17 Jan 2024

Explore 8QY9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8QY9 contains 16 α-helices and 47 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: 2 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	12-15	4	14
β-strand	20-23	4	14
α-helix	25-28	4
α-helix	36-38	3

Chain H: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	7
β-strand	11-12	2	8
β-strand	18-25	8	7
α-helix	29-31	3
β-strand	34-39	6	9
β-strand	45-51	7	9
β-strand	58-59	2	9
β-strand	68-73	6	7
α-helix	74-76	3
β-strand	78-83	6	7
α-helix	88-90	3
β-strand	92-97	6	9
β-strand	101-102	2	10
β-strand	105-106	2	10
β-strand	114-116	3	9
β-strand	117-118	2	8
α-helix	122-123	2
β-strand	124	1	11
β-strand	127-131	5	12
α-helix	132	1
β-strand	142-152	11	12
β-strand	153	1	11
β-strand	158-159	2	13
α-helix	162-164	3
β-strand	170-172	3	12
α-helix	173-175	3
β-strand	177	1	12
β-strand	183-192	10	12
β-strand	201-207	7	13
β-strand	212-218	7	13

Chain L: 7 helices, 22 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	45-48	4	2
β-strand	54	1	2
β-strand	62-67	6	1
β-strand	70-75	6	1
α-helix	80-82	3
β-strand	85-90	6	2
β-strand	98	1	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	145-148	4	5
β-strand	149	1	6
β-strand	154	1	6
β-strand	159-163	5	4
α-helix	164-167	4
β-strand	173-182	10	4
α-helix	183-187	5
β-strand	192-197	6	5
β-strand	205-209	5	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fab light chain of J22.9-H	L	protein	211	Mus musculus
Fab heavy chain of J22.9-H	H	protein	221	Mus musculus
Tumor necrosis factor receptor superfamily member 17	A	protein	35	Homo sapiens	Q02223 (AlphaFold model)

Sequence of entity 1 (L), FASTA

>8QY9_1 Fab light chain of J22.9-H (chains L)
EIVMTQSPATLSVSPGERATLSCKASQSVDSNVAWYQQKPGQAPRALIYSASLRFSGIPA
RFSGSGSGTEFTLTISSLQSEDFAVYYCQQYNNYPLTFGAGTKLELKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNR

Sequence of entity 2 (H), FASTA

>8QY9_2 Fab heavy chain of J22.9-H (chains H)
EVQLVESGGGLVQPGGSLRLSCAASGFTFSRYWMSWVRQAPGKGLVWVGEINPDSSTINY
APSLKDKFTISRDNAKNTLYLQMNSLRAEDTAVYYCASLYYDYGDAMDYWGQGTLVTVSS
ASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSS
GLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPA

Sequence of entity 3 (A), FASTA

>8QY9_3 Tumor necrosis factor receptor superfamily member 17 (chains A)
QCSANEYFDSLLHACIPCQLRCSSATPPATCAAYC

Ligands and cofactors

ID	Name	Formula	Copies
CU	Copper (II) ion	Cu	2

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
8QYA 2.72 Å, J22.9-FNY, fully humanized, CDR optimized Fab Fragment based on chimeric J22.9-xi IgG…
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…
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

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