8QY9

J22.9-H, fully humanized Fab Fragment based on chimeric J22.9-xi IgG against BCMA

• PDB DOI: https://doi.org/10.2210/pdb8QY9/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus, Homo sapiens
• Expression System: Homo sapiens, Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2023-10-25 Released: 2024-01-17 
• Deposition Author(s): Marino, S.F., Daumke, O.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.301 
• R-Value Work: 0.254 
• R-Value Observed: 0.256 

Starting Model: experimental

Literature

Structure-based humanization of a therapeutic antibody for Multiple Myeloma

Marino, S.F., Daumke, O.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: surface plasmon resonance

Macromolecule Content

• Total Structure Weight: 50.48 kDa 
• Atom Count: 3,504 
• Modelled Residue Count: 461 
• Deposited Residue Count: 467 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab light chain of J22.9-H	A [auth L]	211	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab heavy chain of J22.9-H	B [auth H]	221	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Tumor necrosis factor receptor superfamily member 17	C [auth A]	35	Homo sapiens	Mutation(s): 5  Gene Names: TNFRSF17, BCM, BCMA
UniProt & NIH Common Fund Data Resources
Find proteins for Q02223 (Homo sapiens) Explore Q02223  Go to UniProtKB:  Q02223
GTEx:  ENSG00000048462

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CU	D [auth L], E [auth H]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.301 
• R-Value Work: 0.254 
• R-Value Observed: 0.256 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.36	α = 90
b = 55.18	β = 121.023
c = 81.16	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-01-17 
Deposition Author(s): Marino, S.F., Daumke, O.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-01-17
  Type: Initial release
  
• Version 2.0: 2024-07-24
  Type: Coordinate replacement
  Reason: Real space R-factor
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Refinement description, Source and taxonomy, Structure summary