9GFH | pdb_00009gfh

BCR Fab from the subset 1 chronic lymphocytic leukaemia case P1173

• PDB DOI: https://doi.org/10.2210/pdb9GFH/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2024-08-09 Released: 2025-08-20 
• Deposition Author(s): Cocomazzi, P.G., Degano, M.
• Funding Organization(s): Italian Association for Cancer Research, Italian Ministry of Health, Worldwide Cancer Research

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.72 Å
• R-Value Free: 
  0.244 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.212 (DCC) 
• R-Value Observed: 
  0.215 (Depositor) 

Starting Model: experimental

Literature

Defective cell-autonomous signalling and antigenic polyreactivity of B-cell receptors from chronic lymphocytic leukaemia stereotyped subset 1

Cocomazzi, P.G., Iatrou, A., Minici, C., Degano, M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 3 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 4 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 193.63 kDa 
• Atom Count: 13,208 
• Modeled Residue Count: 1,704 
• Deposited Residue Count: 1,760 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BCR P1173 light chain	A [auth L], C [auth B], D, E [auth F]	215	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
BCR P1173 heavy chain	B [auth A], F [auth H], G [auth C], H [auth E]	225	Homo sapiens	Mutation(s): 0
Glycosylation
Glycosylation Sites: 1

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	I [auth G]	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB GlyCosmos:  G21290RB GlyGen:  G21290RB

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	J [auth A], L [auth C], M [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
CIT	K [auth H]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.72 Å
• R-Value Free:  0.244 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.212 (DCC) 
• R-Value Observed: 0.215 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.416	α = 90
b = 128.509	β = 90
c = 134.65	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
STARANISO	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-08-20 
Deposition Author(s): Cocomazzi, P.G., Degano, M.

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Funding Organization	Location	Grant Number
Italian Association for Cancer Research	Italy	IG17032
Italian Association for Cancer Research	Italy	IG25764
Italian Ministry of Health	Italy	RF-2018-12368231
Worldwide Cancer Research	United Kingdom	19-0096

Revision History  

• Version 1.0: 2025-08-20
  Type: Initial release