6XY2

Crystal structure of CTLA-4 complexed with the Fab of HL32 antibody

• PDB DOI: https://doi.org/10.2210/pdb6XY2/pdb

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


• Deposited: 2020-01-29 Released: 2020-12-09 
• Deposition Author(s): Gao, H., Zhou, A.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.05 Å
• R-Value Free: 0.292 
• R-Value Work: 0.249 
• R-Value Observed: 0.251 

Starting Model: experimental

Literature

Structure of CTLA-4 complexed with a pH-sensitive cancer immunotherapeutic antibody.

Gao, H., Cai, H., Liu, J., Wang, X., Zheng, P., Devenport, M., Xu, T., Dou, F., Liu, Y., Zhou, A.

(2020) Cell Discov 6: 79-79

• PubMed: 33298884 
• DOI: https://doi.org/10.1038/s41421-020-00202-9
• Primary Citation of Related Structures:  
  6XY2

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Organizational Affiliation: 

State Key Laboratory of Cognitive Neuroscience and Learning, and Beijing Key Laboratory of Genetic Engineering Drugs and Biotechnology, College of Life Sciences, Beijing Normal University, Beijing, 100875, China.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 63.5 kDa 
• Atom Count: 4,163 
• Modelled Residue Count: 553 
• Deposited Residue Count: 584 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytotoxic T-lymphocyte protein 4	A	123	Homo sapiens	Mutation(s): 0  Gene Names: CTLA4, CD152
UniProt & NIH Common Fund Data Resources
Find proteins for P16410 (Homo sapiens) Explore P16410  Go to UniProtKB:  P16410
PHAROS:  P16410 GTEx:  ENSG00000163599
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P16410-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain	B [auth H]	247	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain	C [auth L]	214	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.05 Å
• R-Value Free: 0.292 
• R-Value Work: 0.249 
• R-Value Observed: 0.251 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 163.862	α = 90
b = 254.478	β = 90
c = 66.935	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
MOSFLM	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-12-09 
Deposition Author(s): Gao, H., Zhou, A.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2020-12-09
  Type: Initial release
  
• Version 1.1: 2020-12-23
  Changes: Database references
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-10-09
  Changes: Structure summary