6XY2 | pdb_00006xy2

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 (Depositor), 0.302 (DCC) 
• R-Value Work: 
  0.249 (Depositor), 0.251 (DCC) 
• R-Value Observed: 
  0.251 (Depositor) 

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 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.
Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
School of Life Science and Technology, Southeast University, Nanjing, Jiangsu, 210096, China.
Alphamab Co. Ltd, Suzhou, Jiangsu, 215125, China.
OncoImmune, Inc., Rockville, MD, 20850, USA.
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. [e-mail].
OncoImmune, Inc., Rockville, MD, 20850, USA. [e-mail].
Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China. [e-mail].

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 
• Modeled 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 (Depositor), 0.302 (DCC) 
• R-Value Work:  0.249 (Depositor), 0.251 (DCC) 
• R-Value Observed: 0.251 (Depositor) 

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