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 8HIT | pdb_00008hit

Crystal structure of anti-CTLA-4 humanized IgG1 MAb--JS007 in complex with human CTLA-4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 
    0.298 (Depositor), 0.300 (DCC) 
  • R-Value Work: 
    0.251 (Depositor), 0.256 (DCC) 
  • R-Value Observed: 
    0.254 (Depositor) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history. 

Literature

Characterization of the high-affinity anti-CTLA-4 monoclonal antibody JS007 for immune checkpoint therapy of cancer.

Guan, J., Liu, H., Chai, Y., Yu, J., Yao, J., Wang, J., Pan, Z., Zhang, J., Zhou, Y., Liu, H., Yao, S., Qi, J., Feng, H., Gao, G.F., Wang, Q., Shi, Y., Tan, S.

(2023) MAbs 15: 2153409-2153409

  • DOI: https://doi.org/10.1080/19420862.2022.2153409
  • Primary Citation Related Structures: 
    8HIT

  • PubMed Abstract: 

    Cytotoxic T lymphocyte-associated antigen 4 (CTLA-4) is a critical inhibitory checkpoint molecule, and monoclonal antibodies (mAbs) targeting CTLA-4 that restore anti-tumor T cell immunity have achieved clinical success. Here, we report a humanized IgG1 mAb, namely JS007, with high binding affinity to CTLA-4. JS007 shows superior binding affinity and T-cell activating efficiency over ipilimumab. Moreover, it demonstrates substantial in vivo tumor suppression efficacy at low doses. The crystal structure of JS007/CTLA-4 complex (PDB: 8HIT) shows JS007 adopts a heavy-chain-dominant binding mode, and mainly contacts the BC loop, DE loop and FG loop of CTLA-4. Notably, two Tyr residues (VH-Y100 and VL-Y32) from the complementarity-determining region loops insert into the two cavities formed by the residues from the loops of CTLA-4, which may contribute to the stabilization of the binding. Comparative analysis with other anti-CTLA-4 mAbs indicates that the double "wedge-into-hole" binding mode is unique for JS007 and may be responsible for the high-affinity binding to CTLA-4. These findings have provided an important molecular understanding of the high-affinity CTLA-4 blockade mAbs and shed light on future development of agents targeting CTLA-4.


  • Organizational Affiliation: 
    • Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), China.

Macromolecule Content 

  • Total Structure Weight: 37.67 kDa 
  • Atom Count: 2,619 
  • Modeled Residue Count: 342 
  • Deposited Residue Count: 345 
  • Unique protein chains: 3

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
JS007-VH118Mus musculusMutation(s): 0 
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
JS007-VL107Mus musculusMutation(s): 0 
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytotoxic T-lymphocyte protein 4120Homo sapiensMutation(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 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP16410
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free:  0.298 (Depositor), 0.300 (DCC) 
  • R-Value Work:  0.251 (Depositor), 0.256 (DCC) 
  • R-Value Observed: 0.254 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.32α = 90
b = 78.32β = 90
c = 123.094γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data collection

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-01
    Type: Initial release
  • Version 1.1: 2024-10-16
    Changes: Data collection, Structure summary