7C88 | pdb_00007c88

Complex structure of JS003 and PD-L1

• PDB DOI: https://doi.org/10.2210/pdb7C88/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus, Homo sapiens
• Expression System: Cricetulus griseus, Escherichia coli
• Mutation(s): No 


• Deposited: 2020-05-29 Released: 2021-04-14 
• Deposition Author(s): Bi, X., Shi, R., Chai, Y., Qi, J., Yan, J., Tan, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.258 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.222 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.224 (Depositor) 

Starting Model: experimental

Literature

Identification of a hotspot on PD-L1 for pH-dependent binding by monoclonal antibodies for tumor therapy.

Liu, H., Bi, X., Zhou, Y., Shi, R., Yao, S., Qi, J., Feng, H., Feng, M., Yan, J., Tan, S.

(2020) Signal Transduct Target Ther 5: 158-158

• PubMed: 32839442 
• DOI: https://doi.org/10.1038/s41392-020-00254-z
• Primary Citation of Related Structures:  
  7C88

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Organizational Affiliation: 
• Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, School of Pharmacy, Fudan University, 201203, Shanghai, China.
Department of Antibody Discovery and Engineering, Shanghai Junshi Biosciences Co., Ltd, 201203, Shanghai, China.
School of Life Sciences, Anhui University, 230601, Hefei, China.
CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China.
CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China.
Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, School of Pharmacy, Fudan University, 201203, Shanghai, China. [e-mail].
School of Life Sciences, Anhui University, 230601, Hefei, China. [e-mail].
CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China. [e-mail].
CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China. [e-mail].
School of Life Sciences, Anhui University, 230601, Hefei, China. [e-mail].
CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, 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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 127.35 kDa 
• Atom Count: 8,992 
• Modeled Residue Count: 1,080 
• Deposited Residue Count: 1,156 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
JS003 Heavy chain	A [auth H], D [auth A]	228	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
JS003 Light chain	B [auth L], E [auth B]	214	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Programmed cell death 1 ligand 1	C [auth M], F [auth C]	136	Homo sapiens	Mutation(s): 0  Gene Names: CD274, B7H1, PDCD1L1, PDCD1LG1, PDL1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NZQ7 (Homo sapiens) Explore Q9NZQ7  Go to UniProtKB:  Q9NZQ7
PHAROS:  Q9NZQ7 GTEx:  ENSG00000120217

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.258 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.222 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.224 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.984	α = 90
b = 65.639	β = 114.47
c = 107.529	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-04-14 
Deposition Author(s): Bi, X., Shi, R., Chai, Y., Qi, J., Yan, J., Tan, S.

Revision History  

• Version 1.0: 2021-04-14
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-09
  Changes: Structure summary