5GRJ | pdb_00005grj

Crystal structure of human PD-L1 with monoclonal antibody avelumab

• PDB DOI: https://doi.org/10.2210/pdb5GRJ/pdb

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


• Deposited: 2016-08-11 Released: 2016-11-02 
• Deposition Author(s): Liu, K., Tan, S., Chai, Y., Chen, D., Song, H., Zhang, C.W.-H., Shi, Y., Liu, J., Tan, W., Lyu, J., Gao, S., Yan, J., Qi, J., Gao, G.F.
• Funding Organization(s): the Ministry of Science and Technology of China, Grand S&T project of China Health and Family Planning Commission

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.21 Å
• R-Value Free: 
  0.238 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Starting Models: experimental

Literature

Structural basis of anti-PD-L1 monoclonal antibody avelumab for tumor therapy.

Liu, K., Tan, S., Chai, Y., Chen, D., Song, H., Zhang, C.W., Shi, Y., Liu, J., Tan, W., Lyu, J., Gao, S., Yan, J., Qi, J., Gao, G.F.

(2017) Cell Res 27: 151-153

• PubMed: 27573173 
• DOI: https://doi.org/10.1038/cr.2016.102
• Primary Citation of Related Structures:  
  5GRJ

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Organizational Affiliation: 
• College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China.
National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing 102206, China.
CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China.
ImmuFucell Biotechnology Co., Ltd., Beijing 100102, China.
CAS Key Laboratory of Bio-medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu 215163, China.
CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

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

Macromolecule Content 

• Total Structure Weight: 49.83 kDa 
• Atom Count: 3,398 
• Modeled Residue Count: 439 
• Deposited Residue Count: 451 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
avelumab H chain	A [auth H]	120	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
avelumab L chain	B [auth L]	110	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Programmed cell death 1 ligand 1	C [auth A]	221	Homo sapiens	Mutation(s): 0  Gene Names: 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: 3.21 Å
• R-Value Free:  0.238 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.87	α = 90
b = 98.151	β = 108.43
c = 62.036	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-11-02 
Deposition Author(s): Liu, K., Tan, S., Chai, Y., Chen, D., Song, H., Zhang, C.W.-H., Shi, Y., Liu, J., Tan, W., Lyu, J., Gao, S., Yan, J., Qi, J., Gao, G.F.

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Funding Organization	Location	Grant Number
the Ministry of Science and Technology of China	China	2013CB531502, 2014CB542503
Grand S&T project of China Health and Family Planning Commission	China	013ZX10004608-002, 2016ZX10004201-009

Revision History  

• Version 1.0: 2016-11-02
  Type: Initial release
  
• Version 1.1: 2017-01-18
  Changes: Database references
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-10-23
  Changes: Structure summary