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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.258 (Depositor), 0.257 (DCC)
R-Value Work:
0.222 (Depositor), 0.223 (DCC)
R-Value Observed:
0.224 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

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 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41392-020-00254-z
Primary Citation Related Structures:
7C88

Organizational Affiliation

Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, School of Pharmacy, Fudan University, 201203, Shanghai, China.

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

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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9NZQ7
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.258 (Depositor), 0.257 (DCC)
R-Value Work: 0.222 (Depositor), 0.223 (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

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Entry History

Deposition Data

Released Date: 2021-04-14

Deposition Author(s):

Revision History (Full details and data files)

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