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- PDB-7c88: Complex structure of JS003 and PD-L1 -

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Basic information

Entry
Database: PDB / ID: 7c88
TitleComplex structure of JS003 and PD-L1
Components
  • JS003 Heavy chain
  • JS003 Light chain
  • Programmed cell death 1 ligand 1
KeywordsIMMUNE SYSTEM / PD-L1 / antibody / pH
Function / homology
Function and homology information


negative regulation of tumor necrosis factor superfamily cytokine production / positive regulation of activated CD8-positive, alpha-beta T cell apoptotic process / negative regulation of CD8-positive, alpha-beta T cell activation / negative regulation of T cell mediated immune response to tumor cell / TRIF-dependent toll-like receptor signaling pathway / negative regulation of CD4-positive, alpha-beta T cell proliferation / STAT3 nuclear events downstream of ALK signaling / negative regulation of interleukin-10 production / negative regulation of activated T cell proliferation / positive regulation of interleukin-10 production ...negative regulation of tumor necrosis factor superfamily cytokine production / positive regulation of activated CD8-positive, alpha-beta T cell apoptotic process / negative regulation of CD8-positive, alpha-beta T cell activation / negative regulation of T cell mediated immune response to tumor cell / TRIF-dependent toll-like receptor signaling pathway / negative regulation of CD4-positive, alpha-beta T cell proliferation / STAT3 nuclear events downstream of ALK signaling / negative regulation of interleukin-10 production / negative regulation of activated T cell proliferation / positive regulation of interleukin-10 production / negative regulation of type II interferon production / PD-1 signaling / positive regulation of T cell proliferation / T cell costimulation / response to cytokine / recycling endosome membrane / actin cytoskeleton / early endosome membrane / cellular response to lipopolysaccharide / adaptive immune response / transcription coactivator activity / cell surface receptor signaling pathway / receptor ligand activity / positive regulation of cell migration / immune response / external side of plasma membrane / signal transduction / extracellular exosome / nucleoplasm / plasma membrane
Similarity search - Function
: / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Programmed cell death 1 ligand 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.997 Å
AuthorsBi, X. / Shi, R. / Chai, Y. / Qi, J. / Yan, J. / Tan, S.
CitationJournal: Signal Transduct Target Ther / Year: 2020
Title: Identification of a hotspot on PD-L1 for pH-dependent binding by monoclonal antibodies for tumor therapy.
Authors: Liu, H. / Bi, X. / Zhou, Y. / Shi, R. / Yao, S. / Qi, J. / Feng, H. / Feng, M. / Yan, J. / Tan, S.
History
DepositionMay 29, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: JS003 Heavy chain
L: JS003 Light chain
M: Programmed cell death 1 ligand 1
A: JS003 Heavy chain
B: JS003 Light chain
C: Programmed cell death 1 ligand 1


Theoretical massNumber of molelcules
Total (without water)127,3496
Polymers127,3496
Non-polymers00
Water11,854658
1
H: JS003 Heavy chain
L: JS003 Light chain
M: Programmed cell death 1 ligand 1


Theoretical massNumber of molelcules
Total (without water)63,6753
Polymers63,6753
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5130 Å2
ΔGint-35 kcal/mol
Surface area23860 Å2
MethodPISA
2
A: JS003 Heavy chain
B: JS003 Light chain
C: Programmed cell death 1 ligand 1


Theoretical massNumber of molelcules
Total (without water)63,6753
Polymers63,6753
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5020 Å2
ΔGint-37 kcal/mol
Surface area23780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.984, 65.639, 107.529
Angle α, β, γ (deg.)90.00, 114.47, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody JS003 Heavy chain


Mass: 24418.326 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody JS003 Light chain


Mass: 23431.971 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster)
#3: Protein Programmed cell death 1 ligand 1 / hPD-L1 / B7 homolog 1 / B7-H1


Mass: 15824.343 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD274, B7H1, PDCD1L1, PDCD1LG1, PDL1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NZQ7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 658 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.84 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1M Na HEPES 7.0, 15% w/v PEG 20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9789 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.996→50 Å / Num. obs: 86422 / % possible obs: 92.61 % / Redundancy: 5.3 % / CC1/2: 0.99 / Net I/σ(I): 1.74
Reflection shellResolution: 2→4.31 Å / Num. unique obs: 93009 / CC1/2: 0.872

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Processing

Software
NameVersionClassification
PHENIX(1.16_3549: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GRJ

5grj


Resolution: 1.997→50 Å / SU ML: 0.26 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 28.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2576 4235 4.9 %
Rwork0.2223 --
obs0.224 86422 92.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.997→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8334 0 0 658 8992
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068520
X-RAY DIFFRACTIONf_angle_d0.93911588
X-RAY DIFFRACTIONf_dihedral_angle_d20.6953092
X-RAY DIFFRACTIONf_chiral_restr0.0541320
X-RAY DIFFRACTIONf_plane_restr0.0051468
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.997-2.01920.3321860.28151785X-RAY DIFFRACTION62
2.0192-2.0430.3096910.30412131X-RAY DIFFRACTION71
2.043-2.06790.63741080.50091925X-RAY DIFFRACTION66
2.0679-2.09410.50671060.48331578X-RAY DIFFRACTION55
2.0941-2.12160.29841420.2672435X-RAY DIFFRACTION82
2.1216-2.15070.28121390.26942494X-RAY DIFFRACTION86
2.1507-2.18140.29091520.26692660X-RAY DIFFRACTION91
2.1814-2.2140.32121510.26672785X-RAY DIFFRACTION95
2.214-2.24860.42161200.37732701X-RAY DIFFRACTION91
2.2486-2.28540.3981480.37782433X-RAY DIFFRACTION84
2.2854-2.32480.28941550.26362874X-RAY DIFFRACTION99
2.3248-2.36710.28671420.24922920X-RAY DIFFRACTION99
2.3671-2.41260.28071360.2492952X-RAY DIFFRACTION100
2.4126-2.46190.27621450.25652968X-RAY DIFFRACTION100
2.4619-2.51540.31821580.25382951X-RAY DIFFRACTION100
2.5154-2.57390.29371450.26342967X-RAY DIFFRACTION100
2.5739-2.63820.29871610.25492934X-RAY DIFFRACTION100
2.6382-2.70960.36981460.28542917X-RAY DIFFRACTION99
2.7096-2.78930.27131510.23522969X-RAY DIFFRACTION100
2.7893-2.87930.2481710.23362945X-RAY DIFFRACTION100
2.8793-2.98220.28951400.22582973X-RAY DIFFRACTION100
2.9822-3.10150.25261230.21652959X-RAY DIFFRACTION100
3.1015-3.24260.25891520.2172990X-RAY DIFFRACTION100
3.2426-3.41350.21911690.21672937X-RAY DIFFRACTION100
3.4135-3.62730.25441480.21382969X-RAY DIFFRACTION100
3.6273-3.90710.2221660.20772935X-RAY DIFFRACTION100
3.9071-4.30.23841460.17242997X-RAY DIFFRACTION100
4.3-4.92130.18931580.15472983X-RAY DIFFRACTION100
4.9213-6.19710.18311330.17173017X-RAY DIFFRACTION100
6.1971-41.5820.21711470.19413103X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 25.0263 Å / Origin y: -0.8502 Å / Origin z: 122.2695 Å
111213212223313233
T0.1975 Å20.0111 Å2-0.0117 Å2-0.1572 Å20.0068 Å2--0.1817 Å2
L0.3013 °2-0.0234 °2-0.0647 °2-0.0583 °20.0331 °2--0.0704 °2
S0.0007 Å °0.0013 Å °-0.008 Å °-0.0277 Å °-0.0108 Å °0.0209 Å °-0.0081 Å °0.0075 Å °0 Å °
Refinement TLS groupSelection details: all

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