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- PDB-7cgw: Complex structure of PD-1 and tislelizumab Fab -

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Basic information

Entry
Database: PDB / ID: 7cgw
TitleComplex structure of PD-1 and tislelizumab Fab
Components
  • Heavy chain of tislelizumab Fab
  • Light chain of tislelizumab Fab
  • Programmed cell death protein 1
KeywordsANTITUMOR PROTEIN / Tislelizumab / PD-1 / antibody
Function / homology
Function and homology information


negative regulation of tolerance induction / regulatory T cell apoptotic process / B cell apoptotic process / negative regulation of immune response / positive regulation of T cell apoptotic process / negative regulation of B cell apoptotic process / humoral immune response / PD-1 signaling / regulation of immune response / Potential therapeutics for SARS ...negative regulation of tolerance induction / regulatory T cell apoptotic process / B cell apoptotic process / negative regulation of immune response / positive regulation of T cell apoptotic process / negative regulation of B cell apoptotic process / humoral immune response / PD-1 signaling / regulation of immune response / Potential therapeutics for SARS / adaptive immune response / external side of plasma membrane / apoptotic process / plasma membrane
Similarity search - Function
Programmed cell death protein 1 / Immunoglobulin V-Type / 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 protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsHong, Y. / Feng, Y.C. / Liu, Y.
CitationJournal: Febs Open Bio / Year: 2021
Title: Tislelizumab uniquely binds to the CC' loop of PD-1 with slow-dissociated rate and complete PD-L1 blockage.
Authors: Hong, Y. / Feng, Y. / Sun, H. / Zhang, B. / Wu, H. / Zhu, Q. / Li, Y. / Zhang, T. / Zhang, Y. / Cui, X. / Li, Z. / Song, X. / Li, K. / Liu, M. / Liu, Y.
History
DepositionJul 2, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heavy chain of tislelizumab Fab
B: Light chain of tislelizumab Fab
C: Programmed cell death protein 1
H: Heavy chain of tislelizumab Fab
L: Light chain of tislelizumab Fab
P: Programmed cell death protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,56113
Polymers130,0136
Non-polymers1,5487
Water0
1
A: Heavy chain of tislelizumab Fab
B: Light chain of tislelizumab Fab
C: Programmed cell death protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,6706
Polymers65,0063
Non-polymers6643
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6720 Å2
ΔGint-20 kcal/mol
Surface area24350 Å2
MethodPISA
2
H: Heavy chain of tislelizumab Fab
L: Light chain of tislelizumab Fab
P: Programmed cell death protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,8917
Polymers65,0063
Non-polymers8854
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6510 Å2
ΔGint-23 kcal/mol
Surface area24590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.638, 145.572, 175.549
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Antibody Heavy chain of tislelizumab Fab


Mass: 24477.336 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody Light chain of tislelizumab Fab


Mass: 23549.080 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein Programmed cell death protein 1 / / hPD-1


Mass: 16979.893 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDCD1, PD1 / Production host: Homo sapiens (human) / References: UniProt: Q15116
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestY

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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: 3.5 Å3/Da / Density % sol: 64.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 0.1M Citric acid, pH4.0, 1M LiCl and 20% PEG6000

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.2→101.88 Å / Num. obs: 30470 / % possible obs: 99.9 % / Redundancy: 11.4 % / Biso Wilson estimate: 95.76 Å2 / CC1/2: 0.994 / Net I/σ(I): 11.8
Reflection shellResolution: 3.2→3.37 Å / Mean I/σ(I) obs: 2.4 / Num. unique obs: 4399 / CC1/2: 0.673

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Tislelizumab Fab

Resolution: 3.2→101.88 Å / SU ML: 0.4264 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.2957
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.254 2005 6.59 %
Rwork0.2179 28418 -
obs0.2203 30423 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 104.54 Å2
Refinement stepCycle: LAST / Resolution: 3.2→101.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8352 0 98 0 8450
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068644
X-RAY DIFFRACTIONf_angle_d1.094911774
X-RAY DIFFRACTIONf_chiral_restr0.21151358
X-RAY DIFFRACTIONf_plane_restr0.00791505
X-RAY DIFFRACTIONf_dihedral_angle_d23.33733115
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.280.30791480.2912008X-RAY DIFFRACTION99.54
3.28-3.370.38811390.28321993X-RAY DIFFRACTION100
3.37-3.470.33591370.27751999X-RAY DIFFRACTION100
3.47-3.580.33591390.26032026X-RAY DIFFRACTION99.95
3.58-3.710.26481360.23542006X-RAY DIFFRACTION100
3.71-3.860.28241470.23142007X-RAY DIFFRACTION99.91
3.86-4.030.29011400.23152029X-RAY DIFFRACTION99.91
4.03-4.240.2431490.20742020X-RAY DIFFRACTION99.77
4.24-4.510.23551380.19012023X-RAY DIFFRACTION99.72
4.51-4.860.2371470.17642031X-RAY DIFFRACTION99.59
4.86-5.350.18321450.17742026X-RAY DIFFRACTION99.72
5.35-6.120.23931440.20332043X-RAY DIFFRACTION99.95
6.12-7.710.21791430.25022068X-RAY DIFFRACTION100
7.71-101.880.26391530.21662139X-RAY DIFFRACTION98.75

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