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- PDB-7wvm: The complex structure of PD-1 and cemiplimab -

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Basic information

Entry
Database: PDB / ID: 7wvm
TitleThe complex structure of PD-1 and cemiplimab
Components
  • Heavy Chain of Cemiplimab
  • Light Chain of Cemiplimab
  • Programmed cell death protein 1
KeywordsIMMUNE SYSTEM/ANTITUMOR PROTEIN / PD-1 / antibody / N58 glycosylation / cemiplimab / immune checkpoint therapy (ICT) / ANTITUMOR PROTEIN / IMMUNE SYSTEM-ANTITUMOR PROTEIN complex
Function / homology
Function and homology information


negative regulation of tolerance induction / regulatory T cell apoptotic process / negative regulation of immune response / negative regulation of T cell mediated immune response to tumor cell / negative regulation of T cell activation / positive regulation of T cell apoptotic process / B cell apoptotic process / negative regulation of B cell apoptotic process / humoral immune response / Co-inhibition by PD-1 ...negative regulation of tolerance induction / regulatory T cell apoptotic process / negative regulation of immune response / negative regulation of T cell mediated immune response to tumor cell / negative regulation of T cell activation / positive regulation of T cell apoptotic process / B cell apoptotic process / negative regulation of B cell apoptotic process / humoral immune response / Co-inhibition by PD-1 / regulation of immune response / signaling receptor activity / 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 ...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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Programmed cell death protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsLu, D. / Xu, Z.P. / Liu, K.F. / Tan, S.G. / Gao, G.F. / Chai, Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31830097 China
National Natural Science Foundation of China (NSFC)32100752 China
CitationJournal: Front Immunol / Year: 2022
Title: PD-1 N58-Glycosylation-Dependent Binding of Monoclonal Antibody Cemiplimab for Immune Checkpoint Therapy.
Authors: Lu, D. / Xu, Z. / Zhang, D. / Jiang, M. / Liu, K. / He, J. / Ma, D. / Ma, X. / Tan, S. / Gao, G.F. / Chai, Y.
History
DepositionFeb 10, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 20, 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
A: Heavy Chain of Cemiplimab
B: Light Chain of Cemiplimab
E: Programmed cell death protein 1
C: Heavy Chain of Cemiplimab
D: Light Chain of Cemiplimab
F: Programmed cell death protein 1


Theoretical massNumber of molelcules
Total (without water)74,8736
Polymers74,8736
Non-polymers00
Water00
1
A: Heavy Chain of Cemiplimab
B: Light Chain of Cemiplimab
E: Programmed cell death protein 1


Theoretical massNumber of molelcules
Total (without water)37,4373
Polymers37,4373
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Heavy Chain of Cemiplimab
D: Light Chain of Cemiplimab
F: Programmed cell death protein 1


Theoretical massNumber of molelcules
Total (without water)37,4373
Polymers37,4373
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)131.545, 131.545, 124.338
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Antibody Heavy Chain of Cemiplimab


Mass: 12751.239 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Antibody Light Chain of Cemiplimab


Mass: 11514.724 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Protein Programmed cell death protein 1 / Protein PD-1 / hPD-1


Mass: 13170.722 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDCD1, PD1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15116
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: 4.22 Å3/Da / Density % sol: 70.84 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Sodium acetate, pH 5.0, 5% w/v PGA (Na+ form, LM), 20% w/v PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. obs: 17566 / % possible obs: 100 % / Redundancy: 8.9 % / Biso Wilson estimate: 68.82 Å2 / Rmerge(I) obs: 0.2 / Net I/σ(I): 9.5
Reflection shellResolution: 3.4→3.52 Å / Rmerge(I) obs: 0.658 / Num. unique obs: 1721

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.13-2998refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GGU, 6KTR

5ggu

6ktr


Resolution: 3.4→43.06 Å / SU ML: 0.4753 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.151
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2874 860 5.02 %
Rwork0.2466 16265 -
obs0.2487 17125 97.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.12 Å2
Refinement stepCycle: LAST / Resolution: 3.4→43.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5176 0 0 0 5176
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00285297
X-RAY DIFFRACTIONf_angle_d0.68547187
X-RAY DIFFRACTIONf_chiral_restr0.051786
X-RAY DIFFRACTIONf_plane_restr0.0053931
X-RAY DIFFRACTIONf_dihedral_angle_d18.45441884
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.610.36961310.35712724X-RAY DIFFRACTION99.62
3.61-3.890.39461510.3482742X-RAY DIFFRACTION99.83
3.89-4.280.27791590.28182711X-RAY DIFFRACTION99.31
4.28-4.90.22281490.1962706X-RAY DIFFRACTION98.28
4.9-6.170.24421400.21132660X-RAY DIFFRACTION95.6
6.17-43.060.29291300.19652722X-RAY DIFFRACTION93.29

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