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- PDB-7cu5: N-Glycosylation of PD-1 and glycosylation dependent binding of PD... -

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Basic information

Entry
Database: PDB / ID: 7cu5
TitleN-Glycosylation of PD-1 and glycosylation dependent binding of PD-1 specific monoclonal antibody camrelizumab
Components
  • Programmed cell death protein 1
  • camrelizumab-scFv
KeywordsIMMUNE SYSTEM / Camrelizumab / glycosylation / PD-1.
Function / homology
Function and homology information


negative regulation of tolerance induction / regulatory T cell apoptotic process / negative regulation of immune response / B cell apoptotic process / 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 / negative regulation of immune response / B cell apoptotic process / 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: 2.81 Å
AuthorsLiu, K.F. / Tan, S.G. / Jin, W.J. / Guan, J.W. / Wang, W.L. / Sun, H. / Qi, J.X. / Yan, J.H. / Chai, Y. / Wang, Z.F. ...Liu, K.F. / Tan, S.G. / Jin, W.J. / Guan, J.W. / Wang, W.L. / Sun, H. / Qi, J.X. / Yan, J.H. / Chai, Y. / Wang, Z.F. / Chu, X.D. / Gao, G.F.
CitationJournal: Embo Rep. / Year: 2020
Title: N-glycosylation of PD-1 promotes binding of camrelizumab.
Authors: Liu, K. / Tan, S. / Jin, W. / Guan, J. / Wang, Q. / Sun, H. / Qi, J. / Yan, J. / Chai, Y. / Wang, Z. / Deng, C. / Gao, G.F.
History
DepositionAug 21, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 31, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: camrelizumab-scFv
E: Programmed cell death protein 1
A: camrelizumab-scFv
Q: Programmed cell death protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,83411
Polymers76,2394
Non-polymers3,5947
Water0
1
Q: Programmed cell death protein 1
hetero molecules

B: camrelizumab-scFv
A: camrelizumab-scFv

E: Programmed cell death protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,83411
Polymers76,2394
Non-polymers3,5947
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_465x-1,y+1,z1
crystal symmetry operation1_366x-2,y+1,z+11
Buried area11230 Å2
ΔGint44 kcal/mol
Surface area32410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.108, 77.622, 96.051
Angle α, β, γ (deg.)69.381, 78.444, 88.566
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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Antibody / Protein , 2 types, 4 molecules BAEQ

#1: Antibody camrelizumab-scFv


Mass: 24791.680 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: Protein Programmed cell death protein 1 / / hPD-1


Mass: 13327.914 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDCD1, PD1 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q15116

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Sugars , 4 types, 7 molecules

#3: Polysaccharide alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 894.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpa1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-2-3/a4-b1_a6-e1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 894.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-2-3/a4-b1_a6-e1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#6: 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.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
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

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Details

Has ligand of interestN

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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: 3.86 Å3/Da / Density % sol: 68.14 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1M cadmium chloride, 0.1M Na acetate, pH4.6, 30 %(v/v) PEG 400 a month later.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 27286 / % possible obs: 98.4 % / Redundancy: 3.4 % / Biso Wilson estimate: 34.4 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 11.2
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.692 / Num. unique obs: 2726

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WT9

5wt9


Resolution: 2.81→29.69 Å / SU ML: 0.3635 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 27.4888
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2515 1234 4.73 %
Rwork0.2123 24880 -
obs0.2141 26114 93.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.7 Å2
Refinement stepCycle: LAST / Resolution: 2.81→29.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5486 0 0 0 5486
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00475610
X-RAY DIFFRACTIONf_angle_d0.67817621
X-RAY DIFFRACTIONf_chiral_restr0.0464881
X-RAY DIFFRACTIONf_plane_restr0.0052956
X-RAY DIFFRACTIONf_dihedral_angle_d20.78722082
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.81-2.920.33271130.29671873X-RAY DIFFRACTION64.19
2.92-3.050.36021620.28772742X-RAY DIFFRACTION93.65
3.05-3.210.36381390.27172899X-RAY DIFFRACTION98.38
3.21-3.410.26821390.25922880X-RAY DIFFRACTION97.8
3.41-3.680.28881410.25042851X-RAY DIFFRACTION96.36
3.68-4.050.2811010.23522909X-RAY DIFFRACTION97.76
4.05-4.630.19891470.16652892X-RAY DIFFRACTION97.78
4.63-5.830.1881500.16152901X-RAY DIFFRACTION99.38
5.83-29.680.2171420.17942933X-RAY DIFFRACTION98.87

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