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- PDB-6umu: Human apo PD-1 triple mutant -

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Basic information

Entry
Database: PDB / ID: 6umu
TitleHuman apo PD-1 triple mutant
ComponentsProgrammed cell death protein 1
KeywordsIMMUNE SYSTEM / PD-1 / immune checkpoint
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 / B cell apoptotic process / positive regulation of T 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 / B cell apoptotic process / positive regulation of T 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 / adaptive immune response / Potential therapeutics for SARS / 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: 1.183 Å
AuthorsTang, S. / Kim, P.S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: A high-affinity human PD-1/PD-L2 complex informs avenues for small-molecule immune checkpoint drug discovery.
Authors: Tang, S. / Kim, P.S.
History
DepositionOct 10, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 11, 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 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Programmed cell death protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5843
Polymers14,5131
Non-polymers712
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint-17 kcal/mol
Surface area6640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.172, 46.172, 89.270
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Programmed cell death protein 1 / hPD-1


Mass: 14513.199 Da / Num. of mol.: 1 / Fragment: UNP residues 33-150 / Mutation: N74G, T76P, A132V
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
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 1.89 Å3/Da / Density % sol: 35.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM sodium chloride, 100 mM Tris-HCl, pH 8.0, 27% w/v PEG5000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 6, 2019
RadiationMonochromator: Liquid nitrogen-cooled double crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.18→50 Å / Num. obs: 36705 / % possible obs: 99.8 % / Redundancy: 10 % / Biso Wilson estimate: 16.72 Å2 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.017 / Rrim(I) all: 0.056 / Χ2: 1.826 / Net I/σ(I): 11.9 / Num. measured all: 365601
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.18-1.260.50917550.8470.2220.5570.52498.6
1.2-1.227.50.50118160.890.1960.5390.5399.9
1.22-1.258.50.44518230.9350.1610.4740.55499.9
1.25-1.2790.41418050.9160.1450.440.609100
1.27-1.390.3517840.9530.1220.3710.62399.9
1.3-1.339.30.31218260.9730.1060.330.66299.5
1.33-1.3610.40.27518000.9790.0890.2890.77100
1.36-1.410.50.22618370.9850.0730.2370.818100
1.4-1.4410.20.1918320.9860.0620.20.913100
1.44-1.4910.20.15818180.9910.0520.1670.98299.9
1.49-1.549.60.13118170.990.0440.1381.26499.5
1.54-1.610.90.11218230.9930.0350.1181.56100
1.6-1.67110.10118190.9950.0320.1061.756100
1.67-1.76110.08918450.9930.0280.0942.015100
1.76-1.8710.40.07618160.9960.0250.082.40999.7
1.87-2.0211.20.06218470.9980.0190.0652.76299.5
2.02-2.2211.50.05618800.9980.0170.0582.866100
2.22-2.5411.20.05118660.9980.0160.0543.266100
2.54-3.210.90.04618870.9990.0140.0493.56299.3
3.2-5010.50.04620090.9980.0140.0485.23599.4

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Processing

Software
NameVersionClassification
HKL-3000data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3RRQ

3rrq


Resolution: 1.183→36.493 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 15.99
RfactorNum. reflection% reflection
Rfree0.1638 2009 5.48 %
Rwork0.1536 --
obs0.1542 36660 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 69.11 Å2 / Biso mean: 23.7131 Å2 / Biso min: 9.98 Å2
Refinement stepCycle: final / Resolution: 1.183→36.493 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms842 0 3 152 997
Biso mean--27.09 38.86 -
Num. residues----112
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091056
X-RAY DIFFRACTIONf_angle_d1.3481476
X-RAY DIFFRACTIONf_chiral_restr0.087171
X-RAY DIFFRACTIONf_plane_restr0.006197
X-RAY DIFFRACTIONf_dihedral_angle_d9.698423
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.183-1.21210.25281400.1972240798
1.2121-1.24490.1821380.17172417100
1.2449-1.28150.19351400.15262460100
1.2815-1.32290.17771400.14142419100
1.3229-1.37020.18851420.13852445100
1.3702-1.4250.18291420.13932453100
1.425-1.48990.17461490.13842478100
1.4899-1.56840.17671340.13432448100
1.5684-1.66670.16771460.13442486100
1.6667-1.79540.16641410.13832483100
1.7954-1.97610.17731450.1401245599
1.9761-2.2620.15351460.14422514100
2.262-2.84970.19341470.17482531100
2.8497-36.4930.14111590.15872655100

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