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- PDB-3rrq: Crystal structure of the extracellular domain of human PD-1 -

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Basic information

Entry
Database: PDB / ID: 3rrq
TitleCrystal structure of the extracellular domain of human PD-1
ComponentsProgrammed cell death protein 1
KeywordsIMMUNE SYSTEM / PD-1 / Programmed death-1 / costimulatory
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 / Immunoglobulins ...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 / Immunoglobulins / Immunoglobulin-like fold / 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: 2.1 Å
AuthorsLazar-Molnar, E. / Ramagopal, U.A. / Nathenson, S.G. / Almo, S.C.
CitationJournal: To be Published
Title: Crystal structure of the extracellular domain of human PD-1
Authors: Lazar-Molnar, E. / Ramagopal, U.A. / Nathenson, S.G. / Almo, S.C.
History
DepositionApr 29, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Programmed cell death protein 1


Theoretical massNumber of molelcules
Total (without water)14,4451
Polymers14,4451
Non-polymers00
Water63135
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.020, 46.020, 187.395
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Detailsmonomer

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Components

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


Mass: 14445.148 Da / Num. of mol.: 1 / Fragment: Residues 32-160 / Mutation: A132L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PD-1, PD1, PDCD1 / Plasmid: pET-3a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) pLysS / References: UniProt: Q15116
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O

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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: 1.98 Å3/Da / Density % sol: 37.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 3.5M Sodium formate, 0.1M Bis-Tris, pH 7.5, Vapor diffusion, Sitting drop, temperature 298K, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 1, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 7612 / Num. obs: 7612 / % possible obs: 99.9 % / Redundancy: 17.4 % / Biso Wilson estimate: 36 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.043 / Χ2: 1.012 / Net I/σ(I): 9.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.1-2.1818.30.5727080.958100
2.18-2.2618.20.4777251.08100
2.26-2.3718.10.3727310.998100
2.37-2.4918.10.2937370.913100
2.49-2.65180.2237460.976100
2.65-2.8517.80.1377510.932100
2.85-3.1417.60.0867461.048100
3.14-3.5917.30.0667771.301100
3.59-4.5216.50.0387900.953100
4.52-5014.90.0269010.95899.3

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NPU

1npu


Resolution: 2.1→36.69 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.935 / WRfactor Rfree: 0.2339 / WRfactor Rwork: 0.2016 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8019 / SU B: 12.869 / SU ML: 0.151 / SU R Cruickshank DPI: 0.2301 / SU Rfree: 0.1883 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2488 350 4.7 %RANDOM
Rwork0.2143 ---
obs0.2159 7526 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 125.6 Å2 / Biso mean: 48.9633 Å2 / Biso min: 20.33 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å20.34 Å20 Å2
2--0.67 Å20 Å2
3----1.01 Å2
Refinement stepCycle: LAST / Resolution: 2.1→36.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms845 0 0 35 880
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.022888
X-RAY DIFFRACTIONr_angle_refined_deg1.5011.9531206
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3615111
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.74322.04544
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.18315145
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6491512
X-RAY DIFFRACTIONr_chiral_restr0.1110.2134
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021689
X-RAY DIFFRACTIONr_mcbond_it2.0192552
X-RAY DIFFRACTIONr_mcangle_it3.2373893
X-RAY DIFFRACTIONr_scbond_it2.2132336
X-RAY DIFFRACTIONr_scangle_it3.2483311
LS refinement shellResolution: 2.1→2.153 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 20 -
Rwork0.197 493 -
all-513 -
obs--99.81 %
Refinement TLS params.Method: refined / Origin x: -18.336 Å / Origin y: 16.204 Å / Origin z: 2.049 Å
111213212223313233
T0.1708 Å20.0315 Å20.0104 Å2-0.3065 Å20.0118 Å2--0.2098 Å2
L5.2692 °20.045 °2-0.0111 °2-3.0542 °21.2036 °2--4.4368 °2
S-0.1689 Å °-0.5647 Å °-0.2113 Å °0.4258 Å °0.1661 Å °0.0476 Å °0.533 Å °0.0517 Å °0.0028 Å °

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