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- PDB-2m2d: Human programmed cell death 1 receptor -

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Basic information

Entry
Database: PDB / ID: 2m2d
TitleHuman programmed cell death 1 receptor
ComponentsProgrammed cell death protein 1
KeywordsAPOPTOSIS / PD-1
Function / homology
Function and homology information


negative regulation of tolerance induction / regulatory T cell apoptotic process / 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 immune response / negative regulation of B cell apoptotic process / humoral immune response / regulation of immune response ...negative regulation of tolerance induction / regulatory T cell apoptotic process / 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 immune response / negative regulation of B cell apoptotic process / humoral immune response / regulation of immune response / PD-1 signaling / 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 / 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)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model detailsclosest to the average, model 11
AuthorsVeverka, V. / Cheng, X. / Waters, L.C. / Muskett, F.W. / Morgan, S. / Lesley, A. / Griffiths, M. / Stubberfield, C. / Griffin, R. / Henry, A.J. ...Veverka, V. / Cheng, X. / Waters, L.C. / Muskett, F.W. / Morgan, S. / Lesley, A. / Griffiths, M. / Stubberfield, C. / Griffin, R. / Henry, A.J. / Robinson, M.K. / Jansson, A. / Ladbury, J.E. / Ikemizu, S. / Davis, S.J. / Carr, M.D.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structure and interactions of the human programmed cell death 1 receptor.
Authors: Cheng, X. / Veverka, V. / Radhakrishnan, A. / Waters, L.C. / Muskett, F.W. / Morgan, S.H. / Huo, J. / Yu, C. / Evans, E.J. / Leslie, A.J. / Griffiths, M. / Stubberfield, C. / Griffin, R. / ...Authors: Cheng, X. / Veverka, V. / Radhakrishnan, A. / Waters, L.C. / Muskett, F.W. / Morgan, S.H. / Huo, J. / Yu, C. / Evans, E.J. / Leslie, A.J. / Griffiths, M. / Stubberfield, C. / Griffin, R. / Henry, A.J. / Jansson, A. / Ladbury, J.E. / Ikemizu, S. / Carr, M.D. / Davis, S.J.
History
DepositionDec 18, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2013Group: Database references
Revision 1.2May 15, 2013Group: Database references
Revision 1.3Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _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)13,2461
Polymers13,2461
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)35 / 100structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

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


Mass: 13245.809 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDCD1, PD1 / Plasmid: pET / Production host: Escherichia coli (E. coli) / References: UniProt: Q15116
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1332D 1H-1H TOCSY
1432D 1H-1H NOESY
1523D HN(CA)CB
1623D CBCA(CO)NH
1723D HNCO
1823D (H)CCH-TOCSY
1913D 1H-15N TOCSY
11023D 1H-13C NOESY
11113D 1H-15N NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-15N] protein, 25 mM potassium phosphate, 100 mM sodium chloride, 95% H2O/5% D2O95% H2O/5% D2O
20.5 mM [U-13C; U-15N] protein, 25 mM potassium phosphate, 100 mM sodium chloride, 95% H2O/5% D2O95% H2O/5% D2O
30.5 mM protein, 25 mM potassium phosphate, 100 mM sodium chloride, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMprotein-1[U-15N]1
25 mMpotassium phosphate-21
100 mMsodium chloride-31
0.5 mMprotein-4[U-13C; U-15N]2
25 mMpotassium phosphate-52
100 mMsodium chloride-62
0.5 mMprotein-73
25 mMpotassium phosphate-83
100 mMsodium chloride-93
Sample conditionsIonic strength: 0.125 / pH: 6.4 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
SparkyGoddarddata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanstructure solution
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 35

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