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- PDB-2ky5: Solution structure of the PECAM-1 cytoplasmic tail with DPC -

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Basic information

Entry
Database: PDB / ID: 2ky5
TitleSolution structure of the PECAM-1 cytoplasmic tail with DPC
ComponentsPlatelet endothelial cell adhesion molecule
KeywordsCELL ADHESION / PECAM-1 / ITIM / signal transduction / membrane association / Structural Genomics / Protein Structure Initiative / PSI / Center for Eukaryotic Structural Genomics / CESG
Function / homology
Function and homology information


positive regulation of protein localization to cell-cell junction / diapedesis / cell recognition / glomerular endothelium development / monocyte extravasation / neutrophil extravasation / platelet alpha granule membrane / cell-cell adhesion via plasma-membrane adhesion molecules / bicellular tight junction assembly / negative regulation of immune response ...positive regulation of protein localization to cell-cell junction / diapedesis / cell recognition / glomerular endothelium development / monocyte extravasation / neutrophil extravasation / platelet alpha granule membrane / cell-cell adhesion via plasma-membrane adhesion molecules / bicellular tight junction assembly / negative regulation of immune response / establishment of endothelial barrier / leukocyte cell-cell adhesion / maintenance of blood-brain barrier / Platelet sensitization by LDL / homophilic cell adhesion via plasma membrane adhesion molecules / PECAM1 interactions / Integrin cell surface interactions / phagocytosis / secretory granule membrane / Cell surface interactions at the vascular wall / cell-cell adhesion / transmembrane signaling receptor activity / positive regulation of peptidyl-tyrosine phosphorylation / cell-cell junction / Platelet degranulation / cell surface receptor signaling pathway / positive regulation of cell migration / positive regulation of protein phosphorylation / immune response / membrane raft / external side of plasma membrane / Neutrophil degranulation / signal transduction / protein homodimerization activity / protein-containing complex / extracellular space / extracellular exosome / plasma membrane
Similarity search - Function
C17orf99, Ig domain / C17orf99 Ig domain / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain ...C17orf99, Ig domain / C17orf99 Ig domain / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Platelet endothelial cell adhesion molecule
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
Model detailslowest energy, model 1
AuthorsLytle, B.L. / Peterson, F.C. / Volkman, B.F. / Paddock, C. / Newman, D.K. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: Blood / Year: 2011
Title: Residues within a lipid-associated segment of the PECAM-1 cytoplasmic domain are susceptible to inducible, sequential phosphorylation.
Authors: Paddock, C. / Lytle, B.L. / Peterson, F.C. / Holyst, T. / Newman, P.J. / Volkman, B.F. / Newman, D.K.
History
DepositionMay 14, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 5, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Platelet endothelial cell adhesion molecule


Theoretical massNumber of molelcules
Total (without water)5,9881
Polymers5,9881
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)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Platelet endothelial cell adhesion molecule / PECAM-1 / EndoCAM / GPIIA' / PECA1


Mass: 5988.368 Da / Num. of mol.: 1 / Fragment: sequence database residues 685-737
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PECAM-1, PECAM1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21[pREP4] / References: UniProt: P16284

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
1313D 13C-separated NOESY (AROMATIC)
NMR detailsText: AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT AND ITERATIVE NOE REFINEMENT.

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Sample preparation

DetailsContents: 1 mM [U-100% 13C; U-100% 15N] PECAM-1, 20 mM sodium phosphate, 50 mM sodium chloride, 2 mM DTT, 600 mM [U-100% 2H] DPC, 95% H2O, 5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMPECAM-1-1[U-100% 13C; U-100% 15N]1
20 mMsodium phosphate-21
50 mMsodium chloride-31
2 mMDTT-41
600 mMDPC-5[U-100% 2H]1
Sample conditionsIonic strength: 52 / pH: 7.0 / Pressure: AMBIENT / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Xplor-NIH2.9.3SCHWIETERS,C.D.,KUSZEWSKI,J.J.,TJANDRA,N.,CLORE,G.M.refinement
TopSpin2.1Brukercollection
NMRPipe2009Delagio,F. et al.processing
XEASY1.3Eccles, C., Guntert, P., Billeter, M., Wuthrich, K.data analysis
GARANT2.1C. Bartelsdata analysis
CYANA2.1Guntert, P.structural calculation
RefinementMethod: molecular dynamics / Software ordinal: 1
Details: STRUCTURES ARE BASED ON A TOTAL OF 164 NOE CONSTRAINTS ( 81 INTRA, 42 SEQUENTIAL, 41 MEDIUM and 0 LONG RANGE CONSTRAINTS) AND 33 PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS.FINAL STRUCTURES WERE ...Details: STRUCTURES ARE BASED ON A TOTAL OF 164 NOE CONSTRAINTS ( 81 INTRA, 42 SEQUENTIAL, 41 MEDIUM and 0 LONG RANGE CONSTRAINTS) AND 33 PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS.FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT.
NMR constraintsNOE constraints total: 164 / NOE intraresidue total count: 81 / NOE medium range total count: 41 / NOE sequential total count: 42
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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