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- PDB-2luv: Structure and Binding Interface of the Cytosolic Tails of aXb2 In... -

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Basic information

Entry
Database: PDB / ID: 2luv
TitleStructure and Binding Interface of the Cytosolic Tails of aXb2 Integrin
ComponentsIntegrin alpha-X
KeywordsCELL ADHESION / MYRISTOYLATED / DPC MICELLES
Function / homology
Function and homology information


positive regulation of endothelial tube morphogenesis / integrin alphaX-beta2 complex / positive regulation of myelination / heterotypic cell-cell adhesion / integrin complex / cell adhesion mediated by integrin / tertiary granule membrane / ficolin-1-rich granule membrane / ECM proteoglycans / Integrin cell surface interactions ...positive regulation of endothelial tube morphogenesis / integrin alphaX-beta2 complex / positive regulation of myelination / heterotypic cell-cell adhesion / integrin complex / cell adhesion mediated by integrin / tertiary granule membrane / ficolin-1-rich granule membrane / ECM proteoglycans / Integrin cell surface interactions / cell-matrix adhesion / secretory granule membrane / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / animal organ morphogenesis / cell-cell adhesion / receptor tyrosine kinase binding / positive regulation of angiogenesis / integrin binding / signaling receptor activity / Interleukin-4 and Interleukin-13 signaling / defense response to virus / cell adhesion / positive regulation of cell migration / external side of plasma membrane / positive regulation of cell population proliferation / Neutrophil degranulation / positive regulation of gene expression / cell surface / membrane / metal ion binding / plasma membrane
Similarity search - Function
: / Integrin alpha-X-like, Ig-like domain 3 / Integrin alpha cytoplasmic region / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / : / Integrin alpha Ig-like domain 2 / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site ...: / Integrin alpha-X-like, Ig-like domain 3 / Integrin alpha cytoplasmic region / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / : / Integrin alpha Ig-like domain 2 / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / Integrins alpha chain signature. / FG-GAP repeat profile. / Integrin alpha (beta-propellor repeats). / FG-GAP repeat / FG-GAP repeat / Integrin domain superfamily / Integrin alpha, N-terminal / von Willebrand factor type A domain / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR
Model detailslowest energy, model1
AuthorsChua, G.L. / Tang, X. / Patra, T.A. / Tan, S.M. / Bhattacharjya, S.
CitationJournal: To be Published
Title: Structure and Binding Interface of the Cytosolic Tails of aXb2 Integrin
Authors: Chua, G.L. / Tang, X. / Patra, T.A. / Tan, S.M. / Bhattacharjya, S.
History
DepositionJun 21, 2012Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jul 4, 2012Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Integrin alpha-X


Theoretical massNumber of molelcules
Total (without water)3,9601
Polymers3,9601
Non-polymers00
Water0
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/peptide Integrin alpha-X / CD11 antigen-like family member C / Leu M5 / Leukocyte adhesion glycoprotein p150 / 95 alpha chain ...CD11 antigen-like family member C / Leu M5 / Leukocyte adhesion glycoprotein p150 / 95 alpha chain / Leukocyte adhesion receptor p150 / 95


Mass: 3960.423 Da / Num. of mol.: 1 / Fragment: Cytoplasmic domain, UNP residues 1129-1163 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P20702
Sequence detailsTHIS PEPTIDE IS CHEMICALLY SYNTHESIZED WITH A N-TERMINAL MYRISTATE GROUP.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D 1H-1H NOESY
1322D 1H-13C HSQC
1422D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
1200mM [U-99% 2H] DPC-1, 10mM sodium phosphate-2, 10% [U-100% 2H] D2O-3, 90% H2O/10% D2O90% H2O/10% D2O
2200mM [U-99% 2H] DPC-4, 10mM sodium phosphate-5, 100% [U-100% 2H] D2O-6, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
200 mMDPC-1[U-99% 2H]1
10 mMsodium phosphate-21
10 %D2O-3[U-100% 2H]1
200 mMDPC-4[U-99% 2H]2
10 mMsodium phosphate-52
100 %D2O-6[U-100% 2H]2
Sample conditionsIonic strength: 0 / pH: 5.6 / Pressure: ambient / Temperature: 308 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospinprocessing
SparkyGoddardchemical shift assignment
CYANA2Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2Guntert, Mumenthaler and Wuthrichrefinement
NMR constraintsNOE constraints total: 263 / NOE intraresidue total count: 74 / NOE long range total count: 3 / NOE medium range total count: 96 / NOE sequential total count: 90 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 29 / Protein psi angle constraints total count: 28
NMR representativeSelection criteria: lowest energy
NMR ensembleAverage torsion angle constraint violation: 8.9 ° / Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0 Å / Maximum torsion angle constraint violation: 8.9 ° / Maximum upper distance constraint violation: 0 Å / Representative conformer: 1
NMR ensemble rmsDistance rms dev: 0 Å / Distance rms dev error: 0 Å

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