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- PDB-2l8s: Solution NMR Structure of Transmembrane and Cytosolic Regions of ... -

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Basic information

Entry
Database: PDB / ID: 2l8s
TitleSolution NMR Structure of Transmembrane and Cytosolic Regions of Integrin Alpha1 in Detergent Micelles
ComponentsIntegrin alpha-1
KeywordsCELL ADHESION / Integrin Alpha1 / Transmembrane Region / Detergent micelle
Function / homology
Function and homology information


cellular extravasation / integrin alpha1-beta1 complex / collagen binding involved in cell-matrix adhesion / Other semaphorin interactions / CHL1 interactions / Laminin interactions / basal part of cell / Platelet Adhesion to exposed collagen / integrin complex / cell adhesion mediated by integrin ...cellular extravasation / integrin alpha1-beta1 complex / collagen binding involved in cell-matrix adhesion / Other semaphorin interactions / CHL1 interactions / Laminin interactions / basal part of cell / Platelet Adhesion to exposed collagen / integrin complex / cell adhesion mediated by integrin / negative regulation of epidermal growth factor receptor signaling pathway / positive regulation of phosphoprotein phosphatase activity / Smooth Muscle Contraction / Integrin cell surface interactions / collagen binding / cell-matrix adhesion / neutrophil chemotaxis / neuron projection morphogenesis / acrosomal vesicle / integrin-mediated signaling pathway / cell-cell adhesion / vasodilation / positive regulation of neuron apoptotic process / integrin binding / perikaryon / protein phosphatase binding / positive regulation of MAPK cascade / negative regulation of cell population proliferation / external side of plasma membrane / focal adhesion / cell surface / extracellular exosome / membrane / metal ion binding / plasma membrane
Similarity search - Function
: / Integrin alpha Ig-like domain 3 / 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. ...: / Integrin alpha Ig-like domain 3 / 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 / simulated annealing
Model detailsclosest to the average, model 1
AuthorsLai, C. / Liu, X. / Tian, C.
CitationJournal: Plos One / Year: 2013
Title: Integrin Alpha1 Has a Long Helix, Extending from the Transmembrane Region to the Cytoplasmic Tail in Detergent Micelles
Authors: Lai, C. / Liu, X. / Tian, C. / Wu, F.
History
DepositionJan 24, 2011Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Feb 1, 2012Provider: repository / Type: Initial release
Revision 1.1May 15, 2013Group: Database references
Revision 1.2Jun 14, 2023Group: Database references / Other
Category: database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _struct_ref_seq_dif.details
Revision 1.3May 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

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Assembly

Deposited unit
A: Integrin alpha-1


Theoretical massNumber of molelcules
Total (without water)6,3441
Polymers6,3441
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)10 / 200structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Integrin alpha-1 / / Integrin Alpha1 / CD49 antigen-like family member A / Laminin and collagen receptor / VLA-1


Mass: 6343.925 Da / Num. of mol.: 1
Fragment: Transmembrane/Cytoplasmic Region, UNP residues 1135-1179
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P56199

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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-15N HSQC
1323D HNCO
1423D HNCA
1523D HN(CA)CB
1623D CBCA(CO)NH
1723D C(CO)NH
1823D HBHA(CO)NH
1923D H(CCO)NH
11023D 1H-15N NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
150mM sodium phosphate; 2mM DTT; 1.0mM [U-15N] Integrin Alpha1; 95% H2O/5% D2O95% H2O/5% D2O
21.0mM [U-13C; U-15N] Integrin Alpha1; 50mM sodium phosphate; 2mM DTT; 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
50 mMsodium phosphate-11
2 mMDTT-21
1.0 mMIntegrin Alpha 1-3[U-15N]1
1.0 mMIntegrin Alpha1-4[U-13C; U-15N]2
50 mMsodium phosphate-52
2 mMDTT-62
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 303 K

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NMR measurement

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

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Processing

NMR software
NameDeveloperClassification
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Xplor-NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
Xplor-NIHrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10 / Representative conformer: 5

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