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- PDB-2m32: Alpha-1 integrin I-domain in complex with GLOGEN triple helical p... -

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Basic information

Entry
Database: PDB / ID: 2m32
TitleAlpha-1 integrin I-domain in complex with GLOGEN triple helical peptide
Components
  • GLOGEN peptide
  • Integrin alpha-1
KeywordsCELL ADHESION / alpha-1 integrin / I-domain / GLOGEN
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 / von Willebrand factor, type A domain / : / Integrin alpha Ig-like domain 2 / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site ...: / Integrin alpha Ig-like domain 3 / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / von Willebrand factor, type A domain / : / 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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsChin, Y. / Headey, S. / Mohanty, B. / McEwan, P. / Swarbrick, J. / Mulhern, T. / Emsley, J. / Simpson, J. / Scanlon, M.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: The Structure of Integrin alpha 1I Domain in Complex with a Collagen-mimetic Peptide.
Authors: Chin, Y.K. / Headey, S.J. / Mohanty, B. / Patil, R. / McEwan, P.A. / Swarbrick, J.D. / Mulhern, T.D. / Emsley, J. / Simpson, J.S. / Scanlon, M.J.
History
DepositionJan 7, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 6, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Integrin alpha-1
B: GLOGEN peptide
C: GLOGEN peptide
D: GLOGEN peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4245
Polymers27,4004
Non-polymers241
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 #1lowest energy

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Components

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


Mass: 21513.334 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGA1 / Production host: Escherichia coli (E. coli) / References: UniProt: P56199
#2: Protein/peptide GLOGEN peptide


Mass: 1962.060 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: synthetically obtained
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCA
1313D HN(CO)CA
1413D HN(CA)CB
1513D HNCO
1613D HBHA(CO)NH
1713D 1H-15N NOESY
1813D 1H-13C NOESY aliphatic
1913D 1H-13C NOESY aromatic

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Sample preparation

DetailsContents: 1.2 mM [U-98% 13C; U-98% 15N] Alpha-1 integrin, 2.4 mM GLOGEN, 50 mM HEPES, 50 mM NaCl, 5 mM MgCl2, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.2 mMentity_1-1[U-98% 13C; U-98% 15N]1
2.4 mMentity_2-21
50 mMHEPES-31
50 mMNaCl-41
5 mMMgCl2-51
Sample conditionsIonic strength: 0.1 / pH: 7.4 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAvance8001
Bruker AvanceBrukerAvance9002

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Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

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