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- PDB-2k1a: Bicelle-embedded integrin alpha(IIB) transmembrane segment -

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Basic information

Entry
Database: PDB / ID: 2k1a
TitleBicelle-embedded integrin alpha(IIB) transmembrane segment
ComponentsIntegrin alpha-IIb
KeywordsCELL ADHESION / single-pass transmembrane segment / Alternative splicing / Calcium / Cleavage on pair of basic residues / Disease mutation / Glycoprotein / Integrin / Polymorphism / Pyrrolidone carboxylic acid / Receptor
Function / homology
Function and homology information


integrin alphaIIb-beta3 complex / platelet alpha granule membrane / fibrinogen binding / extracellular matrix binding / positive regulation of leukocyte migration / integrin complex / cell adhesion mediated by integrin / p130Cas linkage to MAPK signaling for integrins / GRB2:SOS provides linkage to MAPK signaling for Integrins / ECM proteoglycans ...integrin alphaIIb-beta3 complex / platelet alpha granule membrane / fibrinogen binding / extracellular matrix binding / positive regulation of leukocyte migration / integrin complex / cell adhesion mediated by integrin / p130Cas linkage to MAPK signaling for integrins / GRB2:SOS provides linkage to MAPK signaling for Integrins / ECM proteoglycans / Integrin cell surface interactions / Integrin signaling / cell-matrix adhesion / Signal transduction by L1 / integrin-mediated signaling pathway / Signaling by high-kinase activity BRAF mutants / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / MAP2K and MAPK activation / cell-cell adhesion / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Signaling by BRAF and RAF1 fusions / integrin binding / Platelet degranulation / angiogenesis / molecular adaptor activity / blood microparticle / external side of plasma membrane / focal adhesion / cell surface / extracellular exosome / metal ion binding / identical protein binding / plasma membrane
Similarity search - Function
Bicelle-embedded integrin alpha(iib) transmembrane segment / : / Integrin alpha Ig-like domain 3 / Integrin alpha cytoplasmic region / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / : ...Bicelle-embedded integrin alpha(iib) transmembrane segment / : / Integrin alpha Ig-like domain 3 / Integrin alpha cytoplasmic region / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / : / Integrin alpha Ig-like domain 2 / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model type detailsminimized average
AuthorsLau, T.-L. / Dua, V. / Ulmer, T.S.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Structure of the Integrin {alpha}IIb Transmembrane Segment.
Authors: Lau, T.L. / Dua, V. / Ulmer, T.S.
History
DepositionFeb 25, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / 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
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 650HELIX DETERMINATION METHOD: AUTHOR

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Integrin alpha-IIb


Theoretical massNumber of molelcules
Total (without water)4,7521
Polymers4,7521
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)21 / 21all calculated structures submitted
RepresentativeModel #1minimized average structure

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Components

#1: Protein/peptide Integrin alpha-IIb / Platelet membrane glycoprotein IIb / GPalpha IIb / GPIIb / CD41 antigen


Mass: 4751.833 Da / Num. of mol.: 1 / Fragment: Transmembrane region
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGA2B, GP2B, ITGAB / Production host: Escherichia coli (E. coli) / References: UniProt: P08514

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D TRIPLE RESONANCE
1213D HNCO-J

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Sample preparation

DetailsContents: 0.6 mM [U-100% 13C; U-100% 15N; 80% 2H] protein, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
SampleConc.: 0.6 mM / Component: entity / Isotopic labeling: [U-100% 13C; U-100% 15N; 80% 2H]
Sample conditionsIonic strength: 0.025 / pH: 7.4 / Pressure: ambient / Temperature: 308.2 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 21 / Conformers submitted total number: 21

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