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- PDB-8rpq: Solution NMR structure of Integrin beta-1 TMD -

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Basic information

Entry
Database: PDB / ID: 8rpq
TitleSolution NMR structure of Integrin beta-1 TMD
ComponentsIntegrin beta-1
KeywordsMEMBRANE PROTEIN / Transmembrane helix
Function / homology
Function and homology information


integrin alpha8-beta1 complex / : / integrin alpha3-beta1 complex / integrin alpha5-beta1 complex / integrin alpha6-beta1 complex / integrin alpha7-beta1 complex / integrin alpha10-beta1 complex / integrin alpha11-beta1 complex / positive regulation of glutamate uptake involved in transmission of nerve impulse / myoblast fate specification ...integrin alpha8-beta1 complex / : / integrin alpha3-beta1 complex / integrin alpha5-beta1 complex / integrin alpha6-beta1 complex / integrin alpha7-beta1 complex / integrin alpha10-beta1 complex / integrin alpha11-beta1 complex / positive regulation of glutamate uptake involved in transmission of nerve impulse / myoblast fate specification / integrin alpha9-beta1 complex / regulation of collagen catabolic process / cardiac cell fate specification / integrin binding involved in cell-matrix adhesion / integrin alpha4-beta1 complex / cell-cell adhesion mediated by integrin / integrin alpha1-beta1 complex / collagen binding involved in cell-matrix adhesion / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / integrin alpha2-beta1 complex / reactive gliosis / formation of radial glial scaffolds / Other semaphorin interactions / cerebellar climbing fiber to Purkinje cell synapse / Formation of the ureteric bud / positive regulation of fibroblast growth factor receptor signaling pathway / CD40 signaling pathway / Fibronectin matrix formation / calcium-independent cell-matrix adhesion / basement membrane organization / regulation of synapse pruning / integrin alphav-beta1 complex / myelin sheath abaxonal region / CHL1 interactions / cardiac muscle cell myoblast differentiation / MET interacts with TNS proteins / Laminin interactions / leukocyte tethering or rolling / cardiac muscle cell differentiation / cell projection organization / germ cell migration / Platelet Adhesion to exposed collagen / myoblast fusion / positive regulation of vascular endothelial growth factor signaling pathway / Elastic fibre formation / mesodermal cell differentiation / axon extension / myoblast differentiation / cell migration involved in sprouting angiogenesis / Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin / positive regulation of fibroblast migration / integrin complex / wound healing, spreading of epidermal cells / heterotypic cell-cell adhesion / regulation of spontaneous synaptic transmission / lamellipodium assembly / sarcomere organization / dendrite morphogenesis / Molecules associated with elastic fibres / MET activates PTK2 signaling / Basigin interactions / Mechanical load activates signaling by PIEZO1 and integrins in osteocytes / negative regulation of vasoconstriction / leukocyte cell-cell adhesion / positive regulation of wound healing / cell adhesion mediated by integrin / muscle organ development / Syndecan interactions / response to muscle activity / positive regulation of neuroblast proliferation / maintenance of blood-brain barrier / negative regulation of Rho protein signal transduction / cell-substrate adhesion / homophilic cell adhesion via plasma membrane adhesion molecules / TGF-beta receptor signaling activates SMADs / establishment of mitotic spindle orientation / cleavage furrow / fibronectin binding / negative regulation of anoikis / cellular response to low-density lipoprotein particle stimulus / RHOG GTPase cycle / glial cell projection / intercalated disc / neuroblast proliferation / negative regulation of neuron differentiation / RAC2 GTPase cycle / ECM proteoglycans / RAC3 GTPase cycle / Integrin cell surface interactions / phagocytosis / cellular defense response / coreceptor activity / laminin binding / cell adhesion molecule binding / ruffle / RAC1 GTPase cycle / extracellular matrix organization / positive regulation of GTPase activity / B cell differentiation / protein tyrosine kinase binding
Similarity search - Function
Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / Integrin beta tail domain / Integrin EGF domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail ...Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / Integrin beta tail domain / Integrin EGF domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / EGF-like domain, extracellular / EGF-like domain / Integrins beta chain EGF (I-EGF) domain profile. / Integrin beta subunit, VWA domain / Integrin beta subunit / Integrin beta N-terminal / Integrin beta chain VWA domain / Integrin plexin domain / Integrins beta chain EGF (I-EGF) domain signature. / Integrin beta subunits (N-terminal portion of extracellular region) / Integrin domain superfamily / PSI domain / domain found in Plexins, Semaphorins and Integrins / von Willebrand factor A-like domain superfamily / EGF-like domain signature 1.
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsMuhle-Goll, C. / Moser, C.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)263531414/FOR 2290 Germany
CitationJournal: Acs Chem Neurosci / Year: 2024
Title: Substrate Selection Criteria in Regulated Intramembrane Proteolysis.
Authors: Moser, C. / Guschtschin-Schmidt, N. / Silber, M. / Flum, J. / Muhle-Goll, C.
History
DepositionJan 16, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release

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Structure visualization

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Assembly

Deposited unit
A: Integrin beta-1


Theoretical massNumber of molelcules
Total (without water)3,8771
Polymers3,8771
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Integrin beta-1 / Fibronectin receptor subunit beta / Glycoprotein IIa / GPIIA / VLA-4 subunit beta


Mass: 3876.872 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P05556

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
113isotropic12D 1H-1H NOESY
123isotropic12D 1H-13C HSQC
133isotropic12D 1H-15N HSQC

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Sample preparation

DetailsType: solution / Contents: 0.5 uM NA Itgb1, trifluoroethanol/water / Label: Itgb1 / Solvent system: trifluoroethanol/water
SampleConc.: 0.5 uM / Component: Itgb1 / Isotopic labeling: NA
Sample conditionsIonic strength: 0 Not defined / Ionic strength err: 0.2 / Label: Itgb1 / pH: 6.5 / PH err: 0.2 / Pressure: 1 atm / Temperature: 300 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz / Details: TXI cryoprobe

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Processing

NMR software
NameVersionDeveloperClassification
CcpNmr Analysis2.4.2CCPNchemical shift assignment
CcpNmr Analysis2.4.2CCPNpeak picking
ARIA2.3.2Linge, O'Donoghue and Nilgesstructure calculation
ARIALinge, O'Donoghue and Nilgesrefinement
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: 20

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