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- PDB-8oxz: Rat alpha5beta1 integrin, headpiece -

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Basic information

Entry
Database: PDB / ID: 8oxz
TitleRat alpha5beta1 integrin, headpiece
Components
  • Integrin beta-1
  • Integrin subunit alpha 5
KeywordsCELL ADHESION / integrin / glycoprotein / membrane protein
Function / homology
Function and homology information


synaptic membrane adhesion to extracellular matrix / Elastic fibre formation / Fibronectin matrix formation / Molecules associated with elastic fibres / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / MET interacts with TNS proteins / response to gonadotropin / Laminin interactions / TGF-beta receptor signaling activates SMADs / MET activates PTK2 signaling ...synaptic membrane adhesion to extracellular matrix / Elastic fibre formation / Fibronectin matrix formation / Molecules associated with elastic fibres / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / MET interacts with TNS proteins / response to gonadotropin / Laminin interactions / TGF-beta receptor signaling activates SMADs / MET activates PTK2 signaling / protein transport within lipid bilayer / Integrin cell surface interactions / Syndecan interactions / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / ECM proteoglycans / negative regulation of cell projection organization / Basigin interactions / Cell surface interactions at the vascular wall / GPER1 signaling / RAC2 GTPase cycle / integrin alpha6-beta1 complex / RHOG GTPase cycle / integrin alpha3-beta1 complex / integrin alpha5-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 / regulation of collagen catabolic process / integrin alpha9-beta1 complex / cardiac cell fate specification / integrin alpha4-beta1 complex / integrin binding involved in cell-matrix adhesion / cell-cell adhesion mediated by integrin / integrin alpha1-beta1 complex / RAC1 GTPase cycle / establishment of Sertoli cell barrier / collagen binding involved in cell-matrix adhesion / integrin alpha2-beta1 complex / hemidesmosome / regulation of synapse pruning / reactive gliosis / formation of radial glial scaffolds / cerebellar climbing fiber to Purkinje cell synapse / Signal transduction by L1 / response to transforming growth factor beta / positive regulation of vascular endothelial growth factor signaling pathway / calcium-independent cell-matrix adhesion / integrin alphav-beta1 complex / positive regulation of fibroblast growth factor receptor signaling pathway / CD40 signaling pathway / basement membrane organization / myelin sheath abaxonal region / regulation of postsynaptic neurotransmitter receptor diffusion trapping / cardiac muscle cell myoblast differentiation / bicellular tight junction assembly / cellular response to vitamin D / maintenance of postsynaptic specialization structure / germ cell migration / tissue homeostasis / leukocyte tethering or rolling / cardiac muscle cell differentiation / cell projection organization / regulation of G protein-coupled receptor signaling pathway / glycinergic synapse / myoblast fusion / mesodermal cell differentiation / cell-substrate junction assembly / axon extension / cell migration involved in sprouting angiogenesis / positive regulation of fibroblast migration / wound healing, spreading of epidermal cells / myoblast differentiation / positive regulation of cell-substrate adhesion / regulation of spontaneous synaptic transmission / response to muscle activity / integrin complex / heterotypic cell-cell adhesion / dendrite morphogenesis / lamellipodium assembly / negative regulation of Rho protein signal transduction / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / cell adhesion mediated by integrin / negative regulation of vasoconstriction / epidermal growth factor receptor binding / sarcomere organization / leukocyte cell-cell adhesion / positive regulation of wound healing / muscle organ development / positive regulation of neuroblast proliferation / cell-substrate adhesion / positive regulation of sprouting angiogenesis / endodermal cell differentiation / alpha-actinin binding / establishment of mitotic spindle orientation / positive regulation of endocytosis / glial cell projection / fibronectin binding / negative regulation of anoikis
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 alpha Ig-like domain 3 / Integrin beta tail domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily ...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 alpha Ig-like domain 3 / Integrin beta tail domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / Integrin beta subunit, VWA domain / Integrin beta subunit / Integrin beta N-terminal / Integrin beta chain VWA domain / Integrin plexin domain / Integrins beta chain cysteine-rich domain signature. / Integrin beta subunits (N-terminal portion of extracellular region) / EGF-like domain, extracellular / EGF-like domain / 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 / 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
Integrin subunit alpha 5 / Integrin beta-1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsRoderer, D. / Dransart, E. / Shafaq-Zadah, M. / Bartels, R. / Johannes, L.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR) France
CitationJournal: To Be Published
Title: Dynamic N-glycan rearrangement nucleates galectin-3 oligomers to determine endocytic fate
Authors: Shafaq-Zadah, M. / Dransart, E. / Wunder, C. / Chambon, V. / Valades-Cruz, C.A. / Leconte, L. / Sarangi, N.K. / Robinson, J. / Bai, S.-K. / Regmi, R. / Di Cicco, A. / Hovasse, A. / Bartels, ...Authors: Shafaq-Zadah, M. / Dransart, E. / Wunder, C. / Chambon, V. / Valades-Cruz, C.A. / Leconte, L. / Sarangi, N.K. / Robinson, J. / Bai, S.-K. / Regmi, R. / Di Cicco, A. / Hovasse, A. / Bartels, R. / Nilsson, U.J. / Cianferani-Sanglier, S. / Leffler, H. / Keyes, T.E. / Levy, D. / Raunser, S. / Roderer, D. / Johannes, L.
History
DepositionMay 3, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
P: Integrin subunit alpha 5
Q: Integrin beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)209,93210
Polymers208,1622
Non-polymers1,7708
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area5590 Å2
ΔGint-4 kcal/mol
Surface area49170 Å2

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Components

#1: Protein Integrin subunit alpha 5


Mass: 119567.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: headpiece, residues 94 - 691 / Source: (natural) Rattus norvegicus (Norway rat) / Organ: Liver / Tissue: Liver / References: UniProt: A0A0G2K1E2
#2: Protein Integrin beta-1 / Beta oligodendroglia / Beta OL / Fibronectin receptor subunit beta / VLA-4 subunit beta


Mass: 88594.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / Organ: Liver / Tissue: Liver / References: UniProt: P49134
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Alpha5beta1 integrin from Rattus norvegicus / Type: COMPLEX / Details: Purified from rat liver and desialated / Entity ID: #1-#2 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Rattus norvegicus (Norway rat) / Organ: Liver
Buffer solutionpH: 7.5
SpecimenConc.: 0.25 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Vitrified immeadiately after elution from NiNTA beads
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Details: Preliminary grid screening was performed manually.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 96000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 42 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1

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Processing

SoftwareName: PHENIX / Version: dev_4778: / Classification: refinement
EM software
IDNameVersionCategory
2EPUimage acquisition
4cryoSPARC3.3CTF correction
7UCSF Chimeramodel fitting
8Cootmodel fitting
10cryoSPARC3.3initial Euler assignment
11cryoSPARC4.03final Euler assignment
13cryoSPARC4.033D reconstruction
14PHENIXdev 4778model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1444502
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 101740 / Symmetry type: POINT
Atomic model buildingB value: 144 / Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: Cross-correlation
Atomic model buildingDetails: Homology model generated from PDB 7NXD / Source name: Modeller / Type: in silico model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0048503
ELECTRON MICROSCOPYf_angle_d0.74211531
ELECTRON MICROSCOPYf_dihedral_angle_d8.3071211
ELECTRON MICROSCOPYf_chiral_restr0.0511276
ELECTRON MICROSCOPYf_plane_restr0.0051523

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