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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 / protein transport within lipid bilayer / response to gonadotropin / Laminin interactions / 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 / protein transport within lipid bilayer / response to gonadotropin / Laminin interactions / MET activates PTK2 signaling / TGF-beta receptor signaling activates SMADs / negative regulation of cell projection organization / Integrin cell surface interactions / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / Syndecan interactions / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / ECM proteoglycans / Basigin interactions / Cell surface interactions at the vascular wall / GPER1 signaling / RAC2 GTPase cycle / RHOG GTPase cycle / RAC1 GTPase cycle / 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 alpha1-beta1 complex / integrin binding involved in cell-matrix adhesion / integrin alpha4-beta1 complex / cell-cell adhesion mediated by integrin / hemidesmosome / establishment of Sertoli cell barrier / collagen binding involved in cell-matrix adhesion / integrin alpha2-beta1 complex / reactive gliosis / formation of radial glial scaffolds / Signal transduction by L1 / response to transforming growth factor beta / cerebellar climbing fiber to Purkinje cell synapse / myelin sheath abaxonal region / CD40 signaling pathway / calcium-independent cell-matrix adhesion / positive regulation of fibroblast growth factor receptor signaling pathway / regulation of synapse pruning / integrin alphav-beta1 complex / basement membrane organization / cardiac muscle cell myoblast differentiation / regulation of postsynaptic neurotransmitter receptor diffusion trapping / maintenance of postsynaptic specialization structure / bicellular tight junction assembly / tissue homeostasis / cardiac muscle cell differentiation / cellular response to vitamin D / germ cell migration / leukocyte tethering or rolling / regulation of G protein-coupled receptor signaling pathway / cell projection organization / positive regulation of vascular endothelial growth factor signaling pathway / myoblast fusion / mesodermal cell differentiation / glycinergic synapse / cell-substrate junction assembly / myoblast differentiation / axon extension / cell migration involved in sprouting angiogenesis / positive regulation of cell-substrate adhesion / regulation of spontaneous synaptic transmission / wound healing, spreading of epidermal cells / epidermal growth factor receptor binding / heterophilic cell-cell adhesion / positive regulation of fibroblast migration / integrin complex / lamellipodium assembly / heterotypic cell-cell adhesion / sarcomere organization / negative regulation of vasoconstriction / leukocyte cell-cell adhesion / muscle organ development / cell adhesion mediated by integrin / positive regulation of wound healing / dendrite morphogenesis / positive regulation of neuroblast proliferation / negative regulation of neuron differentiation / negative regulation of Rho protein signal transduction / response to muscle activity / positive regulation of sprouting angiogenesis / cell-substrate adhesion / endodermal cell differentiation / alpha-actinin binding / establishment of mitotic spindle orientation / 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 tail domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / : / Integrin alpha Ig-like domain 3 / Integrin EGF domain / Integrin beta subunit, tail ...Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta subunit, cytoplasmic domain / Integrin beta tail domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / : / Integrin alpha Ig-like domain 3 / 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 alpha-2 / Integrin alpha Ig-like domain 1 / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / Integrins alpha chain signature. / Integrin alpha chain / Integrin alpha beta-propellor / : / Integrin alpha Ig-like domain 2 / 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: Nat Commun / Year: 2025
Title: Spatial N-glycan rearrangement on αβ integrin nucleates galectin-3 oligomers to determine endocytic fate.
Authors: Massiullah Shafaq-Zadah / Estelle Dransart / Ilyes Hamitouche / Christian Wunder / Valérie Chambon / Cesar A Valades-Cruz / Ludovic Leconte / Nirod Kumar Sarangi / Jack Robinson / Siau-Kun ...Authors: Massiullah Shafaq-Zadah / Estelle Dransart / Ilyes Hamitouche / Christian Wunder / Valérie Chambon / Cesar A Valades-Cruz / Ludovic Leconte / Nirod Kumar Sarangi / Jack Robinson / Siau-Kun Bai / Raju Regmi / Aurélie Di Cicco / Agnès Hovasse / Richard Bartels / Ulf J Nilsson / Sarah Cianférani-Sanglier / Hakon Leffler / Tia E Keyes / Daniel Lévy / Stefan Raunser / Daniel Roderer / Ludger Johannes /
Abstract: Membrane glycoproteins frequently adopt different conformations when altering between active and inactive states. Here, we discover a molecular switch that exploits dynamic spatial rearrangements of ...Membrane glycoproteins frequently adopt different conformations when altering between active and inactive states. Here, we discover a molecular switch that exploits dynamic spatial rearrangements of N-glycans during such conformational transitions to control protein function. For the conformationally switchable cell adhesion glycoprotein αβ integrin, we find that only the bent-closed state arranges N-glycans to nucleate the formation of up to tetrameric oligomers of the glycan-binding protein galectin-3. We propose a structural model of how these galectin-3 oligomers are built and how they clamp the bent-closed state to select it for endocytic uptake and subsequent retrograde trafficking to the Golgi for polarized distribution in cells. Our findings reveal the dynamic regulation of the glycan landscape at the cell surface to achieve oligomerization of galectin-3. Galectin-3 oligomers are thereby identified as functional decoders of defined spatial patterns of N-glycans on specifically the bent-closed conformational state of αβ integrin and possibly other integrin family members.
History
DepositionMay 3, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2024Group: Data collection / Category: em_admin / Item: _em_admin.last_update
Revision 1.2Nov 26, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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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