[English] 日本語
Yorodumi
- PDB-8oxz: Rat alpha5beta1 integrin, headpiece -

+
Open data


ID or keywords:

Loading...

-
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 / 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 / RAC1 GTPase cycle / 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 / hemidesmosome / establishment of Sertoli cell barrier / collagen binding involved in cell-matrix adhesion / integrin alpha2-beta1 complex / reactive gliosis / formation of radial glial scaffolds / cerebellar climbing fiber to Purkinje cell synapse / response to transforming growth factor beta / Signal transduction by L1 / positive regulation of vascular endothelial growth factor signaling pathway / calcium-independent cell-matrix adhesion / positive regulation of fibroblast growth factor receptor signaling pathway / CD40 signaling pathway / basement membrane organization / regulation of synapse pruning / integrin alphav-beta1 complex / myelin sheath abaxonal region / regulation of postsynaptic neurotransmitter receptor diffusion trapping / cardiac muscle cell myoblast differentiation / maintenance of postsynaptic specialization structure / bicellular tight junction assembly / cellular response to vitamin D / leukocyte tethering or rolling / tissue homeostasis / cardiac muscle cell differentiation / germ cell migration / cell projection organization / glycinergic synapse / regulation of G protein-coupled receptor signaling pathway / myoblast fusion / mesodermal cell differentiation / cell-substrate junction assembly / axon extension / cell migration involved in sprouting angiogenesis / myoblast differentiation / positive regulation of fibroblast migration / positive regulation of cell-substrate adhesion / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / regulation of spontaneous synaptic transmission / wound healing, spreading of epidermal cells / integrin complex / heterotypic cell-cell adhesion / epidermal growth factor receptor binding / lamellipodium assembly / dendrite morphogenesis / negative regulation of vasoconstriction / cell adhesion mediated by integrin / leukocyte cell-cell adhesion / sarcomere organization / positive regulation of wound healing / muscle organ development / response to muscle activity / positive regulation of neuroblast proliferation / positive regulation of sprouting angiogenesis / negative regulation of Rho protein signal transduction / cell-substrate adhesion / endodermal cell differentiation / alpha-actinin binding / establishment of mitotic spindle orientation / positive regulation of endocytosis / fibronectin binding / basement membrane
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 alpha Ig-like domain 3 / 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 beta tail domain / : / Integrin alpha Ig-like domain 3 / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / 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) / 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
Revision 1.1Nov 27, 2024Group: Data collection / Category: em_admin / Item: _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more