[English] 日本語
Yorodumi
- PDB-6vgu: Crystal structure of FERM-folded talin head domain bound to the N... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6vgu
TitleCrystal structure of FERM-folded talin head domain bound to the NPLY motif of beta3-integrin
ComponentsIntegrin beta-3,Talin-1
KeywordsSIGNALING PROTEIN / talin / FERM-fold / NPLY motif / integrin
Function / homology
Function and homology information


Elastic fibre formation / Syndecan interactions / C-X3-C chemokine binding / Signal transduction by L1 / Molecules associated with elastic fibres / PECAM1 interactions / TGF-beta receptor signaling activates SMADs / cell projection morphogenesis / neuregulin binding / ECM proteoglycans ...Elastic fibre formation / Syndecan interactions / C-X3-C chemokine binding / Signal transduction by L1 / Molecules associated with elastic fibres / PECAM1 interactions / TGF-beta receptor signaling activates SMADs / cell projection morphogenesis / neuregulin binding / ECM proteoglycans / integrin alpha9-beta1 complex / GRB2:SOS provides linkage to MAPK signaling for Integrins / Integrin signaling / p130Cas linkage to MAPK signaling for integrins / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / MAP2K and MAPK activation / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / Integrin cell surface interactions / LIM domain binding / regulation of serotonin uptake / positive regulation of adenylate cyclase-inhibiting opioid receptor signaling pathway / Smooth Muscle Contraction / alpha9-beta1 integrin-ADAM8 complex / regulation of trophoblast cell migration / integrin alphaIIb-beta3 complex / regulation of postsynaptic neurotransmitter receptor diffusion trapping / Platelet degranulation / maintenance of postsynaptic specialization structure / cortical microtubule organization / regulation of extracellular matrix organization / positive regulation of glomerular mesangial cell proliferation / vinculin binding / integrin alphav-beta3 complex / negative regulation of lipoprotein metabolic process / alphav-beta3 integrin-PKCalpha complex / integrin activation / fibrinogen binding / alphav-beta3 integrin-HMGB1 complex / blood coagulation, fibrin clot formation / vascular endothelial growth factor receptor 2 binding / insulin-like growth factor I binding / negative regulation of lipid transport / VEGFA-VEGFR2 Pathway / positive regulation of vascular endothelial growth factor signaling pathway / glycinergic synapse / regulation of release of sequestered calcium ion into cytosol / positive regulation of osteoclast differentiation / mesodermal cell differentiation / cell-substrate junction assembly / alphav-beta3 integrin-IGF-1-IGF1R complex / filopodium membrane / extracellular matrix binding / apolipoprotein A-I-mediated signaling pathway / positive regulation of cell adhesion mediated by integrin / apoptotic cell clearance / cortical actin cytoskeleton organization / heterotypic cell-cell adhesion / positive regulation of fibroblast migration / positive regulation of smooth muscle cell migration / smooth muscle cell migration / positive regulation of cell-matrix adhesion / negative chemotaxis / cellular response to insulin-like growth factor stimulus / cell adhesion mediated by integrin / positive regulation of osteoblast proliferation / phosphatidylserine binding / microvillus membrane / regulation of postsynaptic neurotransmitter receptor internalization / protein disulfide isomerase activity / platelet-derived growth factor receptor signaling pathway / fibroblast growth factor binding / lamellipodium membrane / positive regulation of bone resorption / fibronectin binding / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / positive regulation of T cell migration / negative regulation of endothelial cell apoptotic process / cellular response to platelet-derived growth factor stimulus / ruffle / positive regulation of endothelial cell proliferation / positive regulation of substrate adhesion-dependent cell spreading / embryo implantation / positive regulation of endothelial cell migration / phosphatidylinositol binding / substrate adhesion-dependent cell spreading / protein kinase C binding / cell-matrix adhesion / response to activity / integrin-mediated signaling pathway / positive regulation of smooth muscle cell proliferation / adherens junction / regulation of actin cytoskeleton organization / synaptic membrane / structural constituent of cytoskeleton / platelet aggregation / ruffle membrane / cellular response to mechanical stimulus / positive regulation of fibroblast proliferation / positive regulation of angiogenesis
Similarity search - Function
Talin VBS2 domain / Vinculin-binding site-containing domain / Talin, central / Talin, central domain superfamily / Talin-1/2, rod-segment / : / : / Vinculin Binding Site / Talin, middle domain / Talin, R4 domain ...Talin VBS2 domain / Vinculin-binding site-containing domain / Talin, central / Talin, central domain superfamily / Talin-1/2, rod-segment / : / : / Vinculin Binding Site / Talin, middle domain / Talin, R4 domain / Talin 1-like, rod segment domain / Talin, N-terminal F0 domain / : / N-terminal or F0 domain of Talin-head FERM / Talin IBS2B domain / I/LWEQ domain / I/LWEQ domain superfamily / I/LWEQ domain / I/LWEQ domain profile. / I/LWEQ domain / Phosphotyrosine-binding domain / IRS-type PTB domain / PTB domain (IRS-1 type) / Alpha-catenin/vinculin-like superfamily / FERM domain signature 1. / FERM conserved site / 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) / FERM domain signature 2. / Integrin domain superfamily / FERM central domain / FERM/acyl-CoA-binding protein superfamily / PSI domain / domain found in Plexins, Semaphorins and Integrins / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / von Willebrand factor A-like domain superfamily / EGF-like domain signature 1. / EGF-like domain signature 2. / PH-like domain superfamily / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Integrin beta-3 / Talin-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.78 Å
AuthorsZhang, P. / Sun, Y. / Wu, J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM119560 United States
American Cancer SocietyRSG-15-167-01-DMC United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Crystal structure of the FERM-folded talin head reveals the determinants for integrin binding.
Authors: Zhang, P. / Azizi, L. / Kukkurainen, S. / Gao, T. / Baikoghli, M. / Jacquier, M.C. / Sun, Y. / Maatta, J.A.E. / Cheng, R.H. / Wehrle-Haller, B. / Hytonen, V.P. / Wu, J.
History
DepositionJan 9, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2020Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 27, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 11, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Integrin beta-3,Talin-1


Theoretical massNumber of molelcules
Total (without water)50,3831
Polymers50,3831
Non-polymers00
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.071, 66.825, 114.466
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Integrin beta-3,Talin-1 / Platelet membrane glycoprotein IIIa / GPIIIa


Mass: 50382.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Itgb3, Tln1, Tln / Plasmid: pET28a
Details (production host): modified to include a TEV cleavage site
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O54890, UniProt: P26039
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 50.77 % / Description: rod, 20um*10um*300um
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M sodium chloride 0.1 M MES pH6.5 10 % w/v PEG 4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 13, 2019
RadiationMonochromator: double crystal Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 2.779→29.62 Å / Num. obs: 12141 / % possible obs: 92.4 % / Redundancy: 2.4 % / Biso Wilson estimate: 63.85 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 12.1
Reflection shellResolution: 2.78→2.85 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.655 / Mean I/σ(I) obs: 1.9 / % possible all: 92.5

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IVF

3ivf


Resolution: 2.78→29.62 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.51
RfactorNum. reflection% reflection
Rfree0.263 611 5.04 %
Rwork0.215 --
obs0.217 12117 91.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 69.71 Å2
Refinement stepCycle: LAST / Resolution: 2.78→29.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3050 0 0 34 3084
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.779-3.05840.35741410.27762878X-RAY DIFFRACTION93
3.0584-3.50030.30261530.24322868X-RAY DIFFRACTION92
3.5003-4.40770.24771720.19552874X-RAY DIFFRACTION92
4.4077-29.620.2421450.20292886X-RAY DIFFRACTION88
Refinement TLS params.Method: refined / Origin x: -25.8421 Å / Origin y: -2.3246 Å / Origin z: 11.0096 Å
111213212223313233
T0.3529 Å2-0.0162 Å2-0.0782 Å2-0.3081 Å2-0.0346 Å2--0.4349 Å2
L2.5198 °20.4972 °2-0.7689 °2-1.0064 °2-0.5155 °2--0.876 °2
S-0.0703 Å °-0.2085 Å °-0.0998 Å °0.0386 Å °0.047 Å °-0.053 Å °0.0428 Å °-0.026 Å °0.0391 Å °
Refinement TLS groupSelection details: ALL

+
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