[English] 日本語
Yorodumi
- PDB-8tee: Crystal structure of Kindlin2 in complex with K794Q mutated beta1... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8tee
TitleCrystal structure of Kindlin2 in complex with K794Q mutated beta1 integrin
Components
  • Fermitin family homolog 2
  • Integrin beta-1
KeywordsCELL ADHESION / kindlin / integrin / acylation
Function / homology
Function and homology information


Localization of the PINCH-ILK-PARVIN complex to focal adhesions / Laminin interactions / MET interacts with TNS proteins / Elastic fibre formation / Cell-extracellular matrix interactions / Fibronectin matrix formation / Syndecan interactions / C-X3-C chemokine binding / Signal transduction by L1 / Molecules associated with elastic fibres ...Localization of the PINCH-ILK-PARVIN complex to focal adhesions / Laminin interactions / MET interacts with TNS proteins / Elastic fibre formation / Cell-extracellular matrix interactions / Fibronectin matrix formation / Syndecan interactions / C-X3-C chemokine binding / Signal transduction by L1 / Molecules associated with elastic fibres / MET activates PTK2 signaling / Basigin interactions / RAC3 GTPase cycle / TGF-beta receptor signaling activates SMADs / ECM proteoglycans / RAC2 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 / adherens junction maintenance / 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 / collagen binding involved in cell-matrix adhesion / integrin alpha2-beta1 complex / reactive gliosis / RAC1 GTPase cycle / protein localization to cell junction / formation of radial glial scaffolds / cerebellar climbing fiber to Purkinje cell synapse / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / myelin sheath abaxonal region / positive regulation of wound healing, spreading of epidermal cells / Integrin cell surface interactions / positive regulation of mesenchymal stem cell proliferation / Cell surface interactions at the vascular wall / CD40 signaling pathway / calcium-independent cell-matrix adhesion / positive regulation of fibroblast growth factor receptor signaling pathway / GPER1 signaling / RHOG GTPase cycle / regulation of synapse pruning / integrin alphav-beta1 complex / basement membrane organization / cardiac muscle cell myoblast differentiation / positive regulation of integrin activation / fibroblast migration / cardiac muscle cell differentiation / type I transforming growth factor beta receptor binding / integrin activation / germ cell migration / leukocyte tethering or rolling / focal adhesion assembly / myoblast fusion / positive regulation of vascular endothelial growth factor signaling pathway / negative regulation of vascular permeability / mesodermal cell differentiation / myoblast differentiation / axon extension / cell migration involved in sprouting angiogenesis / protein localization to membrane / I band / limb development / cardiac muscle tissue development / central nervous system neuron differentiation / regulation of spontaneous synaptic transmission / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of fibroblast migration / sarcomere organization / heterotypic cell-cell adhesion / negative regulation of vasoconstriction / leukocyte cell-cell adhesion / muscle organ development / cell adhesion mediated by integrin / positive regulation of wound healing / dendrite morphogenesis / negative regulation of neuron differentiation / positive regulation of neuroblast proliferation / negative regulation of Rho protein signal transduction / negative regulation of fat cell differentiation / positive regulation of Rho protein signal transduction / response to muscle activity / SMAD binding / phosphatidylinositol-3,4,5-trisphosphate binding / establishment of mitotic spindle orientation / fibronectin binding / lamellipodium membrane / negative regulation of anoikis / intercalated disc / cellular response to low-density lipoprotein particle stimulus / neuroblast proliferation
Similarity search - Function
Kindlin/fermitin, PH domain / Kindlin/fermitin / Kindlin-2, N-terminal / Kindlin-2 N-terminal domain / Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta tail domain / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt ...Kindlin/fermitin, PH domain / Kindlin/fermitin / Kindlin-2, N-terminal / Kindlin-2 N-terminal domain / Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta tail domain / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / 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 / FERM central domain / PSI domain / domain found in Plexins, Semaphorins and Integrins / FERM central domain / FERM superfamily, second domain / Band 4.1 domain / Band 4.1 homologues / PH domain / PH domain profile. / von Willebrand factor A-like domain superfamily / Pleckstrin homology domain. / Pleckstrin homology domain / EGF-like domain signature 1. / PH-like domain superfamily
Similarity search - Domain/homology
Integrin beta-1 / Fermitin family homolog 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsZhang, P.F. / Wu, J.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Iscience / Year: 2024
Title: Acetyl-NPKY of integrin-beta 1 binds KINDLIN2 to control endothelial cell proliferation and junctional integrity.
Authors: Sidibe, A. / Mykuliak, V.V. / Zhang, P. / Hytonen, V.P. / Wu, J. / Wehrle-Haller, B.
History
DepositionJul 6, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fermitin family homolog 2
B: Fermitin family homolog 2
C: Integrin beta-1
D: Integrin beta-1


Theoretical massNumber of molelcules
Total (without water)119,4354
Polymers119,4354
Non-polymers00
Water1,76598
1
A: Fermitin family homolog 2
C: Integrin beta-1

B: Fermitin family homolog 2
D: Integrin beta-1


Theoretical massNumber of molelcules
Total (without water)119,4354
Polymers119,4354
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area6680 Å2
ΔGint-56 kcal/mol
Surface area40660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.971, 98.291, 76.003
Angle α, β, γ (deg.)90.00, 96.42, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Fermitin family homolog 2 / Kindlin-2 / Pleckstrin homology domain-containing family C member 1


Mass: 58094.777 Da / Num. of mol.: 2 / Fragment: UNP residues 1-336,513-680
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Fermt2, Plekhc1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8CIB5
#2: Protein/peptide Integrin beta-1 / Fibronectin receptor subunit beta / VLA-4 subunit beta


Mass: 1622.816 Da / Num. of mol.: 2 / Mutation: K794Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Itgb1 / Production host: Escherichia coli (E. coli) / References: UniProt: P09055
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Tris, pH 8.5, 10% isopropanal

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.91975 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 12, 2020
RadiationMonochromator: double crystal Si(111) monochromator with horizontal axis
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91975 Å / Relative weight: 1
ReflectionResolution: 2.49→29.94 Å / Num. obs: 36657 / % possible obs: 97.4 % / Redundancy: 6.8 % / CC1/2: 0.99 / Rmerge(I) obs: 0.124 / Net I/σ(I): 8.6
Reflection shellResolution: 2.49→2.55 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.623 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2159 / CC1/2: 0.875 / % possible all: 77.5

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5XPY

5xpy


Resolution: 2.49→29.94 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 32.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2747 1853 5.07 %
Rwork0.2274 --
obs0.2298 36564 98.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.49→29.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6729 0 0 98 6827
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036881
X-RAY DIFFRACTIONf_angle_d0.5699370
X-RAY DIFFRACTIONf_dihedral_angle_d15.279921
X-RAY DIFFRACTIONf_chiral_restr0.041078
X-RAY DIFFRACTIONf_plane_restr0.0041184
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.49-2.560.40221200.3482438X-RAY DIFFRACTION90
2.56-2.640.43451370.32852685X-RAY DIFFRACTION98
2.64-2.720.37851360.3122683X-RAY DIFFRACTION99
2.72-2.820.28271430.29532645X-RAY DIFFRACTION98
2.82-2.930.29131550.27242671X-RAY DIFFRACTION99
2.93-3.070.34021420.26932656X-RAY DIFFRACTION99
3.07-3.230.32371310.26512696X-RAY DIFFRACTION99
3.23-3.430.27331510.23932679X-RAY DIFFRACTION99
3.43-3.690.29771410.21972693X-RAY DIFFRACTION99
3.69-4.060.26421430.21722694X-RAY DIFFRACTION99
4.06-4.650.21571570.18942693X-RAY DIFFRACTION99
4.65-5.850.2661470.20852727X-RAY DIFFRACTION99
5.85-29.940.24211500.18912751X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 5.5949 Å / Origin y: -14.766 Å / Origin z: 25.6037 Å
111213212223313233
T0.4806 Å20.0195 Å20.0172 Å2-0.6192 Å2-0.0006 Å2--0.4523 Å2
L0.7888 °2-0.0688 °20.4691 °2-0.0522 °20.004 °2--0.0588 °2
S-0.0201 Å °-0.0509 Å °-0.051 Å °-0.0294 Å °0.0507 Å °-0.0051 Å °-0.0134 Å °-0.0226 Å °-0.0334 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