[English] 日本語
Yorodumi
- PDB-8tec: Crystal structure of Kindlin2 in complex with acylated beta1 inte... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8tec
TitleCrystal structure of Kindlin2 in complex with acylated beta1 integrin peptide
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 / protein transport within lipid bilayer / Elastic fibre formation / Cell-extracellular matrix interactions / Syndecan interactions / C-X3-C chemokine binding / Molecules associated with elastic fibres / Fibronectin matrix formation ...Localization of the PINCH-ILK-PARVIN complex to focal adhesions / Laminin interactions / MET interacts with TNS proteins / protein transport within lipid bilayer / Elastic fibre formation / Cell-extracellular matrix interactions / Syndecan interactions / C-X3-C chemokine binding / Molecules associated with elastic fibres / Fibronectin matrix formation / negative regulation of cell projection organization / Signal transduction by L1 / MET activates PTK2 signaling / Basigin interactions / RAC3 GTPase cycle / ECM proteoglycans / TGF-beta receptor signaling activates SMADs / RAC2 GTPase cycle / integrin alpha3-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 / adherens junction maintenance / integrin alpha5-beta1 complex / integrin alpha9-beta1 complex / regulation of collagen catabolic process / integrin alpha1-beta1 complex / integrin binding involved in cell-matrix adhesion / integrin alpha4-beta1 complex / hemidesmosome / cell adhesion receptor activity / collagen binding involved in cell-matrix adhesion / integrin alpha2-beta1 complex / RAC1 GTPase cycle / protein localization to cell junction / cell-cell adhesion mediated by integrin / formation of radial glial scaffolds / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / cerebellar climbing fiber to Purkinje cell synapse / Integrin cell surface interactions / Cell surface interactions at the vascular wall / positive regulation of mesenchymal stem cell proliferation / positive regulation of wound healing, spreading of epidermal cells / CD40 signaling pathway / calcium-independent cell-matrix adhesion / RHOG GTPase cycle / positive regulation of fibroblast growth factor receptor signaling pathway / GPER1 signaling / reactive gliosis / myelin sheath abaxonal region / integrin alphav-beta1 complex / basement membrane organization / regulation of synapse pruning / positive regulation of integrin activation / regulation of postsynaptic neurotransmitter receptor diffusion trapping / maintenance of postsynaptic specialization structure / bicellular tight junction assembly / tissue homeostasis / primordial germ cell migration / integrin activation / leukocyte tethering or rolling / type I transforming growth factor beta receptor binding / focal adhesion assembly / myoblast fusion / regulation of G protein-coupled receptor signaling pathway / positive regulation of cell-substrate adhesion / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of vascular endothelial growth factor signaling pathway / cell migration involved in sprouting angiogenesis / axon extension / cardiac muscle cell differentiation / myoblast differentiation / regulation of cell morphogenesis / mesodermal cell differentiation / glycinergic synapse / cell fate specification / cell projection organization / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of vascular permeability / positive regulation of fibroblast migration / negative regulation of Rho protein signal transduction / cardiac muscle tissue development / protein localization to membrane / integrin complex / regulation of spontaneous synaptic transmission / cell adhesion mediated by integrin / heterotypic cell-cell adhesion / lamellipodium assembly / I band / negative regulation of vasoconstriction / sarcomere organization / muscle organ development / leukocyte cell-cell adhesion / dendrite morphogenesis / negative regulation of neuron differentiation / positive regulation of wound healing / response to muscle activity / limb development
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 subunit, cytoplasmic domain / Integrin beta tail 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 subunit, cytoplasmic domain / Integrin beta tail domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / : / Integrin EGF domain / EGF-like domain, extracellular / EGF-like domain / 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) / FERM central domain / Integrin domain superfamily / 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 profile. / Pleckstrin homology domain. / Pleckstrin homology domain / EGF-like domain signature 1. / von Willebrand factor A-like domain superfamily / 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: 2.04 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
Revision 1.1Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
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


Theoretical massNumber of molelcules
Total (without water)124,2173
Polymers124,2173
Non-polymers00
Water4,396244
1
A: Fermitin family homolog 2
C: Integrin beta-1

B: Fermitin family homolog 2


Theoretical massNumber of molelcules
Total (without water)124,2173
Polymers124,2173
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area5470 Å2
ΔGint-45 kcal/mol
Surface area40970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.487, 102.093, 76.029
Angle α, β, γ (deg.)90.00, 96.81, 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: 61276.211 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: 1664.896 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: P09055
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M Tris, pH 8.5, 10% isopropanal

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 7, 2020
RadiationMonochromator: Cryogenically-cooled single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.04→102.09 Å / Num. obs: 69860 / % possible obs: 98.8 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.028 / Rrim(I) all: 0.075 / Net I/σ(I): 12.8
Reflection shellResolution: 2.04→2.09 Å / Redundancy: 6.1 % / Rmerge(I) obs: 1.728 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 3942 / CC1/2: 0.394 / % possible all: 87.4

-
Processing

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

5xpy


Resolution: 2.04→75.49 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2302 3350 4.83 %
Rwork0.1938 --
obs0.1955 69366 98.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.04→75.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6797 0 0 244 7041
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076972
X-RAY DIFFRACTIONf_angle_d0.8129484
X-RAY DIFFRACTIONf_dihedral_angle_d21.5462445
X-RAY DIFFRACTIONf_chiral_restr0.0491089
X-RAY DIFFRACTIONf_plane_restr0.0071191
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.04-2.070.46691200.45082167X-RAY DIFFRACTION79
2.07-2.10.46081340.40552766X-RAY DIFFRACTION98
2.1-2.140.37311350.40062671X-RAY DIFFRACTION97
2.14-2.170.40191360.36162726X-RAY DIFFRACTION97
2.17-2.210.43371340.33722765X-RAY DIFFRACTION100
2.21-2.250.40431380.36972785X-RAY DIFFRACTION99
2.25-2.290.36541490.34912759X-RAY DIFFRACTION99
2.29-2.340.3731380.31872747X-RAY DIFFRACTION100
2.34-2.390.32951440.29482771X-RAY DIFFRACTION100
2.39-2.450.35111610.26862789X-RAY DIFFRACTION100
2.45-2.510.33781550.23932739X-RAY DIFFRACTION100
2.51-2.580.27851450.22092752X-RAY DIFFRACTION100
2.58-2.650.23891210.20832815X-RAY DIFFRACTION100
2.65-2.740.24771470.20462800X-RAY DIFFRACTION100
2.74-2.830.2231540.20172780X-RAY DIFFRACTION100
2.83-2.950.26231250.20372793X-RAY DIFFRACTION100
2.95-3.080.26161200.20292760X-RAY DIFFRACTION98
3.08-3.240.20941540.19462774X-RAY DIFFRACTION99
3.24-3.450.22721720.18222764X-RAY DIFFRACTION100
3.45-3.710.22641320.17262804X-RAY DIFFRACTION100
3.71-4.090.19531280.16032814X-RAY DIFFRACTION99
4.09-4.680.17151370.1452802X-RAY DIFFRACTION100
4.68-5.890.21911260.18092814X-RAY DIFFRACTION99
5.9-75.490.18031450.16422859X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -8.3364 Å / Origin y: -5.0603 Å / Origin z: 13.5829 Å
111213212223313233
T0.4846 Å2-0.0161 Å20.0217 Å2-0.5313 Å2-0.0214 Å2--0.4639 Å2
L0.6976 °2-0.0624 °20.4545 °2-0.1632 °20.0317 °2--0.018 °2
S0.0028 Å °0.0728 Å °-0.1163 Å °-0.0262 Å °0.0364 Å °-0.0075 Å °0.05 Å °0.0202 Å °-0.0403 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