[English] 日本語
Yorodumi
- PDB-5xq0: Structural basis of kindlin-mediated integrin recognition and act... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5xq0
TitleStructural basis of kindlin-mediated integrin recognition and activation
ComponentsFermitin family homolog 2,Integrin beta-1
KeywordsSIGNALING PROTEIN / Integrin Binding / Multi-domain containing protein
Function / homology
Function and homology information


protein transport within lipid bilayer / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / Elastic fibre formation / MET interacts with TNS proteins / Syndecan interactions / Cell-extracellular matrix interactions / Laminin interactions / Fibronectin matrix formation / Molecules associated with elastic fibres / Signal transduction by L1 ...protein transport within lipid bilayer / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / Elastic fibre formation / MET interacts with TNS proteins / Syndecan interactions / Cell-extracellular matrix interactions / Laminin interactions / Fibronectin matrix formation / Molecules associated with elastic fibres / Signal transduction by L1 / negative regulation of cell projection organization / TGF-beta receptor signaling activates SMADs / MET activates PTK2 signaling / RAC3 GTPase cycle / integrin alpha3-beta1 complex / integrin alpha5-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 / regulation of inward rectifier potassium channel activity / Basigin interactions / regulation of collagen catabolic process / integrin alpha9-beta1 complex / RAC2 GTPase cycle / cell-cell adhesion mediated by integrin / C-X3-C chemokine binding / cardiac cell fate specification / integrin binding involved in cell-matrix adhesion / ECM proteoglycans / integrin alpha1-beta1 complex / adherens junction maintenance / collagen binding involved in cell-matrix adhesion / integrin alpha2-beta1 complex / regulation of synapse pruning / hemidesmosome / reactive gliosis / RAC1 GTPase cycle / formation of radial glial scaffolds / cerebellar climbing fiber to Purkinje cell synapse / RHOG GTPase cycle / protein localization to cell junction / CD40 signaling pathway / positive regulation of wound healing, spreading of epidermal cells / positive regulation of mesenchymal stem cell proliferation / positive regulation of vascular endothelial growth factor signaling pathway / calcium-independent cell-matrix adhesion / integrin alphav-beta1 complex / positive regulation of fibroblast growth factor receptor signaling pathway / Integrin cell surface interactions / basement membrane organization / Cell surface interactions at the vascular wall / GPER1 signaling / myelin sheath abaxonal region / regulation of postsynaptic neurotransmitter receptor diffusion trapping / cardiac muscle cell myoblast differentiation / positive regulation of integrin activation / bicellular tight junction assembly / tissue homeostasis / germ cell migration / maintenance of postsynaptic specialization structure / leukocyte tethering or rolling / type I transforming growth factor beta receptor binding / cardiac muscle cell differentiation / cell projection organization / integrin activation / regulation of G protein-coupled receptor signaling pathway / glycinergic synapse / myoblast fusion / protein localization to membrane / mesodermal cell differentiation / focal adhesion assembly / negative regulation of vascular permeability / axon extension / positive regulation of fibroblast migration / cell migration involved in sprouting angiogenesis / I band / regulation of spontaneous synaptic transmission / heterotypic cell-cell adhesion / myoblast differentiation / integrin complex / positive regulation of cell-substrate adhesion / dendrite morphogenesis / limb development / muscle organ development / negative regulation of Rho protein signal transduction / lamellipodium assembly / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / cell adhesion mediated by integrin / negative regulation of vasoconstriction / positive regulation of wound healing / sarcomere organization / positive regulation of neuroblast proliferation / negative regulation of fat cell differentiation / SMAD binding / alpha-actinin binding / positive regulation of endocytosis / establishment of mitotic spindle orientation / positive regulation of focal adhesion assembly
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 cytoplasmic domain / Integrin_b_cyt / Integrin beta tail domain ...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 cytoplasmic domain / Integrin_b_cyt / Integrin beta tail domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / Integrin beta subunit, VWA domain / Integrin beta subunit / Integrin beta N-terminal / Integrin beta chain VWA domain / Integrin plexin domain / Integrins beta chain cysteine-rich domain signature. / Integrin beta subunits (N-terminal portion of extracellular region) / EGF-like domain, extracellular / EGF-like domain / Integrin domain superfamily / PSI domain / domain found in Plexins, Semaphorins and Integrins / FERM central domain / FERM central domain / FERM superfamily, second domain / Band 4.1 domain / Band 4.1 homologues / PH domain / von Willebrand factor A-like domain superfamily / PH domain profile. / Pleckstrin homology domain. / EGF-like domain signature 1. / Pleckstrin homology domain / 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: 2.75 Å
AuthorsLi, H. / Yang, H. / Sun, K. / Zhang, Z. / Yu, C. / Wei, Z.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structural basis of kindlin-mediated integrin recognition and activation
Authors: Li, H. / Deng, Y. / Sun, K. / Yang, H. / Liu, J. / Wang, M. / Zhang, Z. / Lin, J. / Wu, C. / Wei, Z. / Yu, C.
History
DepositionJun 5, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation_author.name
Revision 1.2Sep 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fermitin family homolog 2,Integrin beta-1
B: Fermitin family homolog 2,Integrin beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,2253
Polymers112,1332
Non-polymers921
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4970 Å2
ΔGint-39 kcal/mol
Surface area39010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.866, 75.866, 384.219
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein Fermitin family homolog 2,Integrin beta-1 / Kindlin-2 / Pleckstrin homology domain-containing family C member 1 / Fibronectin receptor subunit ...Kindlin-2 / Pleckstrin homology domain-containing family C member 1 / Fibronectin receptor subunit beta / VLA-4 subunit beta


Mass: 56066.676 Da / Num. of mol.: 2 / Fragment: UNP residues 784-798 / Mutation: 168-217 deletion, 337-512 deletion
Source method: isolated from a genetically manipulated source
Details: Beta-integrin tail sequence was fused to the C-terminus of kindlin2
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Fermt2, Plekhc1, Itgb1 / Plasmid: pSUMO / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: Q8CIB5, UniProt: P09055
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 2.85 Å3/Da / Density % sol: 56.79 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M potassium chloride, 0.05 M HEPES pH 7.5, 35% v/v pentaerythritol propoxylate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 34443 / % possible obs: 98.7 % / Redundancy: 4 % / Biso Wilson estimate: 67.25 Å2 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.045 / Rrim(I) all: 0.098 / Χ2: 2.621 / Net I/σ(I): 12 / Num. measured all: 139053
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.75-2.84.40.7880.5160.4130.8951.42599.8
2.8-2.854.40.6710.7010.3540.7641.479100
2.85-2.94.20.5270.7220.2820.6021.46699.9
2.9-2.964.30.4830.7570.2570.551.52699.3
2.96-3.034.10.3830.8490.2070.4391.60799.9
3.03-3.14.20.3230.8760.1720.3681.64899.6
3.1-3.174.10.2620.9290.1410.31.87999.7
3.17-3.264.20.2070.9730.110.2362.08199.4
3.26-3.3640.1770.9660.0960.2032.18199.8
3.36-3.463.90.1530.9680.0840.1762.47498.9
3.46-3.593.90.1260.980.0690.1452.77598.7
3.59-3.733.80.1130.9840.0620.133.27598.8
3.73-3.93.70.0980.9860.0550.1143.49698.2
3.9-4.113.60.0840.990.0480.0973.75897.9
4.11-4.363.50.0740.9920.0420.0853.88996.9
4.36-4.73.50.0670.9920.0380.0773.9796.3
4.7-5.173.60.0630.9940.0350.0733.7796.6
5.17-5.923.70.0630.9940.0350.0733.60197.8
5.92-7.464.40.0590.9960.030.0673.60399.3
7.46-5050.0480.9970.0220.0533.48997.5

-
Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XPZ

5xpz


Resolution: 2.75→45.858 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.8
RfactorNum. reflection% reflection
Rfree0.2845 1733 5.05 %
Rwork0.2315 --
obs0.2341 34335 98.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 207.14 Å2 / Biso mean: 74.5935 Å2 / Biso min: 27.57 Å2
Refinement stepCycle: final / Resolution: 2.75→45.858 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6635 0 6 29 6670
Biso mean--77.23 56.69 -
Num. residues----834
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026787
X-RAY DIFFRACTIONf_angle_d0.4869201
X-RAY DIFFRACTIONf_chiral_restr0.021050
X-RAY DIFFRACTIONf_plane_restr0.0021145
X-RAY DIFFRACTIONf_dihedral_angle_d12.1382433
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.747-2.82780.39421320.31912680281299
2.8278-2.91910.3141270.307127352862100
2.9191-3.02340.31551680.294126502818100
3.0234-3.14440.33571470.270326992846100
3.1444-3.28750.32771370.253127092846100
3.2875-3.46080.27921510.24952709286099
3.4608-3.67750.30451300.23482670280099
3.6775-3.96130.24771490.22632690283998
3.9613-4.35960.27541540.21712672282697
4.3596-4.98980.25931540.20092657281196
4.9898-6.28410.28191450.22992784292998
6.2841-45.86450.28041390.21082947308698
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8937-0.071-0.74650.9918-0.24553.7469-0.04490.2084-0.0018-0.03750.0098-0.09840.1152-0.0130.05710.3550.0583-0.03080.3376-0.00010.3817.55924.5286-63.6227
21.6609-0.3508-0.19861.58160.24771.1479-0.0488-0.08340.20560.1365-0.0071-0.1818-0.00220.17110.04810.42490.1061-0.10150.3265-0.00160.413617.64398.4483-41.9136
30.2559-0.20180.07930.9102-0.44340.2599-0.5049-1.77680.0919-0.21810.22960.10250.9754-0.33720.14191.57250.02810.18081.797-0.14040.7558-3.302538.832819.5073
41.8552-0.04380.12342.80071.32982.25550.082-0.3043-0.0340.9397-0.42350.52680.5019-0.24920.28840.84040.02750.27020.61290.07660.5304-3.438436.1724-10.6425
50.1020.4863-0.05733.98660.5636-0.13550.0667-0.17070.2895-0.081-0.26670.46510.0037-0.47490.17770.51120.19980.00820.6149-0.07350.5185-7.400511.7361-34.2188
60.7671.06960.28624.17031.33861.00140.0417-0.1064-0.0039-0.2496-0.333-0.32470.042-0.02610.38470.40860.12350.07430.46080.00350.4550.085428.3981-26.6436
72.54030.5725-0.05582.30550.84681.5899-0.10340.00730.21780.2351-0.0456-0.2307-0.06160.44260.07760.6109-0.0009-0.0250.54270.13540.424714.399449.3367-16.4968
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 18 through 310 )A18 - 310
2X-RAY DIFFRACTION2chain 'A' and (resid 311 through 797 )A311 - 797
3X-RAY DIFFRACTION3chain 'B' and (resid 20 through 79 )B20 - 79
4X-RAY DIFFRACTION4chain 'B' and (resid 80 through 310 )B80 - 310
5X-RAY DIFFRACTION5chain 'B' and (resid 311 through 531 )B311 - 531
6X-RAY DIFFRACTION6chain 'B' and (resid 532 through 583 )B532 - 583
7X-RAY DIFFRACTION7chain 'B' and (resid 584 through 797 )B584 - 797

+
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://pdbjlvh1.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