[English] 日本語
Yorodumi
- PDB-1u6h: Vinculin head (0-258) in complex with the talin vinculin binding ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1u6h
TitleVinculin head (0-258) in complex with the talin vinculin binding site 2 (849-879)
Components
  • Talin
  • Vinculin
KeywordsCELL ADHESION / Protein-protein complex
Function / homology
Function and homology information


muscle tendon junction / Platelet degranulation / Smooth Muscle Contraction / regulation of protein localization to adherens junction / podosome ring / outer dense plaque of desmosome / inner dense plaque of desmosome / terminal web / epithelial cell-cell adhesion / zonula adherens ...muscle tendon junction / Platelet degranulation / Smooth Muscle Contraction / regulation of protein localization to adherens junction / podosome ring / outer dense plaque of desmosome / inner dense plaque of desmosome / terminal web / epithelial cell-cell adhesion / zonula adherens / dystroglycan binding / vinculin binding / muscle alpha-actinin binding / MAP2K and MAPK activation / alpha-catenin binding / fascia adherens / cell-cell contact zone / costamere / apical junction assembly / regulation of establishment of endothelial barrier / adherens junction assembly / axon extension / protein localization to cell surface / lamellipodium assembly / regulation of focal adhesion assembly / alpha-actinin binding / brush border / skeletal muscle myofibril / stress fiber / regulation of cell migration / ruffle / cell projection / Neutrophil degranulation / morphogenesis of an epithelium / adherens junction / sarcolemma / neuromuscular junction / structural constituent of cytoskeleton / cell-cell adhesion / ruffle membrane / Z disc / beta-catenin binding / actin filament binding / cell-cell junction / actin cytoskeleton / integrin binding / scaffold protein binding / mitochondrial inner membrane / cytoskeleton / cell adhesion / cadherin binding / focal adhesion / ubiquitin protein ligase binding / structural molecule activity / cell surface / protein homodimerization activity / protein-containing complex / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / Talin, R4 domain / Vinculin-binding site-containing domain / Talin, central / Talin, N-terminal F0 domain / Talin, central domain superfamily / Talin-1/2, rod-segment / Vinculin Binding Site / Talin, middle domain / N-terminal or F0 domain of Talin-head FERM ...: / Talin, R4 domain / Vinculin-binding site-containing domain / Talin, central / Talin, N-terminal F0 domain / Talin, central domain superfamily / Talin-1/2, rod-segment / Vinculin Binding Site / Talin, middle domain / N-terminal or F0 domain of Talin-head FERM / Vinculin repeated domain signature. / Vinculin / Alpha-catenin/vinculin-like / I/LWEQ domain / I/LWEQ domain superfamily / I/LWEQ domain / I/LWEQ domain profile. / I/LWEQ domain / Vinculin, conserved site / Vinculin family talin-binding region signature. / Phosphotyrosine-binding domain / Vinculin/alpha-catenin / Vinculin family / Alpha-catenin/vinculin-like superfamily / FERM, N-terminal / FERM N-terminal domain / FERM domain signature 1. / FERM conserved site / FERM domain signature 2. / FERM central domain / FERM/acyl-CoA-binding protein superfamily / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / Four Helix Bundle (Hemerythrin (Met), subunit A) / PH-like domain superfamily / Ubiquitin-like domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Vinculin / Talin-1 / Talin-1
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsFillingham, I. / Gingras, A.R. / Papagrigoriou, E. / Patel, B. / Emsley, J. / Roberts, G.C.K. / Critchley, D.R. / Barsukov, I.L.
CitationJournal: Structure / Year: 2005
Title: A vinculin binding domain from the talin rod unfolds to form a complex with the vinculin head.
Authors: Fillingham, I. / Gingras, A.R. / Papagrigoriou, E. / Patel, B. / Emsley, J. / Critchley, D.R. / Roberts, G.C. / Barsukov, I.L.
History
DepositionJul 30, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Vinculin
B: Talin


Theoretical massNumber of molelcules
Total (without water)34,4612
Polymers34,4612
Non-polymers00
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-26 kcal/mol
Surface area14210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.122, 69.154, 96.162
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Vinculin /


Mass: 31327.104 Da / Num. of mol.: 1 / Fragment: Residues 0-258
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: VCL, VINC1 / Plasmid: pET-15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P12003
#2: Protein/peptide Talin


Mass: 3133.639 Da / Num. of mol.: 1 / Fragment: Vinculin Binding Site 2 (residues 849-879) / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in Gallus gallus (chicken).
References: UniProt: Q8AWI0, UniProt: P54939*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.5 Å3/Da / Density % sol: 50.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG 8000, Tris-HCl, magnesium chloride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 17, 2004 / Details: Toroidal Zerodur mirror, radii of 4.9km and 79mm
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.38→30 Å / Num. all: 14457 / Num. obs: 14457 / % possible obs: 99.68 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.116 / Net I/σ(I): 10.97
Reflection shellResolution: 2.38→2.442 Å / % possible all: 99.23

-
Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: unpublished data

Resolution: 2.38→30 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.875 / SU B: 12.17 / SU ML: 0.273 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.385 / ESU R Free: 0.311 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.3223 717 5 %RANDOM
Rwork0.24196 ---
all0.24574 14457 --
obs0.24574 13740 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.795 Å2
Baniso -1Baniso -2Baniso -3
1--2.28 Å20 Å20 Å2
2--7.68 Å20 Å2
3----5.4 Å2
Refinement stepCycle: LAST / Resolution: 2.38→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2115 0 0 57 2172
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0222138
X-RAY DIFFRACTIONr_angle_refined_deg2.1151.9722892
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2235274
X-RAY DIFFRACTIONr_dihedral_angle_2_deg45.45825.12282
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.75215412
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3151513
X-RAY DIFFRACTIONr_chiral_restr0.1380.2361
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021522
X-RAY DIFFRACTIONr_nbd_refined0.2650.21120
X-RAY DIFFRACTIONr_nbtor_refined0.3110.21474
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2010.281
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2320.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1570.26
X-RAY DIFFRACTIONr_mcbond_it1.0451.51427
X-RAY DIFFRACTIONr_mcangle_it1.77222240
X-RAY DIFFRACTIONr_scbond_it2.6063786
X-RAY DIFFRACTIONr_scangle_it4.254.5652
LS refinement shellResolution: 2.38→2.442 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.437 51 -
Rwork0.353 979 -
obs-979 99.23 %

+
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