[English] 日本語
Yorodumi
- PDB-1qkr: Crystal structure of the vinculin tail and a pathway for activation -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1qkr
TitleCrystal structure of the vinculin tail and a pathway for activation
ComponentsVINCULIN
KeywordsACTIN CYTOSKELETON / CELL ADHESION / HELICAL BUNDLE / LIPID BINDING
Function / homology
Function and homology information


muscle tendon junction / Platelet degranulation / Smooth Muscle Contraction / regulation of protein localization to adherens junction / outer dense plaque of desmosome / inner dense plaque of desmosome / podosome ring / terminal web / epithelial cell-cell adhesion / zonula adherens ...muscle tendon junction / Platelet degranulation / Smooth Muscle Contraction / regulation of protein localization to adherens junction / outer dense plaque of desmosome / inner dense plaque of desmosome / podosome ring / terminal web / epithelial cell-cell adhesion / zonula adherens / fascia adherens / MAP2K and MAPK activation / dystroglycan binding / muscle alpha-actinin binding / alpha-catenin binding / vinculin binding / cell-cell contact zone / apical junction assembly / costamere / regulation of establishment of endothelial barrier / axon extension / adherens junction assembly / 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 / Neutrophil degranulation / morphogenesis of an epithelium / cell projection / adherens junction / neuromuscular junction / sarcolemma / beta-catenin binding / Z disc / actin filament binding / cell-cell junction / actin cytoskeleton / scaffold protein binding / cytoskeleton / cell adhesion / mitochondrial inner membrane / cadherin binding / focal adhesion / ubiquitin protein ligase binding / structural molecule activity / protein homodimerization activity / protein-containing complex / plasma membrane / cytoplasm
Similarity search - Function
Vinculin repeated domain signature. / Vinculin / Alpha-catenin/vinculin-like / Vinculin, conserved site / Vinculin family talin-binding region signature. / Vinculin/alpha-catenin / Vinculin family / Alpha-catenin/vinculin-like superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesGALLUS GALLUS (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.8 Å
AuthorsBakolitsa, C. / De Pereda, J.M. / Bagshaw, C.R. / Critchley, D.R. / Liddington, R.C.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1999
Title: Crystal Structure of the Vinculin Tail and a Pathway for Activation
Authors: Bakolitsa, C. / De Pereda, J.M. / Bagshaw, C.R. / Critchley, D.R. / Liddington, R.C.
History
DepositionAug 4, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 4, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: VINCULIN
B: VINCULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4514
Polymers43,2592
Non-polymers1922
Water5,693316
1
A: VINCULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7262
Polymers21,6291
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: VINCULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7262
Polymers21,6291
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)39.600, 87.770, 50.630
Angle α, β, γ (deg.)90.00, 91.27, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein VINCULIN / TAIL DOMAIN


Mass: 21629.486 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GALLUS GALLUS (chicken) / Tissue: MUSCLE / Gene: VCL / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P12003
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 316 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 44 %
Crystal growpH: 5
Details: 25% (W/V) PEG 2000, 0.2 M (NH4)2SO4, 0.1 M CH3COO PH 5.0
Crystal
*PLUS
Density % sol: 44 %
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 8 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
16 mg/mlprotein1drop
2150 mM1dropNaCl
320 mMTris1drop
44 mMdithiothreitol1drop
525 %(w/v)PEG20001reservoir
60.2 Mammonium sulfate1reservoir
70.1 Msodium acetate1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 1.488
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 1.8→10 Å / Num. obs: 30415 / % possible obs: 95.5 % / Redundancy: 2.6 % / Biso Wilson estimate: 18.4 Å2 / Rsym value: 0.064 / Net I/σ(I): 16.6
Reflection shellResolution: 1.8→1.91 Å / Mean I/σ(I) obs: 3 / Rsym value: 0.27 / % possible all: 88.3
Reflection
*PLUS
Lowest resolution: 25 Å / % possible obs: 98.6 % / Rmerge(I) obs: 0.064
Reflection shell
*PLUS
Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 3

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CNS0.5phasing
SOLVEphasing
CNS0.5refinement
RefinementMethod to determine structure: SIRAS / Resolution: 1.8→10 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1508 5 %RANDOM
Rwork0.2 ---
obs0.2 30415 95.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 70.2752 Å2 / ksol: 0.426906 e/Å3
Displacement parametersBiso mean: 25.9 Å2
Baniso -1Baniso -2Baniso -3
1--3.42 Å20 Å2-3.27 Å2
2--5.39 Å20 Å2
3----1.96 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.2 Å
Luzzati d res low-10 Å
Luzzati sigma a0.12 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2805 0 10 316 3131
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d17.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.051.5
X-RAY DIFFRACTIONc_mcangle_it3.142
X-RAY DIFFRACTIONc_scbond_it4.472
X-RAY DIFFRACTIONc_scangle_it6.962.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.28 226 4.9 %
Rwork0.244 4422 -
obs--88.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.2 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg17.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.74
LS refinement shell
*PLUS
Rfactor Rfree: 0.28

+
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