[English] 日本語
Yorodumi
- PDB-1tr2: Crystal structure of human full-length vinculin (residues 1-1066) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1tr2
TitleCrystal structure of human full-length vinculin (residues 1-1066)
ComponentsVINCULIN ISOFORM 1
KeywordsCELL ADHESION / ACTIN-BINDING
Function / homology
Function and homology information


regulation of protein localization to adherens junction / outer dense plaque of desmosome / inner dense plaque of desmosome / podosome ring / terminal web / cell-substrate junction / epithelial cell-cell adhesion / zonula adherens / dystroglycan binding / alpha-catenin binding ...regulation of protein localization to adherens junction / outer dense plaque of desmosome / inner dense plaque of desmosome / podosome ring / terminal web / cell-substrate junction / epithelial cell-cell adhesion / zonula adherens / dystroglycan binding / alpha-catenin binding / fascia adherens / cell-cell contact zone / apical junction assembly / costamere / regulation of establishment of endothelial barrier / adherens junction assembly / axon extension / protein localization to cell surface / lamellipodium assembly / regulation of focal adhesion assembly / maintenance of blood-brain barrier / brush border / Smooth Muscle Contraction / negative regulation of cell migration / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / cell-matrix adhesion / morphogenesis of an epithelium / cell projection / adherens junction / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / sarcolemma / beta-catenin binding / platelet aggregation / specific granule lumen / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Signaling by BRAF and RAF1 fusions / Signaling by ALK fusions and activated point mutants / cell-cell junction / Platelet degranulation / extracellular vesicle / actin binding / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / secretory granule lumen / molecular adaptor activity / ficolin-1-rich granule lumen / cytoskeleton / cell adhesion / cadherin binding / membrane raft / focal adhesion / ubiquitin protein ligase binding / Neutrophil degranulation / structural molecule activity / protein-containing complex / extracellular exosome / extracellular region / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Vinculin, Vh2 four-helix bundle / 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) ...Vinculin, Vh2 four-helix bundle / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsBorgon, R.A. / Vonrhein, C. / Bricogne, G. / Bois, P.R. / Izard, T.
CitationJournal: Structure / Year: 2004
Title: Crystal Structure of Human Vinculin
Authors: Borgon, R.A. / Vonrhein, C. / Bricogne, G. / Bois, P.R. / Izard, T.
History
DepositionJun 19, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: VINCULIN ISOFORM 1
B: VINCULIN ISOFORM 1


Theoretical massNumber of molelcules
Total (without water)237,1282
Polymers237,1282
Non-polymers00
Water3,927218
1
A: VINCULIN ISOFORM 1


Theoretical massNumber of molelcules
Total (without water)118,5641
Polymers118,5641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: VINCULIN ISOFORM 1


Theoretical massNumber of molelcules
Total (without water)118,5641
Polymers118,5641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.740, 154.080, 108.950
Angle α, β, γ (deg.)90.00, 90.44, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein VINCULIN ISOFORM 1


Mass: 118563.750 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VCL / Plasmid: PET3 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) and BL21(DE3) / References: UniProt: P18206
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 11

-
Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.97 %

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97927
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97927 Å / Relative weight: 1
ReflectionResolution: 2.9→56.86 Å / Num. obs: 48752 / % possible obs: 100 % / Redundancy: 23.7 % / Biso Wilson estimate: 103.211 Å2 / Rmerge(I) obs: 0.154 / Net I/σ(I): 21
Reflection shellResolution: 2.9→2.98 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 1.4 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
BUSTER-TNT1.1.1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.9→56.86 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: SOME OF THE WATER MOLECULES ARE PLACED IN DISORDERED DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.3005 2507 5.15 %RANDOM
Rwork0.2322 ---
obs0.2356 48752 100 %-
Displacement parametersBiso mean: 92.83 Å2
Baniso -1Baniso -2Baniso -3
1--13.42714954 Å20 Å2-0.9340888 Å2
2--3.12342373 Å20 Å2
3---10.30372581 Å2
Refine analyzeLuzzati coordinate error obs: 0.4897 Å
Refinement stepCycle: LAST / Resolution: 2.9→56.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15815 0 0 218 16033
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.006159882
X-RAY DIFFRACTIONt_angle_deg0.945214832
X-RAY DIFFRACTIONt_dihedral_angle_d20.42499670
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle24.07781
X-RAY DIFFRACTIONt_trig_c_planes0.0054972
X-RAY DIFFRACTIONt_gen_planes0.0122715
X-RAY DIFFRACTIONt_it1.7141596420
X-RAY DIFFRACTIONt_nbd0.0549715
LS refinement shellResolution: 2.9→3.07 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.3356 423 5.47 %
Rwork0.2809 7304 -
all28.39 7727 -
obs--99.8 %

+
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