[English] 日本語
Yorodumi
- PDB-1syq: Human vinculin head domain VH1, residues 1-258, in complex with h... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1syq
TitleHuman vinculin head domain VH1, residues 1-258, in complex with human talin's vinculin binding site 1, residues 607-636
Components
  • Talin 1
  • vinculin isoform VCL
KeywordsCELL ADHESION / cytoskeleton / vinculin / talin
Function / homology
Function and homology information


regulation of protein localization to adherens junction / podosome ring / outer dense plaque of desmosome / inner dense plaque of desmosome / cell-substrate junction / terminal web / epithelial cell-cell adhesion / zonula adherens / LIM domain binding / dystroglycan binding ...regulation of protein localization to adherens junction / podosome ring / outer dense plaque of desmosome / inner dense plaque of desmosome / cell-substrate junction / terminal web / epithelial cell-cell adhesion / zonula adherens / LIM domain binding / dystroglycan binding / vinculin binding / alpha-catenin binding / XBP1(S) activates chaperone genes / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / fascia adherens / integrin activation / cell-cell contact zone / costamere / apical junction assembly / regulation of establishment of endothelial barrier / cell-substrate junction assembly / adherens junction assembly / axon extension / protein localization to cell surface / cell-cell junction assembly / lamellipodium assembly / cortical actin cytoskeleton organization / regulation of focal adhesion assembly / maintenance of blood-brain barrier / phosphatidylserine binding / p130Cas linkage to MAPK signaling for integrins / brush border / GRB2:SOS provides linkage to MAPK signaling for Integrins / Signaling by ALK fusions and activated point mutants / Smooth Muscle Contraction / ruffle / phosphatidylinositol binding / cell-matrix adhesion / Integrin signaling / negative regulation of cell migration / cell projection / integrin-mediated signaling pathway / morphogenesis of an epithelium / adherens junction / sarcolemma / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / structural constituent of cytoskeleton / cell-cell adhesion / platelet aggregation / ruffle membrane / beta-catenin binding / specific granule lumen / extracellular vesicle / 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 / actin filament binding / cell-cell junction / Signaling by BRAF and RAF1 fusions / integrin binding / Platelet degranulation / actin binding / secretory granule lumen / ficolin-1-rich granule lumen / molecular adaptor activity / cytoskeleton / cell adhesion / cadherin binding / membrane raft / focal adhesion / ubiquitin protein ligase binding / Neutrophil degranulation / structural molecule activity / cell surface / protein-containing complex / extracellular exosome / extracellular region / 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 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsIzard, T. / Vonrhein, C.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Structural basis for amplifying vinculin activation by talin
Authors: Izard, T. / Vonrhein, C.
History
DepositionApr 1, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2004Provider: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: vinculin isoform VCL
B: Talin 1


Theoretical massNumber of molelcules
Total (without water)32,1882
Polymers32,1882
Non-polymers00
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-29 kcal/mol
Surface area14700 Å2
MethodPISA
2
A: vinculin isoform VCL
B: Talin 1
x 6


Theoretical massNumber of molelcules
Total (without water)193,12812
Polymers193,12812
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation16_545y+1/3,x-1/3,-z+2/31
crystal symmetry operation17_555x-y+1/3,-y+2/3,-z+2/31
crystal symmetry operation18_655-x+4/3,-x+y+2/3,-z+2/31
Buried area29200 Å2
ΔGint-213 kcal/mol
Surface area72890 Å2
MethodPISA
3
A: vinculin isoform VCL
B: Talin 1
x 6


Theoretical massNumber of molelcules
Total (without water)193,12812
Polymers193,12812
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation16_544y+1/3,x-1/3,-z-1/31
crystal symmetry operation17_554x-y+1/3,-y+2/3,-z-1/31
crystal symmetry operation18_654-x+4/3,-x+y+2/3,-z-1/31
Buried area31080 Å2
ΔGint-216 kcal/mol
Surface area71010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.098, 141.098, 104.920
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

-
Components

#1: Protein vinculin isoform VCL


Mass: 29766.275 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: peT3d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P18206
#2: Protein/peptide Talin 1


Mass: 2421.792 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: UniProt: Q9Y490
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 3.12 Å3/Da / Density % sol: 60.59 %

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97889
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97889 Å / Relative weight: 1
ReflectionResolution: 2.42→50 Å / Num. obs: 15061 / % possible obs: 97.6 % / Redundancy: 18 % / Biso Wilson estimate: 34.9 Å2 / Rmerge(I) obs: 0.179 / Net I/σ(I): 8.3
Reflection shellResolution: 2.42→2.51 Å / Rmerge(I) obs: 0.485 / Mean I/σ(I) obs: 3 / % possible all: 80.8

-
Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.42→32.25 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2709941.09 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.236 774 5.1 %RANDOM
Rwork0.188 ---
all0.188 ---
obs0.194 15060 98 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.5471 Å2 / ksol: 0.322653 e/Å3
Displacement parametersBiso mean: 56.3 Å2
Baniso -1Baniso -2Baniso -3
1-4.25 Å23.85 Å20 Å2
2--4.25 Å20 Å2
3----8.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.42→32.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2199 0 0 190 2389
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.014
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.92
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.751.5
X-RAY DIFFRACTIONc_mcangle_it5.262
X-RAY DIFFRACTIONc_scbond_it11.672
X-RAY DIFFRACTIONc_scangle_it14.962.5
LS refinement shellResolution: 2.42→2.57 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.258 118 5.4 %
Rwork0.226 2071 -
obs--85.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER-TOPOLOGY
X-RAY DIFFRACTION4ION.PARAMION.TOP

+
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