[English] 日本語
Yorodumi
- PDB-3zdl: Vinculin head (1-258) in complex with a RIAM fragment -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3zdl
TitleVinculin head (1-258) in complex with a RIAM fragment
Components
  • AMYLOID BETA A4 PRECURSOR PROTEIN-BINDING FAMILY B MEMBER 1-INTERACTING PROTEIN
  • VINCULIN
KeywordsCELL ADHESION
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 / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / epithelial cell-cell adhesion ...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 / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / epithelial cell-cell adhesion / zonula adherens / muscle alpha-actinin binding / dystroglycan binding / MAP2K and MAPK activation / alpha-catenin binding / fascia adherens / vinculin binding / cell-cell contact zone / apical junction assembly / costamere / adherens junction assembly / regulation of establishment of endothelial barrier / axon extension / protein localization to cell surface / lamellipodium assembly / regulation of focal adhesion assembly / T cell receptor complex / p130Cas linkage to MAPK signaling for integrins / alpha-actinin binding / brush border / GRB2:SOS provides linkage to MAPK signaling for Integrins / skeletal muscle myofibril / stress fiber / regulation of cell migration / Integrin signaling / positive regulation of cell adhesion / Neutrophil degranulation / cell projection / morphogenesis of an epithelium / adherens junction / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / neuromuscular junction / sarcolemma / Z disc / beta-catenin binding / 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 / Signaling by BRAF and RAF1 fusions / cell-cell junction / actin cytoskeleton / lamellipodium / scaffold protein binding / mitochondrial inner membrane / cytoskeleton / cell adhesion / cadherin binding / focal adhesion / ubiquitin protein ligase binding / structural molecule activity / signal transduction / protein homodimerization activity / protein-containing complex / plasma membrane / cytosol / cytoplasm
Similarity search - Function
GRB/APBB1IP / APBB1IP, PH domain / RA like domain / Vinculin repeated domain signature. / Vinculin / Alpha-catenin/vinculin-like / Ras association (RalGDS/AF-6) domain / Vinculin, conserved site / Vinculin family talin-binding region signature. / Vinculin/alpha-catenin ...GRB/APBB1IP / APBB1IP, PH domain / RA like domain / Vinculin repeated domain signature. / Vinculin / Alpha-catenin/vinculin-like / Ras association (RalGDS/AF-6) domain / Vinculin, conserved site / Vinculin family talin-binding region signature. / Vinculin/alpha-catenin / Vinculin family / Ras-associating (RA) domain profile. / Ras-associating (RA) domain / Alpha-catenin/vinculin-like superfamily / PH domain / Four Helix Bundle (Hemerythrin (Met), subunit A) / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / Ubiquitin-like domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Vinculin / Amyloid beta A4 precursor protein-binding family B member 1-interacting protein
Similarity search - Component
Biological speciesGALLUS GALLUS (chicken)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsZacharchenko, T. / Elliott, P.R. / Goult, B.T. / Bate, N. / Critchely, D.R. / Barsukov, I.L.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Riam and Vinculin Binding to Talin are Mutually Exclusive and Regulate Adhesion Assembly and Turnover.
Authors: Goult, B.T. / Zacharchenko, T. / Bate, N. / Tsang, R. / Hey, F. / Gingras, A.R. / Elliott, P.R. / Roberts, G.C. / Ballestrem, C. / Critchley, D.R. / Barsukov, I.L.
History
DepositionNov 28, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 13, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2013Group: Database references
Revision 1.2Mar 6, 2013Group: Derived calculations / Other
Revision 1.3Apr 10, 2013Group: Derived calculations / Other
Revision 1.4Apr 17, 2013Group: Database references
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: VINCULIN
B: AMYLOID BETA A4 PRECURSOR PROTEIN-BINDING FAMILY B MEMBER 1-INTERACTING PROTEIN


Theoretical massNumber of molelcules
Total (without water)34,8672
Polymers34,8672
Non-polymers00
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-27.8 kcal/mol
Surface area14660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.730, 70.030, 95.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein VINCULIN / METAVINCULIN


Mass: 31327.104 Da / Num. of mol.: 1 / Fragment: VD1 DOMAIN, RESIDUES 1-259
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GALLUS GALLUS (chicken) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P12003
#2: Protein/peptide AMYLOID BETA A4 PRECURSOR PROTEIN-BINDING FAMILY B MEMBER 1-INTERACTING PROTEIN / APBB1-INTERACTING PROTEIN 1 / PROLINE-RICH EVH1 LIGAND 1 / PREL-1 / PROLINE-RICH PROTEIN 73 / RAP1- ...APBB1-INTERACTING PROTEIN 1 / PROLINE-RICH EVH1 LIGAND 1 / PREL-1 / PROLINE-RICH PROTEIN 73 / RAP1-GTP-INTERACTING ADAPTER MOLECULE / RIAM / RETINOIC ACID-RESPONSIVE PROLINE-RICH PROTEIN 1 / RARP-1


Mass: 3539.914 Da / Num. of mol.: 1 / Fragment: N TERMINAL DOMAIN, RESIUDES 1-32 / Mutation: YES / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q7Z5R6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsC TERMINAL TYROSINE NON NATIVE

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.96 % / Description: NONE
Crystal growDetails: 1.2M AMMONIUM SULPHATE, 0.05M TRI-SODIUM CITRATE, 3% ISOPROPANOL

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9778
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 7, 2011
RadiationMonochromator: ACCEL FIXED EXIT DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 2.3→56.49 Å / Num. obs: 16055 / % possible obs: 100 % / Observed criterion σ(I): 2.9 / Redundancy: 5.6 % / Biso Wilson estimate: 34.31 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 7.8
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 3 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8_1069)refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XWJ

1xwj


Resolution: 2.3→47.8 Å / SU ML: 0.29 / σ(F): 1.34 / Phase error: 23.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2298 801 5 %
Rwork0.1881 --
obs0.1901 16016 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→47.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2204 0 0 57 2261
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082230
X-RAY DIFFRACTIONf_angle_d1.093018
X-RAY DIFFRACTIONf_dihedral_angle_d15.857852
X-RAY DIFFRACTIONf_chiral_restr0.064371
X-RAY DIFFRACTIONf_plane_restr0.005384
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.44410.3491090.24232491X-RAY DIFFRACTION100
2.4441-2.63280.25821440.20942487X-RAY DIFFRACTION100
2.6328-2.89770.24921480.19912494X-RAY DIFFRACTION100
2.8977-3.3170.26371360.18312516X-RAY DIFFRACTION100
3.317-4.17860.18951300.16762552X-RAY DIFFRACTION100
4.1786-47.81040.2081340.18442675X-RAY DIFFRACTION100
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)
10.7701-0.53351.16640.644-0.68361.08890.08980.1576-0.0243-0.1971-0.0721-0.03550.05060.07420.01120.11890.02120.01760.14730.03810.1037-11.0375-13.693823.4492
21.01560.3822-0.41052.2228-0.86013.57010.0662-0.0446-0.08380.04240.22030.07950.2479-0.40660.08890.3363-0.0166-0.16590.20540.02750.7093-11.5667-27.7443.7533
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:256)
2X-RAY DIFFRACTION2(CHAIN B AND RESID 7:32)

+
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