[English] 日本語
Yorodumi
- PDB-3fyq: Structure of Drosophila melanogaster talin IBS2 domain (residues ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3fyq
TitleStructure of Drosophila melanogaster talin IBS2 domain (residues 1981-2168)
ComponentsCG6831-PA (Talin)
KeywordsCELL ADHESION / 5-helix bundle
Function / homology
Function and homology information


Integrin signaling / maintenance of epithelial integrity, open tracheal system / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / lumen formation, open tracheal system / cardiac muscle cell-cardiac muscle cell adhesion / apposition of dorsal and ventral imaginal disc-derived wing surfaces / terminal branching, open tracheal system / muscle attachment / germ-band shortening / Platelet degranulation ...Integrin signaling / maintenance of epithelial integrity, open tracheal system / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / lumen formation, open tracheal system / cardiac muscle cell-cardiac muscle cell adhesion / apposition of dorsal and ventral imaginal disc-derived wing surfaces / terminal branching, open tracheal system / muscle attachment / germ-band shortening / Platelet degranulation / border follicle cell migration / larval somatic muscle development / cell adhesion mediated by integrin / sarcomere organization / ruffle / structural constituent of cytoskeleton / Z disc / cell-cell adhesion / actin filament binding / integrin binding / cytoskeleton / cell adhesion / focal adhesion / negative regulation of DNA-templated transcription / plasma membrane
Similarity search - Function
Talin, central domain / IRS-type PTB domain / PTB domain (IRS-1 type) / A middle domain of Talin 1 / 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, central domain / IRS-type PTB domain / PTB domain (IRS-1 type) / A middle domain of Talin 1 / 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 / I/LWEQ domain / I/LWEQ domain superfamily / I/LWEQ domain / I/LWEQ domain profile. / I/LWEQ domain / Alpha-catenin/vinculin-like superfamily / FERM domain signature 1. / FERM conserved site / 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 / PH-like domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.95 Å
AuthorsCheung, T.Y.S. / Fairchild, M.J. / Zarivach, R. / Tanentzapf, G. / Van Petegem, F.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Crystal structure of the talin integrin binding domain 2.
Authors: Cheung, T.Y. / Fairchild, M.J. / Zarivach, R. / Tanentzapf, G. / Van Petegem, F.
History
DepositionJan 22, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CG6831-PA (Talin)


Theoretical massNumber of molelcules
Total (without water)21,3261
Polymers21,3261
Non-polymers00
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.919, 40.079, 57.547
Angle α, β, γ (deg.)90.00, 112.87, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-53-

HOH

-
Components

#1: Protein CG6831-PA (Talin)


Mass: 21325.990 Da / Num. of mol.: 1 / Fragment: IBS2 domain, UNP residues 1981-2168
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: rhea, CG6831, Dmel_CG6831 / Plasmid: pET41b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLacI / References: UniProt: Q9VSL8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.27 Å3/Da / Density % sol: 45.81 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 9.95
Details: 0.1M Bicine pH 9.95, 1-2M magnesium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 294K

-
Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9808, 0.9811, 0.9694
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 3, 2008
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.98081
20.98111
30.96941
ReflectionResolution: 1.95→50 Å / Num. obs: 13427 / % possible obs: 92.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.95→2.02 Å / % possible all: 54

-
Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXDphasing
REFMAC5.5.0070refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.95→36.15 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.908 / SU B: 3.971 / SU ML: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.179 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25548 678 5 %RANDOM
Rwork0.20625 ---
obs0.20875 12749 94.82 %-
all-13505 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.455 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20 Å2-0.46 Å2
2--1.37 Å20 Å2
3----2.11 Å2
Refinement stepCycle: LAST / Resolution: 1.95→36.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1279 0 0 76 1355
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0211287
X-RAY DIFFRACTIONr_angle_refined_deg1.741.9511753
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.355182
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.11225.95242
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.09915213
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.155155
X-RAY DIFFRACTIONr_chiral_restr0.1150.2234
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02917
X-RAY DIFFRACTIONr_mcbond_it1.1281.5898
X-RAY DIFFRACTIONr_mcangle_it2.07821432
X-RAY DIFFRACTIONr_scbond_it4.1683389
X-RAY DIFFRACTIONr_scangle_it6.8774.5320
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 28 -
Rwork0.267 653 -
obs--63.47 %

+
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://pdbjlvh1.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