[English] 日本語
Yorodumi
- PDB-6u4k: Human talin2 residues 1-403 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6u4k
TitleHuman talin2 residues 1-403
ComponentsTalin-2
KeywordsCELL ADHESION / actin / cytoskeleton / integrin / lipid-binding protein / talin / tumor suppressor gene / vinculin
Function / homology
Function and homology information


cell-cell junction assembly / ruffle / structural constituent of cytoskeleton / cell-cell adhesion / actin filament binding / actin cytoskeleton / integrin binding / actin binding / cell adhesion / focal adhesion ...cell-cell junction assembly / ruffle / structural constituent of cytoskeleton / cell-cell adhesion / actin filament binding / actin cytoskeleton / integrin binding / actin binding / cell adhesion / focal adhesion / synapse / structural molecule activity / plasma membrane / cytoplasm
Similarity search - Function
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 ...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 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 / PH-like domain superfamily / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.555 Å
AuthorsIzard, T. / Rangarajan, E.S. / Colgan, L. / Yasuda, R. / Chinthalapudi, K.
CitationJournal: J.Biol.Chem. / Year: 2020
Title: A distinct talin2 structure directs isoform specificity in cell adhesion.
Authors: Rangarajan, E.S. / Primi, M.C. / Colgan, L.A. / Chinthalapudi, K. / Yasuda, R. / Izard, T.
History
DepositionAug 26, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Sep 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Talin-2


Theoretical massNumber of molelcules
Total (without water)46,9771
Polymers46,9771
Non-polymers00
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Monomer by SEC-MALS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.885, 58.885, 203.799
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

-
Components

#1: Protein Talin-2


Mass: 46976.738 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TLN2, KIAA0320 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9Y4G6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.18 Å3/Da / Density % sol: 43.51 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / Details: 8% PEG8000, Hepes pH 7.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.0043 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Oct 26, 2016
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0043 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.06
ReflectionResolution: 2.555→101.9 Å / Num. obs: 12969 / % possible obs: 100 % / Redundancy: 10.1 % / CC1/2: 0.998 / Rpim(I) all: 0.044 / Net I/σ(I): 15.7
Reflection shellResolution: 2.555→2.76 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 2.7 / Num. unique obs: 1876 / CC1/2: 0.734 / Rpim(I) all: 0.381 / % possible all: 100

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.555→50.996 Å / Cross valid method: THROUGHOUT / σ(F): 3.41 / Phase error: 27.55 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2468 637 5.02 %
Rwork0.1925 12254 -
obs0.1977 12904 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 188.54 Å2 / Biso mean: 61.1146 Å2 / Biso min: 17.41 Å2
Refinement stepCycle: final / Resolution: 2.555→50.996 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3193 0 0 117 3310
Biso mean---54.08 -
Num. residues----391
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5552-2.75250.35351300.32438256895
2.7525-3.02940.27581230.25262435255895
3.0294-3.46760.2821460.21792464261094
3.4676-4.36830.20751320.17012422255495
4.3683-45.61110.2421170.16592495261295
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)
16.0164-0.1087-0.97687.241-0.59848.3020.21910.30.2995-0.1871-0.0982-0.1532-0.42130.0936-0.12010.2984-0.0578-0.04310.3226-0.0390.256234.81743.839553.613
27.16160.528-0.58196.3893-0.07627.9721-0.18871.0392-0.56530.29770.42150.42861.0213-1.2022-0.20120.419-0.1252-0.08070.47640.00570.463127.85923.302578.6533
31.4595-2.2667-2.12195.20094.55455.84350.00190.0111-0.098-0.597-0.1095-0.1149-0.4985-0.62710.04940.4498-0.0353-0.04260.3410.00930.246433.094312.675481.5726
41.0733-0.97091.29891.6171-2.93095.85240.4328-0.1853-0.1502-0.3302-0.35650.14991.1050.3483-0.08470.83740.03860.03190.6228-0.07480.613746.9287-11.488197.5094
52.0931-2.73980.43457.1832.0712.06410.13370.8413-0.44340.55780.40130.04411.21730.2009-0.42060.5443-0.0029-0.02810.4256-0.07820.432739.01141.263774.6439
65.2140.88531.67161.9192-0.86651.3249-0.4768-0.37840.16960.2850.2840.315-0.08560.1240.18790.4063-0.0355-0.00490.42710.04550.215734.89812.948391.6988
74.33381.6786-0.52592.2113-2.70944.0547-0.2471-0.48-0.11071.27250.21010.8567-0.1759-0.6199-0.1230.42130.07190.06080.60440.05870.244920.274327.673289.5206
83.97730.07281.97724.3706-0.40412.5511-0.03810.17070.0487-0.45260.12440.21960.185-0.2108-0.08770.40130.0256-0.02590.40480.01890.163720.691931.836675.837
93.56390.62341.24077.70230.45964.2761-0.03730.19490.35170.51280.2248-0.2448-0.96150.1726-0.06470.54280.06810.01220.4927-0.07620.269633.716851.318490.1539
106.62132.85972.88122.50142.49167.8829-0.06230.4364-0.2091-0.14510.1623-0.47520.22370.70390.02460.38150.09450.07080.4434-0.02110.37437.569243.773990.138
118.8171-3.32255.31699.6568-3.85683.6188-0.3151-0.36480.5980.67-0.0753-0.6431-0.76340.69260.35880.58610.0563-0.03120.7363-0.06970.347140.177751.8654102.465
129.6409-0.3434-1.01312.1071-1.94617.16280.3198-0.4723-0.06110.1483-0.33110.3233-0.18670.49720.15810.61110.05020.03060.5421-0.10820.253635.286448.7603102.0014
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 86 )A1 - 86
2X-RAY DIFFRACTION2chain 'A' and (resid 87 through 107)A87 - 107
3X-RAY DIFFRACTION3chain 'A' and (resid 108 through 132 )A108 - 132
4X-RAY DIFFRACTION4chain 'A' and (resid 133 through 176 )A133 - 176
5X-RAY DIFFRACTION5chain 'A' and (resid 177 through 191)A177 - 191
6X-RAY DIFFRACTION6chain 'A' and (resid 192 through 209)A192 - 209
7X-RAY DIFFRACTION7chain 'A' and (resid 210 through 229 )A210 - 229
8X-RAY DIFFRACTION8chain 'A' and (resid 230 through 310 )A230 - 310
9X-RAY DIFFRACTION9chain 'A' and (resid 311 through 336 )A311 - 336
10X-RAY DIFFRACTION10chain 'A' and (resid 337 through 357 )A337 - 357
11X-RAY DIFFRACTION11chain 'A' and (resid 358 through 375 )A358 - 375
12X-RAY DIFFRACTION12chain 'A' and (resid 377 through 402 )A377 - 402

+
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