[English] 日本語
Yorodumi
- PDB-5umz: Structure of TNRC6A NLS in complex with importin-alpha -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5umz
TitleStructure of TNRC6A NLS in complex with importin-alpha
Components
  • Importin subunit alpha-1
  • TNRC6A
KeywordsPROTEIN TRANSPORT / mRNA decay / miRNA ARM repeat / nuclear transport
Function / homology
Function and homology information


Post-transcriptional silencing by small RNAs / Transcriptional regulation by small RNAs / endoderm development / maintenance of protein location in cell / Sensing of DNA Double Strand Breaks / regulation of transcription by glucose / miRNA-mediated post-transcriptional gene silencing / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / NLS-dependent protein nuclear import complex ...Post-transcriptional silencing by small RNAs / Transcriptional regulation by small RNAs / endoderm development / maintenance of protein location in cell / Sensing of DNA Double Strand Breaks / regulation of transcription by glucose / miRNA-mediated post-transcriptional gene silencing / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / NLS-dependent protein nuclear import complex / miRNA-mediated gene silencing by inhibition of translation / postsynapse to nucleus signaling pathway / RISC complex / regulatory ncRNA-mediated gene silencing / NLS-bearing protein import into nucleus / nuclear import signal receptor activity / nuclear localization sequence binding / non-canonical NF-kappaB signal transduction / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / positive regulation of type I interferon production / cellular response to starvation / protein import into nucleus / P-body / histone deacetylase binding / cytoplasmic stress granule / host cell / nuclear membrane / DNA-binding transcription factor binding / molecular adaptor activity / postsynaptic density / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / Golgi apparatus / glutamatergic synapse / RNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
TNRC6A, RNA recognition motif / TNRC6, PABC binding domain / TNRC6-PABC binding domain / Argonaute hook domain / : / Argonaute hook / Importin subunit alpha / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain superfamily / Importin beta binding domain ...TNRC6A, RNA recognition motif / TNRC6, PABC binding domain / TNRC6-PABC binding domain / Argonaute hook domain / : / Argonaute hook / Importin subunit alpha / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain superfamily / Importin beta binding domain / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain / IBB domain profile. / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / RNA-binding domain superfamily / Alpha Horseshoe / Armadillo-like helical / Armadillo-type fold / Nucleotide-binding alpha-beta plait domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Importin subunit alpha-1 / Trinucleotide repeat-containing gene 6A protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsChaston, J. / Stewart, A.G. / Christie, M.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)DE160100608 Australia
National Health and Medical Research Council (NHMRC, Australia)APP1090408 Australia
CitationJournal: PLoS ONE / Year: 2017
Title: Structural characterisation of TNRC6A nuclear localisation signal in complex with importin-alpha.
Authors: Chaston, J.J. / Stewart, A.G. / Christie, M.
History
DepositionJan 30, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Importin subunit alpha-1
E: TNRC6A
D: TNRC6A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4957
Polymers58,1273
Non-polymers3684
Water7,314406
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.791, 89.980, 99.280
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsAs per the authors the biological assembly is a dimer, the second peptide bound is an artifact of the purification/crystallisation process

-
Components

#1: Protein Importin subunit alpha-1 / Importin alpha P1 / Karyopherin subunit alpha-2 / Pendulin / Pore targeting complex 58 kDa subunit ...Importin alpha P1 / Karyopherin subunit alpha-2 / Pendulin / Pore targeting complex 58 kDa subunit / PTAC58 / RAG cohort protein 1 / SRP1-alpha


Mass: 55121.301 Da / Num. of mol.: 1 / Fragment: UNP residues 70-528
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kpna2, Rch1 / Production host: Escherichia coli (E. coli) / References: UniProt: P52293
#2: Protein/peptide TNRC6A


Mass: 1502.770 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: Q3UHK8*PLUS
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 406 / 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: 3.03 Å3/Da / Density % sol: 59.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: sodium citrate, Hepes 7.0, 10mM DTT

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 4, 2016
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.9→59.28 Å / Num. obs: 56250 / % possible obs: 100 % / Redundancy: 6.9 % / Rpim(I) all: 0.032 / Net I/σ(I): 19.8
Reflection shellRpim(I) all: 0.377

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PJN

1pjn


Resolution: 1.9→44.99 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 0.02 / Phase error: 18.11
RfactorNum. reflection% reflection
Rfree0.1816 2666 4.73 %
Rwork0.1516 --
obs0.153 386273 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→44.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3342 0 24 406 3772
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0163572
X-RAY DIFFRACTIONf_angle_d1.2444892
X-RAY DIFFRACTIONf_dihedral_angle_d16.8572230
X-RAY DIFFRACTIONf_chiral_restr0.095590
X-RAY DIFFRACTIONf_plane_restr0.008629
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.92160.29011450.25773439X-RAY DIFFRACTION100
1.9216-1.94420.28911720.24113364X-RAY DIFFRACTION100
1.9442-1.96790.25141830.23193441X-RAY DIFFRACTION100
1.9679-1.99280.25791810.22363399X-RAY DIFFRACTION100
1.9928-2.0190.25141680.21243420X-RAY DIFFRACTION100
2.019-2.04670.27241420.193397X-RAY DIFFRACTION100
2.0467-2.07590.21451810.17883430X-RAY DIFFRACTION100
2.0759-2.10690.23751950.18353343X-RAY DIFFRACTION100
2.1069-2.13980.19521780.16483430X-RAY DIFFRACTION100
2.1398-2.17490.20321620.1663405X-RAY DIFFRACTION100
2.1749-2.21240.21571660.16533410X-RAY DIFFRACTION100
2.2124-2.25270.15781470.15833469X-RAY DIFFRACTION100
2.2527-2.2960.18661530.15093436X-RAY DIFFRACTION100
2.296-2.34290.16512110.1443354X-RAY DIFFRACTION100
2.3429-2.39380.18581840.14753430X-RAY DIFFRACTION100
2.3938-2.44950.18631530.14423377X-RAY DIFFRACTION100
2.4495-2.51070.18451510.14353422X-RAY DIFFRACTION100
2.5107-2.57860.19931860.14953402X-RAY DIFFRACTION100
2.5786-2.65450.18251640.15423419X-RAY DIFFRACTION100
2.6545-2.74010.17911600.15123419X-RAY DIFFRACTION100
2.7401-2.83810.17561800.14633411X-RAY DIFFRACTION100
2.8381-2.95170.18121450.14933417X-RAY DIFFRACTION100
2.9517-3.0860.17311600.1573444X-RAY DIFFRACTION100
3.086-3.24860.181770.15623408X-RAY DIFFRACTION100
3.2486-3.45210.21661700.15643425X-RAY DIFFRACTION100
3.4521-3.71850.17691700.14193404X-RAY DIFFRACTION100
3.7185-4.09250.16141950.1273375X-RAY DIFFRACTION100
4.0925-4.68420.1381780.1173402X-RAY DIFFRACTION100
4.6842-5.89950.1391620.15033406X-RAY DIFFRACTION100
5.8995-45.00270.18981590.14763407X-RAY DIFFRACTION99
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)
10.74350.58770.38780.29980.26560.32310.09580.0271-0.11890.0404-0.00320.0023-0.0359-0.00490.00210.18370.01330.01110.1733-0.0140.172739.314373.65757.9052
20.2476-0.07220.06620.0652-0.06090.15450.22240.6646-0.3555-0.42370.1728-0.21080.19630.43510.34290.41110.02770.14790.7171-0.24330.350531.963249.581621.9152
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'B' and resid 72 through 409)
2X-RAY DIFFRACTION2(chain 'B' and resid 410 through 497)

+
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