[English] 日本語
Yorodumi
- PDB-3zip: minor-site specific NLS (A58) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3zip
Titleminor-site specific NLS (A58)
Components
  • A58NLS
  • IMPORTIN SUBUNIT ALPHA-2
KeywordsTRANSPORT PROTEIN / NUCLEAR IMPORT / NUCLEAR LOCALIZATION SIGNALS
Function / homology
Function and homology information


Sensing of DNA Double Strand Breaks / 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 / postsynapse to nucleus signaling pathway / nuclear import signal receptor activity / cytoplasmic stress granule / protein import into nucleus / host cell / DNA-binding transcription factor binding ...Sensing of DNA Double Strand Breaks / 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 / postsynapse to nucleus signaling pathway / nuclear import signal receptor activity / cytoplasmic stress granule / protein import into nucleus / host cell / DNA-binding transcription factor binding / postsynaptic density / glutamatergic synapse / nucleoplasm / cytosol
Similarity search - Function
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 ...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 / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Importin subunit alpha-1
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsChang, C.-W. / Counago, R.M. / Williams, S.J. / Kobe, B.
CitationJournal: Traffic / Year: 2013
Title: Distinctive Conformation of Minor Site-Specific Nuclear Localization Signals Bound to Importin-Alpha
Authors: Chang, C.-W. / Counago, R.M. / Williams, S.J. / Boden, M. / Kobe, B.
History
DepositionJan 10, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 1.2Dec 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: IMPORTIN SUBUNIT ALPHA-2
B: A58NLS
C: A58NLS


Theoretical massNumber of molelcules
Total (without water)52,9803
Polymers52,9803
Non-polymers00
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.140, 90.180, 99.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein IMPORTIN SUBUNIT ALPHA-2 / 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: 49872.836 Da / Num. of mol.: 1 / Fragment: RESIDUES 72-497
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P52293
#2: Protein/peptide A58NLS


Mass: 1553.769 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 3.23 Å3/Da / Density % sol: 61.89 % / Description: NONE
Crystal growpH: 6.5
Details: 0.75 M SODIUM CITRATE, 0.1 M HEPES BUFFER (PH 6.5) AND 10 MM DTT

-
Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537
DetectorDate: Sep 2, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.4→19.87 Å / Num. obs: 28437 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 7.2 % / Biso Wilson estimate: 52.74 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 15
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.95 / Mean I/σ(I) obs: 2.1 / % possible all: 100

-
Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IAL

1ial


Resolution: 2.4→19.83 Å / Cor.coef. Fo:Fc: 0.9561 / Cor.coef. Fo:Fc free: 0.9425 / SU R Cruickshank DPI: 0.199 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.204 / SU Rfree Blow DPI: 0.163 / SU Rfree Cruickshank DPI: 0.162
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.1905 1435 5.05 %RANDOM
Rwork0.1643 ---
obs0.1656 28389 99.99 %-
Displacement parametersBiso mean: 58.31 Å2
Baniso -1Baniso -2Baniso -3
1-0.9631 Å20 Å20 Å2
2--4.2164 Å20 Å2
3----5.1795 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: LAST / Resolution: 2.4→19.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3394 0 0 49 3443
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013455HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.014700HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1612SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes89HARMONIC2
X-RAY DIFFRACTIONt_gen_planes489HARMONIC5
X-RAY DIFFRACTIONt_it3455HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.54
X-RAY DIFFRACTIONt_other_torsion3.04
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion479SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4261SEMIHARMONIC4
LS refinement shellResolution: 2.4→2.49 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.2461 151 5.17 %
Rwork0.1985 2768 -
all0.2009 2919 -
obs--99.99 %
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)
11.8606-0.41861.36546.5694-2.25113.78310.1450.1573-0.1911-0.4499-0.0214-0.28840.26630.2538-0.1235-0.02220.0373-0.0471-0.0942-0.0076-0.0499-5.6006-8.258515.3859
21.85440.92610.42552.6665-0.51650.87340.0849-0.12770.12610.22580.01070.0208-0.0703-0.0528-0.0956-0.03560.0034-0.0028-0.066-0.0044-0.0307-4.863914.833816.4526
32.170.1602-0.64594.211-1.12282.25930.09360.0760.11790.17230.00290.2196-0.21230.0035-0.0965-0.0769-0.00490.0446-0.06580.02770.02933.43428.8265.8779
42.33330.3455-1.07282.8208-0.91332.9099-0.00480.78810.3178-0.42420.17240.3825-0.0567-0.536-0.1676-0.1617-0.0057-0.03760.02730.1517-0.07738.400337.4981-19.2805
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|72 - 156}
2X-RAY DIFFRACTION2{A|157 - 262}
3X-RAY DIFFRACTION3{A|263 - 329}
4X-RAY DIFFRACTION4{A|330 - 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