[English] 日本語
Yorodumi
- PDB-1qgk: STRUCTURE OF IMPORTIN BETA BOUND TO THE IBB DOMAIN OF IMPORTIN ALPHA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1qgk
TitleSTRUCTURE OF IMPORTIN BETA BOUND TO THE IBB DOMAIN OF IMPORTIN ALPHA
Components
  • PROTEIN (IMPORTIN ALPHA-2 SUBUNIT)
  • PROTEIN (IMPORTIN BETA SUBUNIT)
KeywordsTRANSPORT RECEPTOR / NUCLEAR IMPORT / HEAT MOTIF / NLS-BINDING
Function / homology
Function and homology information


RNA import into nucleus / Inhibition of nitric oxide production / mitotic chromosome movement towards spindle pole / Sensing of DNA Double Strand Breaks / endoplasmic reticulum tubular network / regulation of DNA recombination / establishment of mitotic spindle localization / astral microtubule organization / entry of viral genome into host nucleus through nuclear pore complex via importin / Transport of Ribonucleoproteins into the Host Nucleus ...RNA import into nucleus / Inhibition of nitric oxide production / mitotic chromosome movement towards spindle pole / Sensing of DNA Double Strand Breaks / endoplasmic reticulum tubular network / regulation of DNA recombination / establishment of mitotic spindle localization / astral microtubule organization / entry of viral genome into host nucleus through nuclear pore complex via importin / Transport of Ribonucleoproteins into the Host Nucleus / positive regulation of viral life cycle / Regulation of cholesterol biosynthesis by SREBP (SREBF) / ribosomal protein import into nucleus / importin-alpha family protein binding / NS1 Mediated Effects on Host Pathways / Initiation of Nuclear Envelope (NE) Reformation / NLS-dependent protein nuclear import complex / Apoptosis induced DNA fragmentation / host cell / Nuclear import of Rev protein / Postmitotic nuclear pore complex (NPC) reformation / nuclear import signal receptor activity / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / nuclear localization sequence binding / DNA metabolic process / CaMK IV-mediated phosphorylation of CREB / NLS-bearing protein import into nucleus / mitotic metaphase chromosome alignment / mitotic spindle assembly / nuclear pore / Assembly of the ORC complex at the origin of replication / Hsp90 protein binding / ISG15 antiviral mechanism / small GTPase binding / cytoplasmic stress granule / protein import into nucleus / histone deacetylase binding / specific granule lumen / SARS-CoV-1 activates/modulates innate immune responses / Interferon alpha/beta signaling / nuclear envelope / nuclear membrane / Estrogen-dependent gene expression / ficolin-1-rich granule lumen / protein domain specific binding / Golgi membrane / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / enzyme binding / RNA binding / extracellular exosome / zinc ion binding / extracellular region / nucleoplasm / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Importin-alpha, importin-beta-binding domain / Importin beta family / HEAT-like repeat / Importin-beta N-terminal domain profile. / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta, N-terminal domain / Importin subunit alpha / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain superfamily ...Importin-alpha, importin-beta-binding domain / Importin beta family / HEAT-like repeat / Importin-beta N-terminal domain profile. / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta, N-terminal domain / 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. / HEAT repeat profile. / HEAT, type 2 / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Importin subunit alpha-1 / Importin subunit beta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsCingolani, G. / Petosa, C. / Weis, K. / Muller, C.W.
CitationJournal: Nature / Year: 1999
Title: Structure of importin-beta bound to the IBB domain of importin-alpha.
Authors: Cingolani, G. / Petosa, C. / Weis, K. / Muller, C.W.
History
DepositionApr 29, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0May 24, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (IMPORTIN BETA SUBUNIT)
B: PROTEIN (IMPORTIN ALPHA-2 SUBUNIT)


Theoretical massNumber of molelcules
Total (without water)102,7072
Polymers102,7072
Non-polymers00
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-6 kcal/mol
Surface area40880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.584, 97.606, 83.194
Angle α, β, γ (deg.)90.00, 91.13, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein PROTEIN (IMPORTIN BETA SUBUNIT) / KARYOPHERIN BETA-1 / NUCLEAR FACTOR P97 / IMPORTIN B


Mass: 97323.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cellular location: CYTOPLASM / Plasmid: PEQ60 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: Q14974
#2: Protein/peptide PROTEIN (IMPORTIN ALPHA-2 SUBUNIT) / IMPORTIN ALPHA-2 SUBUNIT / KARYOPHERIN ALPHA-2 SUBUNIT / SRP1-ALPHA


Mass: 5383.339 Da / Num. of mol.: 1 / Fragment: IBB DOMAIN / Source method: obtained synthetically
Details: This protein is chemically synthesized. The sequence of this protein is naturally found in the cytoplasm of homo sapiens (human).
References: UniProt: P52292
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.55 Å3/Da / Density % sol: 51.4 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
150 mg/mlprotein1drop
218-22 %PEG80001reservoir
350 mMpotassium acetate1reservoir
410 mMbeta-mercaptoethanol1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID2 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 34788 / % possible obs: 97.5 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 15.7
Reflection shellResolution: 2.5→2.57 Å / Rmerge(I) obs: 0.302 / Mean I/σ(I) obs: 2.5 / Rsym value: 0.302 / % possible all: 97.5
Reflection shell
*PLUS
% possible obs: 97.5 %

-
Processing

Software
NameVersionClassification
SOLVEphasing
CNS0.4refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.5→30 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1759 5 %RANDOM
Rwork0.221 ---
obs-34788 97.5 %-
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7185 0 0 44 7229
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.41.5
X-RAY DIFFRACTIONc_mcangle_it52
X-RAY DIFFRACTIONc_scbond_it5.72
X-RAY DIFFRACTIONc_scangle_it7.92.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:PROTEIN_REP.PA
X-RAY DIFFRACTION2CNS_TOPPAR:WATER_REP.PARA
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 30 Å / Rfactor obs: 0.221
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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