[English] 日本語
Yorodumi
- PDB-4b8p: rImp_alpha_A89NLS -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4b8p
TitlerImp_alpha_A89NLS
Components
  • A89NLS
  • IMPORTIN SUBUNIT ALPHA-1A
KeywordsPROTEIN TRANSPORT / NUCLEAR LOCALIZATION SIGNAL
Function / homology
Function and homology information


nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / perinuclear region of cytoplasm / nucleus
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 / Leucine-rich Repeat Variant ...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 / Leucine-rich Repeat Variant / Armadillo/beta-catenin-like repeats / Armadillo / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Importin subunit alpha-1a
Similarity search - Component
Biological speciesORYZA SATIVA JAPONICA GROUP (Japanese rice)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsChang, C.-W. / Counago, R.L.M. / Williams, S.J. / Boden, M. / Kobe, B.
CitationJournal: Plant Cell / Year: 2012
Title: Crystal Structure of Rice Importin-Alpha and Structural Basis of its Interaction with Plant-Specific Nuclear Localization Signals.
Authors: Chang, C.-W. / Counago, R.L.M. / Williams, S.J. / Boden, M. / Kobe, B.
History
DepositionAug 29, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 9, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 20, 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-1A
B: IMPORTIN SUBUNIT ALPHA-1A
C: A89NLS
D: A89NLS


Theoretical massNumber of molelcules
Total (without water)109,0934
Polymers109,0934
Non-polymers00
Water3,963220
1
A: IMPORTIN SUBUNIT ALPHA-1A
C: A89NLS


Theoretical massNumber of molelcules
Total (without water)54,5472
Polymers54,5472
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-0.2 kcal/mol
Surface area18440 Å2
MethodPISA
2
B: IMPORTIN SUBUNIT ALPHA-1A
D: A89NLS


Theoretical massNumber of molelcules
Total (without water)54,5472
Polymers54,5472
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-0.5 kcal/mol
Surface area18520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.425, 140.967, 73.167
Angle α, β, γ (deg.)90.00, 89.98, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein IMPORTIN SUBUNIT ALPHA-1A


Mass: 53026.848 Da / Num. of mol.: 2 / Fragment: NLS BINDING DOMAIN, RESIDUES 73-526
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ORYZA SATIVA JAPONICA GROUP (Japanese rice)
Plasmid: PET30A_RIMPALPHA1A_DIBB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q71VM4
#2: Protein/peptide A89NLS


Mass: 1519.854 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Plasmid: PGEX2T-A89NLS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 2.95 Å3/Da / Density % sol: 58.29 % / Description: NONE
Crystal growpH: 7
Details: 0.1 M BIS-TRIS PROPANE PH 7.0, 15% PEG 3350, 0.2 M NDSB-221 AND 0.2 M NAF

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.5
ReflectionResolution: 2.3→19.82 Å / Num. obs: 55804 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 4.5
Reflection shellResolution: 2.3→19.82 Å / Redundancy: 3 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2 / % possible all: 98.7

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8_1069)refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EE4

1ee4


Resolution: 2.3→19.818 Å / σ(F): 1.38 / Phase error: 20.6 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2038 2848 5.1 %
Rwork0.1888 --
obs0.1896 55640 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→19.818 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6560 0 0 220 6780
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096668
X-RAY DIFFRACTIONf_angle_d1.1459072
X-RAY DIFFRACTIONf_dihedral_angle_d14.0092460
X-RAY DIFFRACTIONf_chiral_restr0.0661088
X-RAY DIFFRACTIONf_plane_restr0.0061170
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.33960.26981440.27332588X-RAY DIFFRACTION93
2.3396-2.38210.23881190.26382589X-RAY DIFFRACTION94
2.3821-2.42780.31541350.25272572X-RAY DIFFRACTION93
2.4278-2.47730.26911360.25372645X-RAY DIFFRACTION94
2.4773-2.5310.2881330.24992659X-RAY DIFFRACTION94
2.531-2.58980.28761390.24212603X-RAY DIFFRACTION94
2.5898-2.65440.25571460.23682613X-RAY DIFFRACTION94
2.6544-2.72590.21221470.22342644X-RAY DIFFRACTION94
2.7259-2.80590.2281530.22042614X-RAY DIFFRACTION94
2.8059-2.89620.22941220.21772668X-RAY DIFFRACTION95
2.8962-2.99930.23631450.22022671X-RAY DIFFRACTION95
2.9993-3.1190.21121330.2142647X-RAY DIFFRACTION95
3.119-3.26020.23851570.21042609X-RAY DIFFRACTION94
3.2602-3.43120.23571380.20422664X-RAY DIFFRACTION95
3.4312-3.64480.1771660.18542637X-RAY DIFFRACTION94
3.6448-3.92410.17911360.16192660X-RAY DIFFRACTION95
3.9241-4.31490.15891470.14042670X-RAY DIFFRACTION95
4.3149-4.93010.18341380.13372662X-RAY DIFFRACTION95
4.9301-6.17690.17051600.16282663X-RAY DIFFRACTION94
6.1769-19.22160.14981370.13932721X-RAY DIFFRACTION95

+
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