[English] 日本語
Yorodumi
- PDB-1ee4: CRYSTAL STRUCTURE OF YEAST KARYOPHERIN (IMPORTIN) ALPHA IN A COMP... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ee4
TitleCRYSTAL STRUCTURE OF YEAST KARYOPHERIN (IMPORTIN) ALPHA IN A COMPLEX WITH A C-MYC NLS PEPTIDE
Components
  • KARYOPHERIN ALPHA
  • MYC PROTO-ONCOGENE PROTEIN
KeywordsTRANSPORT PROTEIN / ARM repeat
Function / homology
Function and homology information


proteasome localization / positive regulation of metanephric cap mesenchymal cell proliferation / positive regulation of acinar cell proliferation / acinar cell proliferation / negative regulation of transcription initiation by RNA polymerase II / SCF ubiquitin ligase complex binding / NK T cell proliferation / Myc-Max complex / regulation of somatic stem cell population maintenance / regulation of cell cycle process ...proteasome localization / positive regulation of metanephric cap mesenchymal cell proliferation / positive regulation of acinar cell proliferation / acinar cell proliferation / negative regulation of transcription initiation by RNA polymerase II / SCF ubiquitin ligase complex binding / NK T cell proliferation / Myc-Max complex / regulation of somatic stem cell population maintenance / regulation of cell cycle process / Binding of TCF/LEF:CTNNB1 to target gene promoters / cellular response to interferon-alpha / RNA polymerase II transcription repressor complex / myotube differentiation / positive regulation of B cell apoptotic process / RUNX3 regulates WNT signaling / TFAP2 (AP-2) family regulates transcription of cell cycle factors / negative regulation of cell division / import into nucleus / negative regulation of monocyte differentiation / detection of mechanical stimulus involved in sensory perception of sound / response to growth factor / response to alkaloid / NLS-dependent protein nuclear import complex / B cell apoptotic process / NLS-bearing protein import into nucleus / transcription regulator activator activity / nuclear localization sequence binding / protein-DNA complex disassembly / Transcription of E2F targets under negative control by DREAM complex / negative regulation of stress-activated MAPK cascade / fibroblast apoptotic process / Regulation of NFE2L2 gene expression / nuclear import signal receptor activity / protein targeting to membrane / positive regulation of mesenchymal cell proliferation / regulation of telomere maintenance / middle ear morphogenesis / skeletal system morphogenesis / Signaling by ALK / branching involved in ureteric bud morphogenesis / negative regulation of gene expression via chromosomal CpG island methylation / pigmentation / rRNA metabolic process / positive regulation of telomere maintenance / E-box binding / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / skeletal muscle cell differentiation / positive regulation of transcription initiation by RNA polymerase II / chromosome organization / negative regulation of fibroblast proliferation / core promoter sequence-specific DNA binding / Cyclin E associated events during G1/S transition / Cyclin A:Cdk2-associated events at S phase entry / ERK1 and ERK2 cascade / positive regulation of epithelial cell proliferation / transcription coregulator binding / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / G1/S transition of mitotic cell cycle / euchromatin / MAPK6/MAPK4 signaling / protein processing / NOTCH1 Intracellular Domain Regulates Transcription / positive regulation of miRNA transcription / DNA-binding transcription repressor activity, RNA polymerase II-specific / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / spindle / cellular response to xenobiotic stimulus / Wnt signaling pathway / Transcriptional regulation of granulopoiesis / positive regulation of fibroblast proliferation / intrinsic apoptotic signaling pathway in response to DNA damage / protein import into nucleus / disordered domain specific binding / cellular response to UV / nuclear envelope / MAPK cascade / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / Interleukin-4 and Interleukin-13 signaling / cellular response to hypoxia / DNA-binding transcription factor binding / Estrogen-dependent gene expression / intracellular iron ion homeostasis / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / protein dimerization activity / Ub-specific processing proteases / nuclear body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin remodeling / response to xenobiotic stimulus / axon / positive regulation of cell population proliferation / DNA damage response / ubiquitin protein ligase binding / positive regulation of gene expression / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process
Similarity search - Function
Leucine zipper, Myc / Myc leucine zipper domain / Transcription regulator Myc / Transcription regulator Myc, N-terminal / : / Myc amino-terminal region / Importin subunit alpha / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain superfamily / Importin beta binding domain ...Leucine zipper, Myc / Myc leucine zipper domain / Transcription regulator Myc / Transcription regulator Myc, N-terminal / : / Myc amino-terminal region / 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. / Helix-loop-helix DNA-binding domain / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Myc proto-oncogene protein / Importin subunit alpha
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsConti, E.
CitationJournal: Structure Fold.Des. / Year: 2000
Title: Crystallographic analysis of the specific yet versatile recognition of distinct nuclear localization signals by karyopherin alpha.
Authors: Conti, E. / Kuriyan, J.
History
DepositionJan 30, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: KARYOPHERIN ALPHA
C: MYC PROTO-ONCOGENE PROTEIN
D: MYC PROTO-ONCOGENE PROTEIN
B: KARYOPHERIN ALPHA
E: MYC PROTO-ONCOGENE PROTEIN
F: MYC PROTO-ONCOGENE PROTEIN


Theoretical massNumber of molelcules
Total (without water)97,7426
Polymers97,7426
Non-polymers00
Water5,405300
1
A: KARYOPHERIN ALPHA
C: MYC PROTO-ONCOGENE PROTEIN
D: MYC PROTO-ONCOGENE PROTEIN


Theoretical massNumber of molelcules
Total (without water)48,8713
Polymers48,8713
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: KARYOPHERIN ALPHA
E: MYC PROTO-ONCOGENE PROTEIN
F: MYC PROTO-ONCOGENE PROTEIN


Theoretical massNumber of molelcules
Total (without water)48,8713
Polymers48,8713
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.680, 85.850, 117.500
Angle α, β, γ (deg.)90.00, 93.42, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein KARYOPHERIN ALPHA / SERINE-RICH RNA POLYMERASE I SUPPRESSOR PROTEIN


Mass: 46870.527 Da / Num. of mol.: 2 / Fragment: ARMADILLO DOMAIN / Mutation: Y397D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: Q02821
#2: Protein/peptide
MYC PROTO-ONCOGENE PROTEIN


Mass: 1000.215 Da / Num. of mol.: 4
Fragment: NLS (NUCLEAR LOCALIZATION SIGNAL) AT THE LARGER (FUNCTIONAL) BINDING SITE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P01106
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 300
Fragment: NLS (NUCLEAR LOCALIZATION SIGNAL) AT THE SMALLER BINDING SITE
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: 2.2 Å3/Da / Density % sol: 44.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal
*PLUS
Density % sol: 43 %
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
2100 mMTris-HCl1reservoir
3200 mMsodium acetate1reservoir
430 %(w/v)PEG40001reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 47949 / % possible obs: 96.9 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 15.8
Reflection shellResolution: 2.1→30 Å
Reflection
*PLUS
Lowest resolution: 30 Å / Num. obs: 47949 / Num. measured all: 152954
Reflection shell
*PLUS
% possible obs: 96.9 % / Rmerge(I) obs: 0.213 / Mean I/σ(I) obs: 6.6

-
Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.1→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh and Huber /
RfactorSelection details
Rfree0.277 random 5%
Rwork0.246 -
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6691 0 0 300 6991
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_angle_deg1.74
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.246
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