[English] 日本語
Yorodumi
- PDB-1pjm: Mouse Importin alpha-bipartite NLS from human retinoblastoma prot... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1pjm
TitleMouse Importin alpha-bipartite NLS from human retinoblastoma protein Complex
Components
  • Importin alpha-2 subunit
  • Retinoblastoma-associated protein
KeywordsPROTEIN TRANSPORT / IMPORTIN ALPHA/KARYOPHERIN ALPHA / NUCLEAR LOCALIZATION SEQUENCE (NLS) RECOGNITION / BIPARTITE NLS / HUMAN RETINOBLASTOMA PROTEIN
Function / homology
Function and homology information


Defective translocation of RB1 mutants to the nucleus / enucleate erythrocyte differentiation / Rb-E2F complex / regulation of lipid kinase activity / positive regulation of collagen fibril organization / negative regulation of myofibroblast differentiation / maintenance of mitotic sister chromatid cohesion / chromatin lock complex / cell morphogenesis involved in neuron differentiation / sister chromatid biorientation ...Defective translocation of RB1 mutants to the nucleus / enucleate erythrocyte differentiation / Rb-E2F complex / regulation of lipid kinase activity / positive regulation of collagen fibril organization / negative regulation of myofibroblast differentiation / maintenance of mitotic sister chromatid cohesion / chromatin lock complex / cell morphogenesis involved in neuron differentiation / sister chromatid biorientation / positive regulation of transcription regulatory region DNA binding / Aberrant regulation of mitotic exit in cancer due to RB1 defects / Sensing of DNA Double Strand Breaks / positive regulation of extracellular matrix organization / : / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / entry of viral genome into host nucleus through nuclear pore complex via importin / glial cell apoptotic process / positive regulation of macrophage differentiation / negative regulation of hepatocyte apoptotic process / positive regulation of viral life cycle / tissue homeostasis / protein localization to chromosome, centromeric region / positive regulation of mitotic metaphase/anaphase transition / importin-alpha family protein binding / NLS-dependent protein nuclear import complex / neuron maturation / postsynapse to nucleus signaling pathway / myoblast differentiation / digestive tract development / Replication of the SARS-CoV-1 genome / aortic valve morphogenesis / nuclear import signal receptor activity / negative regulation of cold-induced thermogenesis / SWI/SNF complex / negative regulation of glial cell proliferation / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / smoothened signaling pathway / hepatocyte apoptotic process / negative regulation of G1/S transition of mitotic cell cycle / Phosphorylation of proteins involved in G1/S transition by active Cyclin E:Cdk2 complexes / RUNX2 regulates osteoblast differentiation / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / negative regulation of cell cycle / negative regulation of apoptotic signaling pathway / skeletal muscle cell differentiation / chondrocyte differentiation / chromosome organization / negative regulation of DNA-binding transcription factor activity / glial cell proliferation / Cyclin E associated events during G1/S transition / negative regulation of protein kinase activity / Cyclin A:Cdk2-associated events at S phase entry / Nuclear events stimulated by ALK signaling in cancer / striated muscle cell differentiation / regulation of mitotic cell cycle / Condensation of Prophase Chromosomes / epithelial cell proliferation / negative regulation of smoothened signaling pathway / RNA polymerase II transcription regulatory region sequence-specific DNA binding / phosphoprotein binding / G1/S transition of mitotic cell cycle / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / negative regulation of cell growth / PML body / Oncogene Induced Senescence / negative regulation of inflammatory response / kinase binding / cellular response to xenobiotic stimulus / spindle / cellular response to insulin stimulus / neuron projection development / protein import into nucleus / cytoplasmic stress granule / negative regulation of epithelial cell proliferation / disordered domain specific binding / Cyclin D associated events in G1 / transcription corepressor activity / heterochromatin formation / host cell / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Replication of the SARS-CoV-2 genome / neuron apoptotic process / spermatogenesis / DNA-binding transcription factor binding / molecular adaptor activity / RNA polymerase II-specific DNA-binding transcription factor binding / Ras protein signal transduction / transcription by RNA polymerase II / cell differentiation / regulation of cell cycle / postsynaptic density / chromatin remodeling / negative regulation of gene expression / cell division / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / regulation of DNA-templated transcription / chromatin / glutamatergic synapse
Similarity search - Function
Rb C-terminal domain / Retinoblastoma-associated protein, B-box / Retinoblastoma-associated protein, A-box / Retinoblastoma-associated protein, C-terminal / Retinoblastoma-associated protein, N-terminal / Retinoblastoma protein family / Retinoblastoma-associated protein B domain / Retinoblastoma-associated protein A domain / Domain of unknown function (DUF3452) / Domain of unknown function (DUF3452) ...Rb C-terminal domain / Retinoblastoma-associated protein, B-box / Retinoblastoma-associated protein, A-box / Retinoblastoma-associated protein, C-terminal / Retinoblastoma-associated protein, N-terminal / Retinoblastoma protein family / Retinoblastoma-associated protein B domain / Retinoblastoma-associated protein A domain / Domain of unknown function (DUF3452) / Domain of unknown function (DUF3452) / Retinoblastoma-associated protein A domain / Rb C-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. / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Retinoblastoma-associated protein / Importin subunit alpha-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.5 Å
AuthorsFontes, M.R.M. / Teh, T. / Jans, D. / Brinkworth, R.I. / Kobe, B.
Citation
Journal: J.Biol.Chem. / Year: 2003
Title: Structural basis for the specificity of bipartite nuclear localization sequence binding by importin-alpha
Authors: Fontes, M.R.M. / Teh, T. / Jans, D. / Brinkworth, R.I. / Kobe, B.
#1: Journal: J.Mol.Biol. / Year: 2000
Title: Structural basis of recognition of monopartite and bipartite nuclear localization sequences by mammalian importin-alpha
Authors: Fontes, M.R.M. / Teh, T. / Kobe, B.
#2: Journal: J.Biol.Chem. / Year: 2001
Title: Biophysical Characterization of Interactions Involving Impostin-alpha during Nuclear Import
Authors: Catimel, B. / Teh, T. / Fontes, M.R.M. / Jennings, I.G. / Jans, D. / Howlett, G.J. / Nice, E.C. / Kobe, B.
#3: Journal: Nat.Struct.Biol. / Year: 1999
Title: Autoinhibition by an internal nuclear localization signal reveled by the crystal structure of mammalian importin alpha
Authors: Kobe, B.
History
DepositionJun 3, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 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 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Retinoblastoma-associated protein
B: Importin alpha-2 subunit


Theoretical massNumber of molelcules
Total (without water)52,0162
Polymers52,0162
Non-polymers00
Water3,117173
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-1 kcal/mol
Surface area18710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.000, 89.179, 100.992
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein/peptide Retinoblastoma-associated protein


Mass: 2129.530 Da / Num. of mol.: 1
Fragment: NLS (nuclear localization signal) bipartite peptide
Source method: obtained synthetically
Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THIS PEPTIDE IS NATURALLY FOUND IN HUMAN RETINOBLASTOMA PROTEIN
References: UniProt: P06400
#2: Protein Importin alpha-2 subunit / Karyopherin alpha-2 subunit


Mass: 49886.633 Da / Num. of mol.: 1 / Fragment: NLS binding domain (70-529)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: KPNA2 OR RCH1 / Plasmid: PET30A / Production host: Escherichia coli (E. coli) / References: UniProt: P52293
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 3.42 Å3/Da / Density % sol: 64.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Sodium Citrate, DTT, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11.7 mg/mlprotein1drop
20.6 Msodium citrate1reservoirpH6.0
310 mMdithiothreitol1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 10, 2000
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→99 Å / Num. all: 25382 / Num. obs: 25382 / % possible obs: 96 % / Observed criterion σ(I): -3 / Redundancy: 9.8 % / Biso Wilson estimate: 53.2 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 19
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.403 / Mean I/σ(I) obs: 2.8 / % possible all: 98.3
Reflection
*PLUS
% possible obs: 96 % / Num. measured all: 249870
Reflection shell
*PLUS
% possible obs: 98.3 %

-
Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY: 1ial

1ial


Resolution: 2.5→29.57 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.239 1169 4.8 %RANDOM
Rwork0.204 ---
obs0.204 24323 96 %-
all-24323 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.52 Å2 / ksol: 0.363607 e/Å3
Displacement parametersBiso mean: 46.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å20 Å20 Å2
2---6.09 Å20 Å2
3---6.69 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.5→29.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3400 0 0 173 3573
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_d18.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.94
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.111.5
X-RAY DIFFRACTIONc_mcangle_it1.852
X-RAY DIFFRACTIONc_scbond_it1.742
X-RAY DIFFRACTIONc_scangle_it2.552.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.299 198 4.9 %
Rwork0.264 3877 -
obs-4075 98.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 30 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.94
LS refinement shell
*PLUS
Highest resolution: 2.5 Å / Rfactor Rfree: 0.292 / Rfactor Rwork: 0.263

+
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