[English] 日本語
Yorodumi
- PDB-2ot8: Karyopherin Beta2/Transportin-hnRNPM NLS Complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ot8
TitleKaryopherin Beta2/Transportin-hnRNPM NLS Complex
Components
  • Heterogeneous nuclear ribonucleoprotein M
  • Transportin-1
KeywordsTRANSPORT PROTEIN / HEAT REPEAT / NUCLEAR IMPORT COMPLEX / KARYOPHERIN
Function / homology
Function and homology information


Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / alternative mRNA splicing, via spliceosome / Intraflagellar transport / paraspeckles / Postmitotic nuclear pore complex (NPC) reformation / FGFR2 alternative splicing / nuclear import signal receptor activity / nuclear localization sequence binding / Processing of Capped Intron-Containing Pre-mRNA / catalytic step 2 spliceosome ...Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / alternative mRNA splicing, via spliceosome / Intraflagellar transport / paraspeckles / Postmitotic nuclear pore complex (NPC) reformation / FGFR2 alternative splicing / nuclear import signal receptor activity / nuclear localization sequence binding / Processing of Capped Intron-Containing Pre-mRNA / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / spliceosomal complex / cilium / small GTPase binding / nuclear matrix / mRNA splicing, via spliceosome / protein import into nucleus / collagen-containing extracellular matrix / protein domain specific binding / mRNA binding / synapse / nucleolus / RNA binding / extracellular exosome / nucleoplasm / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
HnRNP M, nuclear localisation signal / hnRNPM, RNA recognition motif 3 / HnRNP M nuclear localisation signal / Importin beta family / HEAT repeat / HEAT repeat / HEAT-like repeat / Importin-beta N-terminal domain profile. / Importin-beta N-terminal domain / Importin-beta N-terminal domain ...HnRNP M, nuclear localisation signal / hnRNPM, RNA recognition motif 3 / HnRNP M nuclear localisation signal / Importin beta family / HEAT repeat / HEAT repeat / HEAT-like repeat / Importin-beta N-terminal domain profile. / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta, N-terminal domain / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Nucleotide-binding alpha-beta plait domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Heterogeneous nuclear ribonucleoprotein M / Transportin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsCansizoglu, A.E. / Chook, Y.M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2007
Title: Structure-based design of a pathway-specific nuclear import inhibitor.
Authors: Cansizoglu, A.E. / Lee, B.J. / Zhang, Z.C. / Fontoura, B.M. / Chook, Y.M.
History
DepositionFeb 7, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999sequence The central loop region of the sequence (Residues 324-366) was replaced by a GGSGG linker.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transportin-1
B: Transportin-1
C: Heterogeneous nuclear ribonucleoprotein M
D: Heterogeneous nuclear ribonucleoprotein M


Theoretical massNumber of molelcules
Total (without water)200,4914
Polymers200,4914
Non-polymers00
Water00
1
A: Transportin-1
C: Heterogeneous nuclear ribonucleoprotein M


Theoretical massNumber of molelcules
Total (without water)100,2462
Polymers100,2462
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-6 kcal/mol
Surface area36660 Å2
MethodPISA
2
B: Transportin-1
D: Heterogeneous nuclear ribonucleoprotein M


Theoretical massNumber of molelcules
Total (without water)100,2462
Polymers100,2462
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-4 kcal/mol
Surface area37190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.197, 155.001, 141.528
Angle α, β, γ (deg.)90.00, 92.57, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Transportin-1 / Importin beta-2 / Karyopherin beta-2 / M9 region interaction protein / MIP


Mass: 96622.641 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNPO1, KPNB2, MIP1, TRN / Plasmid: pGEX4t3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q92973
#2: Protein/peptide Heterogeneous nuclear ribonucleoprotein M / hnRNP M


Mass: 3623.091 Da / Num. of mol.: 2 / Fragment: hnRNPM NLS fragment (residues 41-70)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HNRPM / Plasmid: pGEX-4t3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P52272

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 4.18 Å3/Da / Density % sol: 70.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM HEPES, 2.7 M potassium formate, 10% glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 18, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 63697 / Redundancy: 3.6 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 20
Reflection shellResolution: 3.1→3.23 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 1.5

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2H4M

2h4m


Resolution: 3.1→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.29 3014 5 %RANDOM
Rwork0.255 ---
obs0.255 59224 98.8 %-
all-59907 --
Displacement parametersBiso mean: 93.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.57 Å0.47 Å
Luzzati sigma a0.79 Å0.65 Å
Refinement stepCycle: LAST / Resolution: 3.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12802 0 0 0 12802
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.19
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.46
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.1→3.21 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.45 259 4.8 %
Rwork0.42 5151 -

+
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://pdbjlvh1.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