[English] 日本語
Yorodumi
- PDB-2z5j: Free Transportin 1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2z5j
TitleFree Transportin 1
ComponentsTransportin-1
KeywordsTRANSPORT PROTEIN / nuclear transport / importin / exportin / karyopherin / nucleocytoplasmic
Function / homology
Function and homology information


Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Intraflagellar transport / Postmitotic nuclear pore complex (NPC) reformation / nuclear import signal receptor activity / nuclear localization sequence binding / cilium / small GTPase binding / protein import into nucleus / RNA binding / extracellular exosome ...Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Intraflagellar transport / Postmitotic nuclear pore complex (NPC) reformation / nuclear import signal receptor activity / nuclear localization sequence binding / cilium / small GTPase binding / protein import into nucleus / RNA binding / extracellular exosome / nucleus / cytosol / cytoplasm
Similarity search - Function
Importin beta family / HEAT-like repeat / HEAT repeat / HEAT 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 ...Importin beta family / HEAT-like repeat / HEAT repeat / HEAT 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 / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsImasaki, T. / Shimizu, T. / Hashimoto, H. / Hidaka, Y. / Yamada, M. / Sato, M.
CitationJournal: Mol.Cell / Year: 2007
Title: Structural basis for substrate recognition and dissociation by human transportin 1
Authors: Imasaki, T. / Shimizu, T. / Hashimoto, H. / Hidaka, Y. / Kose, S. / Imamoto, N. / Yamada, M. / Sato, M.
History
DepositionJul 13, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 23, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transportin-1


Theoretical massNumber of molelcules
Total (without water)101,4081
Polymers101,4081
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.467, 107.467, 194.772
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

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


Mass: 101408.438 Da / Num. of mol.: 1 / Fragment: Transportin 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX6P3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q92973
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.64 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 9.8
Details: 6% PEG 8000, 0.1M sodium dihidrogen phosphate, 0.1M CAPSO pH 9.8, 0.04M spermidine, VAPOR DIFFUSION, HANGING DROP, temperature 300K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 9, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.4→94 Å / Num. all: 15598 / Num. obs: 14806 / % possible obs: 94.8 % / Rmerge(I) obs: 0.085
Reflection shellResolution: 3.4→3.52 Å / Rmerge(I) obs: 0.374 / Mean I/σ(I) obs: 1.7 / % possible all: 72.2

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QBK

1qbk


Resolution: 3.4→49.36 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.871 / SU B: 94.867 / SU ML: 0.648 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.714 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30301 778 5 %RANDOM
Rwork0.23226 ---
obs0.2358 14806 95.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 127.231 Å2
Baniso -1Baniso -2Baniso -3
1-1.29 Å20 Å20 Å2
2--1.29 Å20 Å2
3----2.57 Å2
Refinement stepCycle: LAST / Resolution: 3.4→49.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6652 0 0 0 6652
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0226796
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1331.9779232
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1415833
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.29125.18305
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.613151220
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0011531
X-RAY DIFFRACTIONr_chiral_restr0.0740.21060
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025073
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2440.23936
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.24794
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2286
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.259
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.040.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2441.54272
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.44626813
X-RAY DIFFRACTIONr_scbond_it0.45732798
X-RAY DIFFRACTIONr_scangle_it0.7984.52419
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.398→3.486 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.479 33 -
Rwork0.439 785 -
obs--69.74 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
112.9262-3.396-2.67590.89240.74548.38510.4709-0.89221.51930.61610.19560.2022-1.5407-0.164-0.66650.0949-0.06050.2848-0.2647-0.30380.1193-30.469460.96586.5742
210.8061-1.69140.68287.5445-0.23639.32620.5448-0.16230.7031-0.1625-0.29970.25920.0686-0.1463-0.2451-0.49750.13530.1284-0.6536-0.0926-0.5712-28.81953.1632-5.9957
32.78380.0171-1.98876.5334-2.44573.2951-0.41820.0042-0.716-0.37310.2619-0.02540.7536-0.03730.1563-0.3149-0.07120.0389-0.4287-0.0494-0.4842-22.906926.3949-16.103
45.45130.0809-1.84221.64790.18052.21590.0766-0.8482-0.80470.1563-0.0883-0.44380.07720.17270.0117-0.2258-0.0878-0.1919-0.38630.3744-0.1627-42.70345.832511.5875
52.50511.52820.60687.37362.36812.7147-0.0725-0.0507-0.2948-0.0082-0.0086-0.0840.34960.03250.0812-0.68970.0340.0864-0.47260.1789-0.6786-73.1475-0.3185-7.6027
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA5 - 575 - 57
2X-RAY DIFFRACTION2AA58 - 12558 - 125
3X-RAY DIFFRACTION3AA126 - 319126 - 319
4X-RAY DIFFRACTION4AA371 - 603371 - 603
5X-RAY DIFFRACTION5AA604 - 890604 - 890

+
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