[English] 日本語
Yorodumi
- PDB-3ukz: Mouse importin alpha: mouse CBP80 cNLS complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ukz
TitleMouse importin alpha: mouse CBP80 cNLS complex
Components
  • Importin subunit alpha-2
  • Nuclear cap-binding protein subunit 1
KeywordsPROTEIN TRANSPORT/PROTEIN BINDING / Arm repeat / Armadillo repeat / nuclear transport / nuclear localisation signal binding / importin beta binding / PROTEIN TRANSPORT-PROTEIN BINDING complex
Function / homology
Function and homology information


Formation of the Early Elongation Complex / SLBP independent Processing of Histone Pre-mRNAs / FGFR2 alternative splicing / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / Processing of Intronless Pre-mRNAs / Formation of RNA Pol II elongation complex / RNA polymerase II transcribes snRNA genes / mRNA Capping / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase II Pre-transcription Events ...Formation of the Early Elongation Complex / SLBP independent Processing of Histone Pre-mRNAs / FGFR2 alternative splicing / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / Processing of Intronless Pre-mRNAs / Formation of RNA Pol II elongation complex / RNA polymerase II transcribes snRNA genes / mRNA Capping / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase II Pre-transcription Events / mRNA Splicing - Minor Pathway / mRNA 3'-end processing / RNA Polymerase II Transcription Termination / Transport of Mature mRNA derived from an Intron-Containing Transcript / snRNA export from nucleus / nuclear cap binding complex / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / mRNA metabolic process / RNA cap binding complex / histone mRNA metabolic process / mRNA Splicing - Major Pathway / positive regulation of mRNA 3'-end processing / cap-dependent translational initiation / : / RNA cap binding / alternative mRNA splicing, via spliceosome / Sensing of DNA Double Strand Breaks / entry of viral genome into host nucleus through nuclear pore complex via importin / regulation of mRNA processing / miRNA-mediated post-transcriptional gene silencing / primary miRNA processing / regulatory ncRNA-mediated post-transcriptional gene silencing / positive regulation of viral life cycle / mRNA 3'-end processing / RNA 7-methylguanosine cap binding / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / positive regulation of mRNA splicing, via spliceosome / RNA catabolic process / regulation of translational initiation / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / spliceosomal complex assembly / 7-methylguanosine mRNA capping / mRNA export from nucleus / host cell / positive regulation of transcription elongation by RNA polymerase II / mRNA transcription by RNA polymerase II / mRNA splicing, via spliceosome / cytoplasmic stress granule / protein import into nucleus / positive regulation of cell growth / DNA-binding transcription factor binding / defense response to virus / postsynaptic density / molecular adaptor activity / ribonucleoprotein complex / mRNA binding / glutamatergic synapse / mitochondrion / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
MIF4G-like, type 1 / MIF4G-like, type 2 / Nuclear cap-binding protein subunit 1 / MIF4G like / MIF4G like / MIF4G domain / Middle domain of eukaryotic initiation factor 4G (eIF4G) / MIF4G-like, type 3 / Importin subunit alpha / Atypical Arm repeat ...MIF4G-like, type 1 / MIF4G-like, type 2 / Nuclear cap-binding protein subunit 1 / MIF4G like / MIF4G like / MIF4G domain / Middle domain of eukaryotic initiation factor 4G (eIF4G) / MIF4G-like, type 3 / 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 / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Importin subunit alpha-1 / Nuclear cap-binding protein subunit 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMarfori, M. / Forwood, J.K. / Lonhienne, T.G. / Kobe, B.
CitationJournal: Traffic / Year: 2012
Title: Structural Basis of High-Affinity Nuclear Localization Signal Interactions with Importin-alpha
Authors: Marfori, M. / Lonhienne, T.G. / Forwood, J.K. / Kobe, B.
History
DepositionNov 10, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Importin subunit alpha-2
C: Nuclear cap-binding protein subunit 1


Theoretical massNumber of molelcules
Total (without water)58,2212
Polymers58,2212
Non-polymers00
Water5,531307
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint6 kcal/mol
Surface area18950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.943, 90.023, 100.497
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Importin subunit alpha-2 / / Importin alpha P1 / Karyopherin subunit alpha-2 / Pendulin / Pore targeting complex 58 kDa subunit ...Importin alpha P1 / Karyopherin subunit alpha-2 / Pendulin / Pore targeting complex 58 kDa subunit / PTAC58 / RAG cohort protein 1 / SRP1-alpha


Mass: 55268.473 Da / Num. of mol.: 1 / Fragment: UNP Residues 70-529
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kpna2 / Production host: Escherichia coli (E. coli) / References: UniProt: P52293
#2: Protein/peptide Nuclear cap-binding protein subunit 1 / Cap-binding protein 80 / CBP80


Mass: 2952.213 Da / Num. of mol.: 1 / Fragment: mCBP80 cNLS peptide, residues 1-23
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cbp80 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3UYV9
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 307 / 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: 3.07 Å3/Da / Density % sol: 59.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.82M sodium citrate, 10mM DTT, 0.1M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.953693 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 23, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953693 Å / Relative weight: 1
ReflectionResolution: 2.3→44.99 Å / Num. obs: 32538 / % possible obs: 72.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1

-
Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIX(phenix.refine: 1.7_650)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PJN

1pjn


Resolution: 2.3→42.39 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.29 / Phase error: 17.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.208 1603 5.04 %RANDOM
Rwork0.1763 ---
obs0.1778 31818 97.95 %-
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 28.887 Å2 / ksol: 0.358 e/Å3
Displacement parametersBiso max: 125.92 Å2 / Biso mean: 27.8817 Å2 / Biso min: 5.55 Å2
Baniso -1Baniso -2Baniso -3
1--0.7519 Å2-0 Å20 Å2
2---2.6499 Å2-0 Å2
3---3.4018 Å2
Refinement stepCycle: LAST / Resolution: 2.3→42.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3448 0 0 307 3755
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053509
X-RAY DIFFRACTIONf_angle_d0.7844772
X-RAY DIFFRACTIONf_chiral_restr0.052567
X-RAY DIFFRACTIONf_plane_restr0.004614
X-RAY DIFFRACTIONf_dihedral_angle_d13.4011294
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3001-2.37440.28821270.21932626275395
2.3744-2.45920.24111640.19632644280896
2.4592-2.55770.21791380.17892665280397
2.5577-2.6740.22791400.17152678281897
2.674-2.8150.20741510.17492734288598
2.815-2.99130.2191340.17082757289199
2.9913-3.22220.22321510.1752754290599
3.2222-3.54630.20341410.17612794293599
3.5463-4.05910.19541560.17592739289598
4.0591-5.11270.15841440.148428563000100
5.1127-42.3970.21081570.19022968312599
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)
10.00920.0043-0.00560.0055-0.00570.0064-0.0079-0.0122-0.00620.0336-0.01920.04060.008-0.0160.01120.3418-0.0843-0.01540.19090.00280.2259-1.6618-16.6368-15.1276
20.04270.0103-0.00060.0081-0.00480.05080.073-0.0249-0.06340.0451-0.0143-0.00710.04050.01470.06070.1407-0.0233-0.11590.0212-0.0681-0.00896.4417-10.027-16.8068
30.016-0.0134-0.00210.01540.0038-0.00060.0498-0.01090.0124-0.0337-0.00560.00240.02170.01180.03940.11430.0019-0.0360.0684-0.02330.02767.89534.9544-15.2447
40.2916-0.0334-0.02220.19370.02160.24070.0666-0.0192-0.0069-0.09940.03460.06360.0208-0.00940.03080.08390.0007-0.02040.0790.01780.08812.492417.251-16.7094
50.0187-0.0272-0.04820.1312-0.00090.18150.0698-0.01970.163-0.07830.0484-0.0911-0.0335-0.0115-0.01110.0501-0.00310.01590.0723-0.01450.1194-2.238727.6859-8.3256
60.14190.04990.16750.04870.0370.23730.0922-0.0880.1251-0.06050.0381-0.1119-0.02660.02160.02630.06430.00940.0460.0615-0.03460.1458-10.80935.07986.6389
70.0159-0.024-0.00470.03830.00680.00250.0216-0.04090.0528-0.00140.0278-0.0461-0.02240.05930.02520.1079-0.01570.00680.1531-0.18310.1639-9.815139.327318.0379
80.02430.00560.00890.00620.01130.02020.0116-0.02470.01050.00930.0072-0.01290.02910.0267-0.0070.21170.0048-0.080.3247-0.15980.2392-4.319635.67125.1705
90.00060.003-0.00380.0142-0.00040.01950.005-0.08460.04730.05760.0349-0.02280.0669-0.0117-0.01830.542-0.03420.00070.6316-0.20920.287-12.442544.995631.1963
100.0541-0.0038-0.0260.005-0.0060.0266-0.0095-0.04730.01150.0436-0.0273-0.00970.00840.0296-0.00030.54940.0759-0.22980.8249-0.1620.4137-0.523636.582135.1183
110.0199-0.0113-0.02180.00640.01250.0241-0.0021-0.00540.00150.009-0.0058-0.00230.00730.00740.00140.37670.0558-0.03870.4373-0.07080.38942.9229.17798.1759
120.0167-0.0126-0.00150.0338-0.00210.00060.0001-0.00080.0073-0.0023-0.01-0.00610.0026-0.00640.00170.21650.0588-0.00420.1876-0.00810.14213.196919.59897.0999
130.0193-0.0097-0.02270.05830.05380.06190.0011-0.0113-0.00650.00360.01060.0018-0.00140.0077-0.00450.10290.0071-0.01580.0827-0.02010.0952-0.659910.6668-4.1978
140.06660.01840.02230.02790.01040.0456-0.00070.02210.0032-0.0051-0.00070.0091-0.010.00660.00120.138-0.0235-0.00170.1829-0.00330.1094-5.0485-0.5647-13.2068
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain B and resid 71:78)B71 - 78
2X-RAY DIFFRACTION2(chain B and resid 79:135)B79 - 135
3X-RAY DIFFRACTION3(chain B and resid 136:202)B136 - 202
4X-RAY DIFFRACTION4(chain B and resid 203:246)B203 - 246
5X-RAY DIFFRACTION5(chain B and resid 247:327)B247 - 327
6X-RAY DIFFRACTION6(chain B and resid 328:391)B328 - 391
7X-RAY DIFFRACTION7(chain B and resid 392:427)B392 - 427
8X-RAY DIFFRACTION8(chain B and resid 428:451)B428 - 451
9X-RAY DIFFRACTION9(chain B and resid 452:472)B452 - 472
10X-RAY DIFFRACTION10(chain B and resid 473:497)B473 - 497
11X-RAY DIFFRACTION11(chain C and resid 2:6)C2 - 6
12X-RAY DIFFRACTION12(chain C and resid 7:11)C7 - 11
13X-RAY DIFFRACTION13(chain C and resid 12:18)C12 - 18
14X-RAY DIFFRACTION14(chain C and resid 19:23)C19 - 23

+
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