[English] 日本語
Yorodumi
- PDB-4c31: Nup1:Sac3:Sus1 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4c31
TitleNup1:Sac3:Sus1 complex
Components
  • NUCLEAR MRNA EXPORT PROTEIN SAC3
  • NUCLEOPORIN NUP1
  • PROTEIN SUS1
KeywordsTRANSPORT PROTEIN / NUCLEAR TRANSPORT / MRNA EXPORT / GENE EXPRESSION PATHWAY INTEGRATION / NUCLEAR PORE
Function / homology
Function and homology information


actin filament-based process / DUBm complex / nuclear pore central transport channel / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / transcription export complex 2 / Transport of Mature mRNA derived from an Intron-Containing Transcript / nuclear pore cytoplasmic filaments / Regulation of HSF1-mediated heat shock response / nuclear mRNA surveillance / SLIK (SAGA-like) complex ...actin filament-based process / DUBm complex / nuclear pore central transport channel / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / transcription export complex 2 / Transport of Mature mRNA derived from an Intron-Containing Transcript / nuclear pore cytoplasmic filaments / Regulation of HSF1-mediated heat shock response / nuclear mRNA surveillance / SLIK (SAGA-like) complex / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore nuclear basket / SUMOylation of SUMOylation proteins / NLS-bearing protein import into nucleus / nuclear localization sequence binding / structural constituent of nuclear pore / mRNA 3'-end processing / SUMOylation of RNA binding proteins / RNA export from nucleus / SUMOylation of chromatin organization proteins / SAGA complex / nucleocytoplasmic transport / poly(A)+ mRNA export from nucleus / ribosomal large subunit export from nucleus / nuclear pore / mRNA export from nucleus / transcription-coupled nucleotide-excision repair / protein export from nucleus / transcription elongation by RNA polymerase II / enzyme activator activity / P-body / protein import into nucleus / nuclear envelope / mitotic cell cycle / protein transport / regulation of protein localization / chromatin organization / ribosomal small subunit biogenesis / nuclear membrane / molecular adaptor activity / transcription coactivator activity / chromatin binding / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Nuclear mRNA export protein Sac3 / SAC3 helical domain / Leucine permease transcriptional regulator helical domain / ENY2/SUS1 / Transcription factor, enhancer of yellow 2 / Transcription factor EnY2 superfamily / Transcription factor e(y)2 / SAC3/GANP/THP3, conserved domain / SAC3/GANP/THP3 / SAC3/GANP family ...Nuclear mRNA export protein Sac3 / SAC3 helical domain / Leucine permease transcriptional regulator helical domain / ENY2/SUS1 / Transcription factor, enhancer of yellow 2 / Transcription factor EnY2 superfamily / Transcription factor e(y)2 / SAC3/GANP/THP3, conserved domain / SAC3/GANP/THP3 / SAC3/GANP family / Serum Albumin; Chain A, Domain 1 / Proteasome component (PCI) domain / PCI domain profile. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Nucleoporin NUP1 / Nuclear mRNA export protein SAC3 / SAGA complex subunit SUS1
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsStewart, M. / Jani, D.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: Structural Basis for Binding the Trex2 Complex to Nuclear Pores, Gal1 Localisation and Mrna Export.
Authors: Jani, D. / Valkov, E. / Stewart, M.
History
DepositionAug 21, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 25, 2014Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NUCLEAR MRNA EXPORT PROTEIN SAC3
B: PROTEIN SUS1
C: NUCLEOPORIN NUP1
D: NUCLEAR MRNA EXPORT PROTEIN SAC3
E: PROTEIN SUS1
F: NUCLEOPORIN NUP1
X: NUCLEOPORIN NUP1
Y: NUCLEOPORIN NUP1


Theoretical massNumber of molelcules
Total (without water)45,8568
Polymers45,8568
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12760 Å2
ΔGint-100 kcal/mol
Surface area14520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.550, 95.550, 105.660
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
/ NCS ensembles :
ID
1
2
3
4

-
Components

#1: Protein/peptide NUCLEAR MRNA EXPORT PROTEIN SAC3 / LEUCINE PERMEASE TRANSCRIPTIONAL REGULATOR / SAC3


Mass: 4062.587 Da / Num. of mol.: 2 / Fragment: RESIDUES 757-787
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: PGEXTEV / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P46674
#2: Protein PROTEIN SUS1 / SUS1


Mass: 11094.497 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: PET30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6WNK7
#3: Protein/peptide
NUCLEOPORIN NUP1 / NUCLEAR PORE PROTEIN NUP1 / NUP1


Mass: 3885.394 Da / Num. of mol.: 4 / Fragment: RESIDUES 322-355
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: PGEXTEV / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P20676
Sequence detailsINITIAL GS ADDED FROM VECTOR

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.04 Å3/Da / Density % sol: 59.49 % / Description: NONE
Crystal growpH: 6 / Details: DESCRIBED IN DETAIL IN PUBLICATION, pH 6.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 9, 2011 / Details: MIRRORS
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3→40 Å / Num. obs: 11573 / % possible obs: 100 % / Observed criterion σ(I): 1.34 / Redundancy: 7.7 % / Biso Wilson estimate: 70.96 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 11.8
Reflection shellResolution: 3→3.16 Å / Redundancy: 8 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.4 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FWB

3fwb


Resolution: 3→47.775 Å / SU ML: 0.4 / σ(F): 1.34 / Phase error: 25.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2435 554 4.8 %
Rwork0.2068 --
obs0.2086 11514 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 20 Å2 / ksol: 0.1 e/Å3
Refinement stepCycle: LAST / Resolution: 3→47.775 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2340 0 0 0 2340
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042364
X-RAY DIFFRACTIONf_angle_d0.6623178
X-RAY DIFFRACTIONf_dihedral_angle_d13.868902
X-RAY DIFFRACTIONf_chiral_restr0.027378
X-RAY DIFFRACTIONf_plane_restr0.003398
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.30180.33321530.28312668X-RAY DIFFRACTION99
3.3018-3.77950.28791430.23642686X-RAY DIFFRACTION100
3.7795-4.7610.2361390.18992735X-RAY DIFFRACTION100
4.761-47.7810.19751190.1872871X-RAY DIFFRACTION100

+
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