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- PDB-4c31: Nup1:Sac3:Sus1 complex -

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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 / : / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore central transport channel / transcription export complex 2 / nuclear mRNA surveillance / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore cytoplasmic filaments / SLIK (SAGA-like) complex ...actin filament-based process / DUBm complex / : / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore central transport channel / transcription export complex 2 / nuclear mRNA surveillance / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore cytoplasmic filaments / SLIK (SAGA-like) complex / nuclear pore nuclear basket / mRNA 3'-end processing / structural constituent of nuclear pore / RNA export from nucleus / SAGA complex / poly(A)+ mRNA export from nucleus / nucleocytoplasmic transport / nuclear localization sequence binding / NLS-bearing protein import into nucleus / enzyme activator activity / ribosomal large subunit export from nucleus / transcription-coupled nucleotide-excision repair / mRNA export from nucleus / nuclear pore / protein export from nucleus / P-body / transcription elongation by RNA polymerase II / ribosomal small subunit biogenesis / protein import into nucleus / regulation of protein localization / protein transport / mitotic cell cycle / nuclear envelope / chromatin organization / nuclear membrane / transcription coactivator activity / molecular adaptor 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 / SAC3/GANP/THP3 / SAC3/GANP/THP3, conserved domain / SAC3/GANP family / ENY2/SUS1 / Transcription factor, enhancer of yellow 2 / Transcription factor EnY2 superfamily / Transcription factor e(y)2 ...Nuclear mRNA export protein Sac3 / SAC3 helical domain / Leucine permease transcriptional regulator helical domain / SAC3/GANP/THP3 / SAC3/GANP/THP3, conserved domain / SAC3/GANP family / ENY2/SUS1 / Transcription factor, enhancer of yellow 2 / Transcription factor EnY2 superfamily / Transcription factor e(y)2 / Nuclear pore complex protein / 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 / Transcription and mRNA export factor 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
Water0
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

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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

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Experimental details

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Experiment

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

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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

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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

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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

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