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- PDB-6b4e: Crystal structure of Saccharomyces cerevisiae Gle1 CTD-Nup42 GBM ... -

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Basic information

Entry
Database: PDB / ID: 6b4e
TitleCrystal structure of Saccharomyces cerevisiae Gle1 CTD-Nup42 GBM complex
Components
  • Nucleoporin GLE1
  • Nucleoporin NUP42
KeywordsTRANSPORT PROTEIN / Complex / Nuclear Pore Complex / mRNA export / DEAD-box helicase
Function / homology
Function and homology information


cellular response to salt stress / mRNA export from nucleus in response to heat stress / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore central transport channel / regulation of translational termination / tRNA export from nucleus / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore cytoplasmic filaments / inositol hexakisphosphate binding / structural constituent of nuclear pore ...cellular response to salt stress / mRNA export from nucleus in response to heat stress / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore central transport channel / regulation of translational termination / tRNA export from nucleus / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore cytoplasmic filaments / inositol hexakisphosphate binding / structural constituent of nuclear pore / regulation of translational initiation / nucleocytoplasmic transport / poly(A)+ mRNA export from nucleus / NLS-bearing protein import into nucleus / enzyme activator activity / mRNA export from nucleus / translation initiation factor binding / nuclear pore / phospholipid binding / mRNA processing / transcription corepressor activity / protein transport / nuclear envelope / nuclear membrane / mitochondrion / nucleus / cytoplasm
Similarity search - Function
GLE1-like / mRNA export factor GLE1-like / GLE1-like superfamily / GLE1-like protein / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
PROLINE / Nucleoporin NUP42 / mRNA export factor GLE1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsLin, D.H. / Correia, A.R. / Cai, S.W. / Huber, F.M. / Jette, C.A. / Hoelz, A.
Funding support United States, 6items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5 T32 GM07616 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM117360 United States
Howard Hughes Medical Institute (HHMI) United States
Heritage Medical Research Institute United States
Sidney Kimmel Foundation for Cancer Research United States
Camille & Henry Dreyfus Foundation United States
CitationJournal: Nat Commun / Year: 2018
Title: Structural and functional analysis of mRNA export regulation by the nuclear pore complex.
Authors: Lin, D.H. / Correia, A.R. / Cai, S.W. / Huber, F.M. / Jette, C.A. / Hoelz, A.
History
DepositionSep 26, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Nucleoporin GLE1
A: Nucleoporin GLE1
C: Nucleoporin NUP42
D: Nucleoporin NUP42
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,0258
Polymers76,6714
Non-polymers3544
Water11,313628
1
B: Nucleoporin GLE1
D: Nucleoporin NUP42
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4513
Polymers38,3352
Non-polymers1151
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-10 kcal/mol
Surface area16110 Å2
MethodPISA
2
A: Nucleoporin GLE1
C: Nucleoporin NUP42
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5755
Polymers38,3352
Non-polymers2393
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-5 kcal/mol
Surface area16100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.470, 67.470, 361.651
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-281-

LEU

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Components

#1: Protein Nucleoporin GLE1 / Nuclear pore protein GLE1 / RNA export factor GLE1


Mass: 34258.738 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: GLE1, BRR3, RSS1, YDL207W, D1049 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12315
#2: Protein/peptide Nucleoporin NUP42 / Nuclear pore protein NUP42


Mass: 4076.666 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: NUP42, RIP1, UIP1, YDR192C, YD9346.04C / Production host: Escherichia coli (E. coli) / References: UniProt: P49686
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PRO / PROLINE / Proline


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 628 / Source method: isolated from a natural source / Formula: H2O

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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: 2.68 Å3/Da / Density % sol: 54.17 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES pH 8.2, 11 % (w/v/) PEG 3350, 0.2 M L-Proline

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.75→47.3 Å / Num. obs: 85335 / % possible obs: 99.3 % / Redundancy: 21.8 % / CC1/2: 0.999 / Rpim(I) all: 0.025 / Rsym value: 0.124 / Net I/σ(I): 16.4
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 10.5 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 7866 / CC1/2: 0.573 / Rpim(I) all: 0.398 / Rsym value: 1.27 / % possible all: 93.5

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Processing

Software
NameVersionClassification
PHENIX(dev_2006: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RRN

3rrn


Resolution: 1.75→47.299 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2107 2000 2.34 %
Rwork0.1849 --
obs0.1855 85312 99.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→47.299 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5353 0 24 628 6005
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076839
X-RAY DIFFRACTIONf_angle_d1.1119266
X-RAY DIFFRACTIONf_dihedral_angle_d13.8952588
X-RAY DIFFRACTIONf_chiral_restr0.0451038
X-RAY DIFFRACTIONf_plane_restr0.0051181
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7501-1.79390.39121300.35775424X-RAY DIFFRACTION92
1.7939-1.84240.36311390.32235767X-RAY DIFFRACTION98
1.8424-1.89660.32811390.27495814X-RAY DIFFRACTION99
1.8966-1.95780.27941420.2335893X-RAY DIFFRACTION100
1.9578-2.02780.23091420.20845925X-RAY DIFFRACTION100
2.0278-2.1090.25061420.20165929X-RAY DIFFRACTION100
2.109-2.20490.25441420.19075896X-RAY DIFFRACTION100
2.2049-2.32120.21551440.18285997X-RAY DIFFRACTION100
2.3212-2.46660.21081410.18125907X-RAY DIFFRACTION100
2.4666-2.6570.21131450.17546003X-RAY DIFFRACTION100
2.657-2.92440.22121450.17676033X-RAY DIFFRACTION100
2.9244-3.34750.19831450.18266057X-RAY DIFFRACTION100
3.3475-4.2170.1771480.15566161X-RAY DIFFRACTION100
4.217-47.3160.17311560.17146506X-RAY DIFFRACTION100

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