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- PDB-6b4g: Crystal structure of Chaetomium thermophilum Gle1 CTD-Nup42 GBM c... -

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Basic information

Entry
Database: PDB / ID: 6b4g
TitleCrystal structure of Chaetomium thermophilum Gle1 CTD-Nup42 GBM complex
Components
  • Nucleoporin AMO1
  • Nucleoporin GLE1
KeywordsTRANSPORT PROTEIN / Complex / Nuclear Pore Complex / mRNA export / DEAD-box helicase
Function / homology
Function and homology information


nuclear pore cytoplasmic filaments / inositol hexakisphosphate binding / poly(A)+ mRNA export from nucleus / mRNA transport / nuclear pore / translation initiation factor binding / phospholipid binding / protein transport / nuclear membrane / zinc ion binding / cytoplasm
Similarity search - Function
E3 ligase, CCCH-type zinc finger / CCCH-type zinc finger / mRNA export factor GLE1-like / GLE1-like superfamily / GLE1-like protein / Zinc finger, CCCH-type superfamily / zinc finger / Zinc finger, CCCH-type / Zinc finger C3H1-type profile.
Similarity search - Domain/homology
Nucleoporin AMO1 / mRNA export factor GLE1
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.648 Å
AuthorsLin, D.H. / Correia, A.R. / Cai, S.W. / Huber, F.M. / Jette, C.A. / Hoelz, A.
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 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleoporin GLE1
B: Nucleoporin AMO1
D: Nucleoporin AMO1
F: Nucleoporin AMO1
H: Nucleoporin AMO1
C: Nucleoporin GLE1
E: Nucleoporin GLE1
G: Nucleoporin GLE1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,61013
Polymers175,6348
Non-polymers9765
Water1,49583
1
A: Nucleoporin GLE1
B: Nucleoporin AMO1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2994
Polymers43,9092
Non-polymers3902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-11 kcal/mol
Surface area17580 Å2
MethodPISA
2
D: Nucleoporin AMO1
C: Nucleoporin GLE1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1043
Polymers43,9092
Non-polymers1951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-7 kcal/mol
Surface area17470 Å2
MethodPISA
3
F: Nucleoporin AMO1
E: Nucleoporin GLE1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1043
Polymers43,9092
Non-polymers1951
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-7 kcal/mol
Surface area17870 Å2
MethodPISA
4
H: Nucleoporin AMO1
G: Nucleoporin GLE1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1043
Polymers43,9092
Non-polymers1951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-6 kcal/mol
Surface area17420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.482, 93.055, 229.669
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 35483.184 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: GLE1, CTHT_0027940 / Production host: Escherichia coli (E. coli) / References: UniProt: G0S7F3
#2: Protein
Nucleoporin AMO1 / Nuclear pore protein AMO1


Mass: 8425.326 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: AMO1, CTHT_0020020 / Production host: Escherichia coli (E. coli) / References: UniProt: G0S381
#3: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.57 Å3/Da / Density % sol: 52.14 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: 0.1M MES pH 6.3, 12% (w/v) PEG 20,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.648→48.9 Å / Num. obs: 53442 / % possible obs: 99.8 % / Redundancy: 13.1 % / CC1/2: 1 / Rpim(I) all: 0.026 / Rsym value: 0.093 / Net I/σ(I): 20.5
Reflection shellResolution: 2.65→2.73 Å / Redundancy: 10.5 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 5142 / CC1/2: 0.669 / Rpim(I) all: 0.45 / Rsym value: 1.487 / % possible all: 97.6

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Processing

Software
NameVersionClassification
PHENIX(dev_2006: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.648→48.864 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.52
RfactorNum. reflection% reflection
Rfree0.2768 1999 3.74 %
Rwork0.2398 --
obs0.2412 53434 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.648→48.864 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11418 0 60 83 11561
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00511726
X-RAY DIFFRACTIONf_angle_d1.03315833
X-RAY DIFFRACTIONf_dihedral_angle_d11.1094477
X-RAY DIFFRACTIONf_chiral_restr0.0431694
X-RAY DIFFRACTIONf_plane_restr0.0042045
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6482-2.71450.35631360.31783490X-RAY DIFFRACTION97
2.7145-2.78780.36261400.29853633X-RAY DIFFRACTION100
2.7878-2.86990.3081420.28383623X-RAY DIFFRACTION100
2.8699-2.96250.32441410.283638X-RAY DIFFRACTION100
2.9625-3.06840.33061420.28133655X-RAY DIFFRACTION100
3.0684-3.19120.30771420.27443644X-RAY DIFFRACTION100
3.1912-3.33640.31441420.27423636X-RAY DIFFRACTION100
3.3364-3.51220.35331420.2693667X-RAY DIFFRACTION100
3.5122-3.73220.28741420.27073665X-RAY DIFFRACTION100
3.7322-4.02030.28921440.23253700X-RAY DIFFRACTION100
4.0203-4.42460.26031430.2173683X-RAY DIFFRACTION100
4.4246-5.06430.2441450.20923709X-RAY DIFFRACTION100
5.0643-6.37820.2521450.24043760X-RAY DIFFRACTION100
6.3782-48.87240.23711530.20673932X-RAY DIFFRACTION100

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