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- PDB-6b4f: Crystal structure of human Gle1 CTD-Nup42 GBM complex -

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Basic information

Entry
Database: PDB / ID: 6b4f
TitleCrystal structure of human Gle1 CTD-Nup42 GBM complex
Components
  • Nucleoporin GLE1
  • Nucleoporin like 2
KeywordsTRANSPORT PROTEIN / Complex / Nuclear Pore Complex / mRNA export / DEAD-box helicase
Function / homology
Function and homology information


nuclear pore cytoplasmic filaments / nuclear export signal receptor activity / inositol hexakisphosphate binding / Nuclear Pore Complex (NPC) Disassembly / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways ...nuclear pore cytoplasmic filaments / nuclear export signal receptor activity / inositol hexakisphosphate binding / Nuclear Pore Complex (NPC) Disassembly / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways / SUMOylation of SUMOylation proteins / Transport of Mature mRNA Derived from an Intronless Transcript / Rev-mediated nuclear export of HIV RNA / SUMOylation of RNA binding proteins / Nuclear import of Rev protein / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / nucleocytoplasmic transport / poly(A)+ mRNA export from nucleus / Viral Messenger RNA Synthesis / SUMOylation of ubiquitinylation proteins / Vpr-mediated nuclear import of PICs / SUMOylation of DNA replication proteins / Regulation of HSF1-mediated heat shock response / mRNA transport / mRNA export from nucleus / nuclear pore / SUMOylation of DNA damage response and repair proteins / translation initiation factor binding / protein export from nucleus / centriole / SUMOylation of chromatin organization proteins / ciliary basal body / HCMV Late Events / Transcriptional regulation by small RNAs / phospholipid binding / ISG15 antiviral mechanism / HCMV Early Events / protein transport / nuclear envelope / snRNP Assembly / nuclear membrane / centrosome / nucleolus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / RNA binding / extracellular space / nucleoplasm / identical protein binding / membrane / nucleus / metal ion binding / cytosol / 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 / Zinc finger, CCCH-type / Zinc finger C3H1-type profile.
Similarity search - Domain/homology
PHOSPHATE ION / Nucleoporin NUP42 / Nucleoporin NUP42 / mRNA export factor GLE1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.811 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 1.2Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 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

Downloads & links

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Assembly

Deposited unit
B: Nucleoporin GLE1
A: Nucleoporin GLE1
C: Nucleoporin like 2
D: Nucleoporin like 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,0648
Polymers83,8034
Non-polymers2614
Water52229
1
B: Nucleoporin GLE1
C: Nucleoporin like 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9373
Polymers41,9022
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-28 kcal/mol
Surface area17840 Å2
MethodPISA
2
A: Nucleoporin GLE1
D: Nucleoporin like 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1275
Polymers41,9022
Non-polymers2253
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-30 kcal/mol
Surface area17900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.660, 69.710, 93.570
Angle α, β, γ (deg.)90.00, 90.66, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Nucleoporin GLE1 / hGLE1 / GLE1-like protein


Mass: 36375.141 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GLE1, GLE1L / Production host: Escherichia coli (E. coli) / References: UniProt: Q53GS7
#2: Protein/peptide Nucleoporin like 2


Mass: 5526.420 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUPL2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3B7J4, UniProt: O15504*PLUS
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 3.2 Å3/Da / Density % sol: 61.61 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 0.2 M sodium potassium phosphate pH 7.6, 26 % (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.8→46.782 Å / Num. obs: 25969 / % possible obs: 99.2 % / Redundancy: 3.8 % / CC1/2: 0.992 / Rpim(I) all: 0.054 / Rsym value: 0.107 / Net I/σ(I): 10.1
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2551 / CC1/2: 0.536 / Rpim(I) all: 0.735 / Rsym value: 1.443 / % possible all: 97.8

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.811→46.782 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.06
RfactorNum. reflection% reflection
Rfree0.2735 1067 5.12 %
Rwork0.2454 --
obs0.2469 20826 79.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.811→46.782 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5794 0 12 29 5835
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035941
X-RAY DIFFRACTIONf_angle_d0.638029
X-RAY DIFFRACTIONf_dihedral_angle_d11.4463589
X-RAY DIFFRACTIONf_chiral_restr0.034880
X-RAY DIFFRACTIONf_plane_restr0.0031017
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8115-2.93940.334140.4012308X-RAY DIFFRACTION10
2.9394-3.09440.4437690.36711175X-RAY DIFFRACTION38
3.0944-3.28820.36941470.33762822X-RAY DIFFRACTION92
3.2882-3.5420.33571780.28763046X-RAY DIFFRACTION99
3.542-3.89830.30551380.25513124X-RAY DIFFRACTION100
3.8983-4.4620.24691670.21483062X-RAY DIFFRACTION100
4.462-5.62010.22861670.20823092X-RAY DIFFRACTION100
5.6201-46.78830.23911870.22793130X-RAY DIFFRACTION99

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