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- PDB-6b4i: Crystal structure of human Gle1 CTD-Nup42 GBM-DDX19B(ADP) complex -

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Basic information

Entry
Database: PDB / ID: 6b4i
TitleCrystal structure of human Gle1 CTD-Nup42 GBM-DDX19B(ADP) complex
Components
  • ATP-dependent RNA helicase DDX19B
  • 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 / Nuclear Pore Complex (NPC) Disassembly / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Transport of Ribonucleoproteins into the Host Nucleus / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways / SUMOylation of SUMOylation proteins ...nuclear pore cytoplasmic filaments / nuclear export signal receptor activity / Nuclear Pore Complex (NPC) Disassembly / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Transport of Ribonucleoproteins into the Host Nucleus / 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 / Nuclear import of Rev protein / SUMOylation of RNA binding proteins / NEP/NS2 Interacts with the Cellular Export Machinery / Transport of Mature mRNA derived from an Intron-Containing Transcript / tRNA processing in the nucleus / inositol hexakisphosphate binding / nucleocytoplasmic transport / Viral Messenger RNA Synthesis / poly(A)+ mRNA export from nucleus / SUMOylation of ubiquitinylation proteins / Vpr-mediated nuclear import of PICs / SUMOylation of DNA replication proteins / Regulation of HSF1-mediated heat shock response / mRNA transport / nuclear pore / mRNA export from nucleus / SUMOylation of DNA damage response and repair proteins / translation initiation factor binding / centriole / protein export from nucleus / SUMOylation of chromatin organization proteins / HCMV Late Events / Transcriptional regulation by small RNAs / helicase activity / phospholipid binding / ISG15 antiviral mechanism / cytoplasmic stress granule / HCMV Early Events / nuclear envelope / protein transport / snRNP Assembly / nuclear membrane / RNA helicase activity / ciliary basal body / RNA helicase / mRNA binding / centrosome / nucleolus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP hydrolysis activity / extracellular space / RNA binding / extracellular exosome / zinc ion binding / nucleoplasm / ATP binding / identical protein binding / nucleus / membrane / cytoplasm / cytosol
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. / RNA helicase, DEAD-box type, Q motif ...: / 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. / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / Nucleoporin NUP42 / Nucleoporin NUP42 / mRNA export factor GLE1 / ATP-dependent RNA helicase DDX19B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.619 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

Downloads & links

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Assembly

Deposited unit
B: Nucleoporin GLE1
C: Nucleoporin like 2
A: Nucleoporin GLE1
D: Nucleoporin like 2
E: ATP-dependent RNA helicase DDX19B
F: ATP-dependent RNA helicase DDX19B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,54314
Polymers181,1196
Non-polymers1,4248
Water00
1
B: Nucleoporin GLE1
C: Nucleoporin like 2
F: ATP-dependent RNA helicase DDX19B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,2727
Polymers90,5603
Non-polymers7124
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Nucleoporin GLE1
D: Nucleoporin like 2
E: ATP-dependent RNA helicase DDX19B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,2727
Polymers90,5603
Non-polymers7124
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.740, 74.650, 146.830
Angle α, β, γ (deg.)90.00, 94.85, 90.00
Int Tables number4
Space group name H-MP1211

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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: Protein ATP-dependent RNA helicase DDX19B / DEAD box RNA helicase DEAD5 / DEAD box protein 19B


Mass: 48658.000 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDX19B, DBP5, DDX19, TDBP / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UMR2, RNA helicase
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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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: 2.65 Å3/Da / Density % sol: 53.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 13 % (w/v) PEG 3350, 0.2 M sodium potassium phosphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0333 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0333 Å / Relative weight: 1
ReflectionResolution: 3.6→50 Å / Num. obs: 21685 / % possible obs: 98.6 % / Redundancy: 6.9 % / CC1/2: 0.997 / Rpim(I) all: 0.061 / Rsym value: 0.159 / Net I/σ(I): 8.5
Reflection shellResolution: 3.6→3.9 Å / Redundancy: 7 % / Mean I/σ(I) obs: 1 / Num. unique obs: 2157 / CC1/2: 0.48 / Rpim(I) all: 0.833 / Rsym value: 2.232 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX(dev_2006: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.619→46.091 Å / SU ML: 0.55 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 33.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.281 1742 9.18 %
Rwork0.2343 --
obs0.2387 18966 86.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.619→46.091 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12506 0 84 0 12590
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00412854
X-RAY DIFFRACTIONf_angle_d1.06917377
X-RAY DIFFRACTIONf_dihedral_angle_d14.6064920
X-RAY DIFFRACTIONf_chiral_restr0.0581939
X-RAY DIFFRACTIONf_plane_restr0.0032250
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6188-3.72530.33260.3354275X-RAY DIFFRACTION17
3.7253-3.84540.3881940.3258919X-RAY DIFFRACTION56
3.8454-3.98280.41741280.30551308X-RAY DIFFRACTION80
3.9828-4.14220.33061580.291620X-RAY DIFFRACTION98
4.1422-4.33060.31681650.28931578X-RAY DIFFRACTION96
4.3306-4.55870.31891500.2611641X-RAY DIFFRACTION99
4.5587-4.8440.31351740.24021634X-RAY DIFFRACTION100
4.844-5.21760.2561690.21851643X-RAY DIFFRACTION99
5.2176-5.74170.30471740.24241647X-RAY DIFFRACTION99
5.7417-6.57050.3231620.24021609X-RAY DIFFRACTION97
6.5705-8.27040.23861690.21991685X-RAY DIFFRACTION99
8.2704-46.09430.231730.19111665X-RAY DIFFRACTION97

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