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- PDB-6b4j: Crystal structure of human Gle1 CTD-Nup42 GBM-DDX19B(AMPPNP) complex -

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Basic information

Entry
Database: PDB / ID: 6b4j
TitleCrystal structure of human Gle1 CTD-Nup42 GBM-DDX19B(AMPPNP) 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 export signal receptor activity / inositol hexakisphosphate binding / nuclear pore cytoplasmic filaments / 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 export signal receptor activity / inositol hexakisphosphate binding / nuclear pore cytoplasmic filaments / 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 / Transport of Mature mRNA derived from an Intron-Containing Transcript / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / 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 / mRNA export from nucleus / SUMOylation of DNA damage response and repair proteins / nuclear pore / translation initiation factor binding / centriole / protein export from nucleus / SUMOylation of chromatin organization proteins / helicase activity / ciliary basal body / HCMV Late Events / Transcriptional regulation by small RNAs / phospholipid binding / ISG15 antiviral mechanism / cytoplasmic stress granule / HCMV Early Events / protein transport / nuclear envelope / snRNP Assembly / nuclear membrane / RNA helicase activity / RNA helicase / centrosome / mRNA binding / nucleolus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP hydrolysis activity / RNA binding / extracellular space / extracellular exosome / nucleoplasm / ATP binding / identical protein binding / membrane / nucleus / metal ion binding / 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 / DEAD-box RNA helicase Q motif profile. ...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 / DEAD/DEAH box helicase domain / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / PHOSPHATE ION / 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: 3.4 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 1.2Nov 21, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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)182,55216
Polymers180,9216
Non-polymers1,63110
Water00
1
B: Nucleoporin GLE1
C: Nucleoporin like 2
F: ATP-dependent RNA helicase DDX19B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,3719
Polymers90,4603
Non-polymers9106
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)91,1817
Polymers90,4603
Non-polymers7204
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.940, 73.560, 145.860
Angle α, β, γ (deg.)90.00, 95.07, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 4 molecules BAEF

#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
#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

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Protein/peptide , 1 types, 2 molecules CD

#2: Protein/peptide Nucleoporin like 2


Mass: 5427.290 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: O15504*PLUS

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Non-polymers , 3 types, 10 molecules

#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*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: 53.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 15 % (w/v) PEG 3350, 0.3 M sodium potassium phosphate pH 6.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. obs: 25636 / % possible obs: 100 % / Redundancy: 10.2 % / CC1/2: 0.997 / Rpim(I) all: 0.093 / Rsym value: 0.298 / Net I/σ(I): 6.6
Reflection shellResolution: 3.4→3.5 Å / Mean I/σ(I) obs: 0.9 / Num. unique obs: 25636 / CC1/2: 0.483 / Rpim(I) all: 1.249 / Rsym value: 4.069 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(dev_2006: ???)refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.4→48.43 Å / SU ML: 0.59 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 37.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3133 1979 9.3 %
Rwork0.2606 --
obs0.2656 21291 82.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.4→48.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12504 0 94 0 12598
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00312842
X-RAY DIFFRACTIONf_angle_d0.99817359
X-RAY DIFFRACTIONf_dihedral_angle_d14.6084916
X-RAY DIFFRACTIONf_chiral_restr0.0691935
X-RAY DIFFRACTIONf_plane_restr0.0032246
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4003-3.48530.4163240.3165175X-RAY DIFFRACTION11
3.4853-3.57950.4862490.3439451X-RAY DIFFRACTION28
3.5795-3.68480.3561870.3603892X-RAY DIFFRACTION53
3.6848-3.80370.37091290.35031187X-RAY DIFFRACTION72
3.8037-3.93960.42921520.3511452X-RAY DIFFRACTION88
3.9396-4.09730.37761680.32091686X-RAY DIFFRACTION99
4.0973-4.28360.36271770.30491634X-RAY DIFFRACTION100
4.2836-4.50930.34131480.27171688X-RAY DIFFRACTION100
4.5093-4.79160.34241850.26011670X-RAY DIFFRACTION100
4.7916-5.16120.30291660.23561675X-RAY DIFFRACTION100
5.1612-5.67990.29851730.26271662X-RAY DIFFRACTION100
5.6799-6.50010.37941730.28881673X-RAY DIFFRACTION100
6.5001-8.1830.25731700.23381729X-RAY DIFFRACTION100
8.183-48.43470.22871780.19191738X-RAY DIFFRACTION100

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