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- PDB-3fhc: Crystal structure of human Dbp5 in complex with Nup214 -

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Basic information

Entry
Database: PDB / ID: 3fhc
TitleCrystal structure of human Dbp5 in complex with Nup214
Components
  • ATP-dependent RNA helicase DDX19B
  • Nuclear pore complex protein Nup214
KeywordsTRANSPORT PROTEIN/HYDROLASE / DEAD-box helicase / mRNA export / Nucleoporin / beta propeller / RecA-like / RNA dependent ATPase / CAN / Ddx19 / Dead-box protein 19b / nuclear pore complex / Glycoprotein / mRNA transport / Nucleus / Phosphoprotein / Protein transport / Proto-oncogene / Translocation / Transport / ATP-binding / Helicase / Hydrolase / Membrane / Nucleotide-binding / RNA-binding / TRANSPORT PROTEIN-HYDROLASE COMPLEX
Function / homology
Function and homology information


cytoplasmic side of nuclear pore / HuR (ELAVL1) binds and stabilizes mRNA / regulation of nucleocytoplasmic transport / nuclear export signal receptor activity / 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 ...cytoplasmic side of nuclear pore / HuR (ELAVL1) binds and stabilizes mRNA / regulation of nucleocytoplasmic transport / nuclear export signal receptor activity / 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 / structural constituent of nuclear pore / 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 / RNA export from nucleus / nucleocytoplasmic transport / Viral Messenger RNA Synthesis / poly(A)+ mRNA export from nucleus / nuclear localization sequence binding / SUMOylation of ubiquitinylation proteins / Vpr-mediated nuclear import of PICs / SUMOylation of DNA replication proteins / Regulation of HSF1-mediated heat shock response / mRNA export from nucleus / SUMOylation of DNA damage response and repair proteins / nuclear pore / protein export from nucleus / SUMOylation of chromatin organization proteins / helicase activity / HCMV Late Events / Transcriptional regulation by small RNAs / ISG15 antiviral mechanism / cytoplasmic stress granule / HCMV Early Events / protein import into nucleus / nuclear envelope / snRNP Assembly / RNA helicase activity / regulation of cell cycle / RNA helicase / mRNA binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP hydrolysis activity / RNA binding / extracellular exosome / nucleoplasm / ATP binding / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
Nuclear pore complex protein Nup214, phenylalanine-glycine (FG) domain / Nucleoporin Nup214 phenylalanine-glycine (FG) domain / Nuclear pore complex protein / 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. ...Nuclear pore complex protein Nup214, phenylalanine-glycine (FG) domain / Nucleoporin Nup214 phenylalanine-glycine (FG) domain / Nuclear pore complex protein / 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 / WD40 repeats / WD40 repeat / WD40/YVTN repeat-like-containing domain superfamily / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Nuclear pore complex protein Nup214 / ATP-dependent RNA helicase DDX19B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
Authorsvon Moeller, H. / Conti, E.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2009
Title: The mRNA export protein DBP5 binds RNA and the cytoplasmic nucleoporin NUP214 in a mutually exclusive manner
Authors: von Moeller, H. / Basquin, C. / Conti, E.
History
DepositionDec 9, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 5, 2014Group: Derived calculations
Revision 1.3Nov 6, 2019Group: Advisory / Data collection / Category: pdbx_unobs_or_zero_occ_atoms / reflns_shell / Item: _reflns_shell.Rmerge_I_obs
Revision 1.4Nov 1, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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: Nuclear pore complex protein Nup214
B: ATP-dependent RNA helicase DDX19B


Theoretical massNumber of molelcules
Total (without water)71,5232
Polymers71,5232
Non-polymers00
Water1,54986
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.409, 134.707, 152.845
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Nuclear pore complex protein Nup214 / Nucleoporin 214kDa / Nup214 / Nucleoporin Nup214 / 214 kDa nucleoporin / Protein CAN


Mass: 44996.781 Da / Num. of mol.: 1 / Fragment: Nterminal beta propeller, UNP residues 1-405
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Nup214 (Residues 1-405) / Plasmid: pETMC / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 / References: UniProt: P35658
#2: Protein ATP-dependent RNA helicase DDX19B / Dead-box helicase 5 / Dbp5 / DEAD box protein 19B / DEAD box RNA helicase DEAD5


Mass: 26525.752 Da / Num. of mol.: 1 / Fragment: Nterminal RecA-like domain, UNP residues 68-302
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Dbp5 (Residues 68-302) / Plasmid: pETMC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q9UMR2, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 4.22 Å3/Da / Density % sol: 70.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 50mM MES pH 6.0, 900mM Na citrate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99988 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 1, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99988 Å / Relative weight: 1
ReflectionResolution: 2.8→47.7 Å / Num. all: 30169 / Num. obs: 30169 / % possible obs: 100 % / Observed criterion σ(I): 3.3 / Redundancy: 14.13 % / Biso Wilson estimate: 45.8 Å2 / Rmerge(I) obs: 0.138 / Net I/σ(I): 11.59
Reflection shellResolution: 2.8→3 Å / Redundancy: 13.6 % / Rmerge(I) obs: 0.364 / Mean I/σ(I) obs: 3.31 / Num. unique all: 5545 / Rsym value: 0.36 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0063refinement
PDB_EXTRACT3.006data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2OIT and 3FHT

2oit

3fht


Resolution: 2.8→47.65 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.866 / Occupancy max: 1 / Occupancy min: 0 / SU B: 13.023 / SU ML: 0.247 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 3.31 / ESU R: 0.436 / ESU R Free: 0.302 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.26 1509 5 %RANDOM
Rwork0.218 ---
obs0.22 30169 100 %-
all-30169 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 85.99 Å2 / Biso mean: 42.137 Å2 / Biso min: 4.39 Å2
Baniso -1Baniso -2Baniso -3
1--1.45 Å20 Å20 Å2
2--3.59 Å20 Å2
3----2.14 Å2
Refinement stepCycle: LAST / Resolution: 2.8→47.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4736 0 0 86 4822
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224778
X-RAY DIFFRACTIONr_angle_refined_deg1.3411.9786490
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6875596
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.54125.131191
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.31315823
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8781517
X-RAY DIFFRACTIONr_chiral_restr0.0830.2747
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213541
X-RAY DIFFRACTIONr_mcbond_it0.6221.53016
X-RAY DIFFRACTIONr_mcangle_it1.18324893
X-RAY DIFFRACTIONr_scbond_it1.41431762
X-RAY DIFFRACTIONr_scangle_it2.554.51597
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 109 -
Rwork0.328 2070 -
all-2179 -
obs--100 %

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