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- PDB-3fmo: Crystal structure of the nucleoporin Nup214 in complex with the D... -

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Basic information

Entry
Database: PDB / ID: 3fmo
TitleCrystal structure of the nucleoporin Nup214 in complex with the DEAD-box helicase Ddx19
Components
  • ATP-dependent RNA helicase DDX19B
  • Nuclear pore complex protein Nup214
KeywordsOncoprotein/Hydrolase / nuclear porin / nuclear pore complex / nucleocytoplasmic transport / mRNA export / protein interaction / helicase / beta-propeller / DEAD box / Glycoprotein / mRNA transport / Nucleus / Phosphoprotein / Protein transport / Proto-oncogene / Translocation / Transport / ATP-binding / Hydrolase / Membrane / Nucleotide-binding / RNA-binding / Protein transport-Hydrolase COMPLEX / Oncoprotein-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 / NEP/NS2 Interacts with the Cellular Export Machinery / Transport of Mature mRNA derived from an Intron-Containing Transcript / 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 / HCMV Late Events / helicase activity / 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 / cytosol / cytoplasm
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
ADENOSINE-5'-DIPHOSPHATE / Nuclear pore complex protein Nup214 / ATP-dependent RNA helicase DDX19B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsNapetschnig, J. / Debler, E.W. / Blobel, G. / Hoelz, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Structural and functional analysis of the interaction between the nucleoporin Nup214 and the DEAD-box helicase Ddx19.
Authors: Napetschnig, J. / Kassube, S.A. / Debler, E.W. / Wong, R.W. / Blobel, G. / Hoelz, A.
History
DepositionDec 22, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nuclear pore complex protein Nup214
B: ATP-dependent RNA helicase DDX19B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,8894
Polymers83,3702
Non-polymers5192
Water57632
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.484, 115.392, 143.461
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailschains A,B

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Components

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


Mass: 49730.020 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUP214, CAIN, CAN, KIAA0023 / Production host: Escherichia coli (E. coli) / References: UniProt: P35658
#2: Protein ATP-dependent RNA helicase DDX19B / DEAD box protein 19B / DEAD box RNA helicase DEAD5


Mass: 33639.629 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDX19B, DBP5, DDX19 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9UMR2, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.95 Å3/Da / Density % sol: 58.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: sodium di-hydrogen phosphate, di-potassium hydrogen phosphate, sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 5, 2008
RadiationMonochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 34373 / Num. obs: 33892 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 13.8 % / Rsym value: 0.105
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 10.8 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 3353 / Rsym value: 0.687 / % possible all: 89.9

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OIT

2oit


Resolution: 2.51→45.79 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.934 / SU B: 20.314 / SU ML: 0.2 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.406 / ESU R Free: 0.267 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24199 1528 4.9 %RANDOM
Rwork0.19898 ---
obs0.20102 29350 91.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 49.485 Å2
Baniso -1Baniso -2Baniso -3
1-8.82 Å20 Å2-0 Å2
2---3.51 Å20 Å2
3----5.31 Å2
Refinement stepCycle: LAST / Resolution: 2.51→45.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5118 0 33 32 5183
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0225265
X-RAY DIFFRACTIONr_bond_other_d0.0010.023590
X-RAY DIFFRACTIONr_angle_refined_deg1.4921.9927156
X-RAY DIFFRACTIONr_angle_other_deg0.87238854
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9985651
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.53925.28214
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.74315936
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6521521
X-RAY DIFFRACTIONr_chiral_restr0.0790.2818
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025712
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02943
X-RAY DIFFRACTIONr_nbd_refined0.2150.2995
X-RAY DIFFRACTIONr_nbd_other0.2020.23623
X-RAY DIFFRACTIONr_nbtor_refined0.1870.22526
X-RAY DIFFRACTIONr_nbtor_other0.0930.23044
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2128
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1640.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2650.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2140.25
X-RAY DIFFRACTIONr_mcbond_it0.9021.54166
X-RAY DIFFRACTIONr_mcbond_other0.1111.51288
X-RAY DIFFRACTIONr_mcangle_it1.06625349
X-RAY DIFFRACTIONr_scbond_it1.36732309
X-RAY DIFFRACTIONr_scangle_it2.0294.51807
LS refinement shellResolution: 2.51→2.573 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 89 -
Rwork0.321 1439 -
obs--78.64 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.2685-0.08950.55511.4607-0.45212.28120.0103-0.05530.0161-0.2448-0.01980.04910.24710.09960.0095-0.15150.03310.0339-0.09470.0256-0.084624.27643.39316.5871
21.0299-0.12080.27072.1876-0.6873.080.14490.0950.03540.131-0.0801-0.02290.02690.1238-0.0648-0.2355-0.0033-0.0029-0.02520.0455-0.031832.7608-13.412943.8545
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA9 - 4289 - 428
2X-RAY DIFFRACTION2BB69 - 30069 - 300

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