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

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Basic information

Entry
Database: PDB / ID: 3fmp
TitleCrystal structure of the nucleoporin Nup214 in complex with the DEAD-box helicase Ddx19
Components
  • ATP-dependent RNA helicase DDX19B
  • Nuclear pore complex protein Nup214Nuclear pore
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 / RNA export from nucleus / structural constituent of nuclear pore / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / SUMOylation of RNA binding proteins / 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 / poly(A)+ mRNA export from nucleus / Viral Messenger RNA Synthesis / 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 / HCMV Early Events / cytoplasmic stress granule / protein import into nucleus / nuclear envelope / snRNP Assembly / RNA helicase activity / regulation of cell cycle / RNA helicase / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 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: 3.19 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_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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
C: Nuclear pore complex protein Nup214
D: ATP-dependent RNA helicase DDX19B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,3046
Polymers207,4494
Non-polymers8542
Water0
1
A: Nuclear pore complex protein Nup214
B: ATP-dependent RNA helicase DDX19B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,1523
Polymers103,7252
Non-polymers4271
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Nuclear pore complex protein Nup214
D: ATP-dependent RNA helicase DDX19B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,1523
Polymers103,7252
Non-polymers4271
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.369, 112.915, 142.573
Angle α, β, γ (deg.)90.00, 89.86, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D
13A
23C

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILEPHEPHEAA9 - 2349 - 234
21ILEILEPHEPHECC9 - 2349 - 234
12LEULEULYSLYSBB70 - 29870 - 298
22LEULEULYSLYSDD70 - 29870 - 298
13HISHISPROPROAA239 - 428239 - 428
23HISHISPROPROCC239 - 428239 - 428

NCS ensembles :
ID
1
2
3
Detailschains A,B / chains C,D

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Components

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


Mass: 49730.020 Da / Num. of mol.: 2
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: 53994.727 Da / Num. of mol.: 2
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-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine 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: 2.38 Å3/Da / Density % sol: 48.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: PEG 3000, CHES buffer, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 8, 2008
RadiationMonochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. all: 32548 / Num. obs: 29717 / % possible obs: 91.3 % / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Rsym value: 0.113 / Net I/σ(I): 14.3
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 3.6 / Num. unique all: 3249 / Rsym value: 0.395 / % possible all: 70.9

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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: 3FMO

3fmo


Resolution: 3.19→50 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.891 / SU B: 45.736 / SU ML: 0.369 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.572 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28317 1504 5.1 %RANDOM
Rwork0.24938 ---
obs0.25114 28125 90.73 %-
all-30998 --
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: 72.611 Å2
Baniso -1Baniso -2Baniso -3
1-16.88 Å2-0 Å20.93 Å2
2---3.14 Å20 Å2
3----13.74 Å2
Refinement stepCycle: LAST / Resolution: 3.19→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10162 0 54 0 10216
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02210446
X-RAY DIFFRACTIONr_bond_other_d0.0020.027110
X-RAY DIFFRACTIONr_angle_refined_deg1.4711.99114204
X-RAY DIFFRACTIONr_angle_other_deg0.899317544
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.52851294
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.13525.308422
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.342151854
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8561540
X-RAY DIFFRACTIONr_chiral_restr0.080.21628
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211334
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021870
X-RAY DIFFRACTIONr_nbd_refined0.2290.22520
X-RAY DIFFRACTIONr_nbd_other0.2010.27613
X-RAY DIFFRACTIONr_nbtor_refined0.190.24986
X-RAY DIFFRACTIONr_nbtor_other0.0910.25858
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2275
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0260.25
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1970.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2690.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1510.27
X-RAY DIFFRACTIONr_mcbond_it0.3081.58321
X-RAY DIFFRACTIONr_mcbond_other0.0691.52560
X-RAY DIFFRACTIONr_mcangle_it0.411210630
X-RAY DIFFRACTIONr_scbond_it0.68834583
X-RAY DIFFRACTIONr_scangle_it1.0474.53574
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A2972tight positional0.030.05
2B3090tight positional0.020.05
3A2509tight positional0.020.05
1A2972tight thermal0.060.5
2B3090tight thermal0.030.5
3A2509tight thermal0.050.5
LS refinement shellResolution: 3.2→3.269 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 74 -
Rwork0.293 1472 -
obs--64.52 %
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)
12.81020.06831.18333.97340.82814.14230.05940.1573-0.31390.3286-0.0623-0.14470.967-0.04480.0029-0.5078-0.110.0811-0.2931-0.0453-0.211836.106159.8469101.0239
21.39590.8636-0.13274.68732.22716.28840.2071-0.07890.0389-0.083-0.11830.04960.0153-0.3254-0.0888-0.17670.0232-0.0061-0.3083-0.0631-0.193428.407643.654763.38
32.72340.4246-1.53683.9-1.40394.32010.06930.11330.30760.2124-0.07380.1668-0.92290.06440.0045-0.5191-0.0717-0.0754-0.28570.0182-0.202556.28754.29529.7425
41.38040.6416-0.1275.7327-2.35337.25430.2306-0.1496-0.0021-0.2415-0.1155-0.07240.1510.315-0.1151-0.39320.0039-0.0632-0.29830.0617-0.174763.678570.4631-7.9101
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 428
2X-RAY DIFFRACTION2B70 - 298
3X-RAY DIFFRACTION3C9 - 428
4X-RAY DIFFRACTION4D70 - 298

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