[English] 日本語
Yorodumi
- PDB-3fmo: Crystal structure of the nucleoporin Nup214 in complex with the D... -

+
Open data


ID or keywords:

Loading...

-
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 / structural constituent of nuclear pore / nuclear localization sequence binding / 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 / RNA export from 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 / nuclear pore / mRNA export from nucleus / SUMOylation of DNA damage response and repair proteins / SUMOylation of chromatin organization proteins / protein export from nucleus / HCMV Late Events / helicase activity / Transcriptional regulation by small RNAs / ISG15 antiviral mechanism / HCMV Early Events / protein import into nucleus / cytoplasmic stress granule / 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 / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
Nuclear pore complex protein Nup214, phenylalanine-glycine (FG) domain / Nucleoporin Nup214 phenylalanine-glycine (FG) domain / Nucleoporin Nup159/Nup146, N-terminal / NUP159/214 beta propeller / Nuclear pore complex protein / 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 ...Nuclear pore complex protein Nup214, phenylalanine-glycine (FG) domain / Nucleoporin Nup214 phenylalanine-glycine (FG) domain / Nucleoporin Nup159/Nup146, N-terminal / NUP159/214 beta propeller / Nuclear pore complex protein / 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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more