[English] 日本語
Yorodumi
- PDB-2jgn: DDX3 helicase domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2jgn
TitleDDX3 helicase domain
ComponentsATP-DEPENDENT RNA HELICASE DDX3X
KeywordsHYDROLASE / PHOSPHORYLATION / NUCLEOTIDE-BINDING / HELICASE / RNA-BINDING / ATP-BINDING / DNA-BINDING / NUCLEAR PROTEIN / HOST-VIRUS INTERACTION
Function / homology
Function and homology information


CTPase activity / positive regulation of toll-like receptor 8 signaling pathway / positive regulation of toll-like receptor 7 signaling pathway / positive regulation of translation in response to endoplasmic reticulum stress / protein localization to cytoplasmic stress granule / eukaryotic initiation factor 4E binding / RNA strand annealing activity / positive regulation of chemokine (C-C motif) ligand 5 production / positive regulation of mitochondrial translation / gamete generation ...CTPase activity / positive regulation of toll-like receptor 8 signaling pathway / positive regulation of toll-like receptor 7 signaling pathway / positive regulation of translation in response to endoplasmic reticulum stress / protein localization to cytoplasmic stress granule / eukaryotic initiation factor 4E binding / RNA strand annealing activity / positive regulation of chemokine (C-C motif) ligand 5 production / positive regulation of mitochondrial translation / gamete generation / positive regulation of protein K63-linked ubiquitination / NLRP3 inflammasome complex / cellular response to arsenic-containing substance / poly(A) binding / gamma-tubulin binding / P granule / cellular response to osmotic stress / negative regulation of non-canonical NF-kappaB signal transduction / cytoplasmic pattern recognition receptor signaling pathway / transcription factor binding / positive regulation of NLRP3 inflammasome complex assembly / negative regulation of intrinsic apoptotic signaling pathway / cell leading edge / lipid homeostasis / positive regulation of interferon-alpha production / positive regulation of translational initiation / ribosomal small subunit binding / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of type I interferon production / positive regulation of G1/S transition of mitotic cell cycle / negative regulation of protein-containing complex assembly / positive regulation of viral genome replication / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / translation initiation factor binding / signaling adaptor activity / stress granule assembly / intrinsic apoptotic signaling pathway / DNA helicase activity / positive regulation of interferon-beta production / ribonucleoside triphosphate phosphatase activity / positive regulation of translation / protein serine/threonine kinase activator activity / cytosolic ribosome assembly / chromosome segregation / translational initiation / positive regulation of non-canonical NF-kappaB signal transduction / negative regulation of cell growth / cellular response to virus / mRNA 5'-UTR binding / response to virus / RNA stem-loop binding / Wnt signaling pathway / cytoplasmic stress granule / positive regulation of canonical Wnt signaling pathway / lamellipodium / positive regulation of cell growth / secretory granule lumen / ficolin-1-rich granule lumen / cell differentiation / RNA helicase activity / negative regulation of translation / intracellular signal transduction / RNA helicase / positive regulation of apoptotic process / cadherin binding / negative regulation of gene expression / innate immune response / GTPase activity / mRNA binding / centrosome / Neutrophil degranulation / positive regulation of gene expression / negative regulation of apoptotic process / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / mitochondrion / DNA binding / RNA binding / extracellular exosome / extracellular region / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / 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-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ATP-dependent RNA helicase DDX3X
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsRodamilans, B. / Montoya, G.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2007
Title: Expression, Purification, Crystallization and Preliminary X-Ray Diffraction Analysis of the Ddx3 RNA Helicase Domain.
Authors: Rodamilans, B. / Montoya, G.
History
DepositionFeb 13, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 30, 2012Group: Other
Revision 1.3Dec 13, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ATP-DEPENDENT RNA HELICASE DDX3X
B: ATP-DEPENDENT RNA HELICASE DDX3X
C: ATP-DEPENDENT RNA HELICASE DDX3X


Theoretical massNumber of molelcules
Total (without water)63,5183
Polymers63,5183
Non-polymers00
Water3,477193
1
A: ATP-DEPENDENT RNA HELICASE DDX3X


Theoretical massNumber of molelcules
Total (without water)21,1731
Polymers21,1731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ATP-DEPENDENT RNA HELICASE DDX3X


Theoretical massNumber of molelcules
Total (without water)21,1731
Polymers21,1731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: ATP-DEPENDENT RNA HELICASE DDX3X


Theoretical massNumber of molelcules
Total (without water)21,1731
Polymers21,1731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.438, 61.032, 89.111
Angle α, β, γ (deg.)90.00, 101.67, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein ATP-DEPENDENT RNA HELICASE DDX3X / DBX / DDX3


Mass: 21172.598 Da / Num. of mol.: 3 / Fragment: HELICASE DOMAIN, RESIDUES 408-579
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PCOLD III / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O00571, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.04 Å3/Da / Density % sol: 34 % / Description: NONE
Crystal growDetails: RESERVOIR: 2M (NH4)2SO4, 0.1M IMIDAZOLE PH 6.4 PLUS 5MM SPERMINE TETRA-HCL PROTEIN: 10MM HEPES, 500MM (NH4)2SO4, PH 8.0.

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9
DetectorType: ADSC CCD / Detector: CCD / Details: MIRROR
RadiationMonochromator: SILICON (1 1 1) CHANNEL- CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.9→87 Å / Num. obs: 105982 / % possible obs: 93.2 % / Observed criterion σ(I): 1 / Redundancy: 3.1 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 15.03
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.53 / % possible all: 72.2

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2DB3

2db3


Resolution: 1.91→34.5 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.926 / SU B: 8.522 / SU ML: 0.126 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.191 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1704 5 %RANDOM
Rwork0.198 ---
obs0.201 32363 93 %-
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: 27.07 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å2-0.16 Å2
2---0.28 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.91→34.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3727 0 0 193 3920
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0223781
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6821.9515104
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0375459
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.62524.541185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.06915670
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5171524
X-RAY DIFFRACTIONr_chiral_restr0.1190.2592
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022805
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2270.21687
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.22577
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.2203
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2220.262
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2510.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2091.52400
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.88923734
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.12231571
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.7914.51370
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.91→1.96 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 88 -
Rwork0.202 1757 -
obs--69.2 %
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)
13.8156-0.04030.56382.06391.00255.15220.1718-0.1067-0.27110.10530.06040.00370.66750.234-0.2322-0.04830.02570.0101-0.0214-0.0246-0.01245.4212.36159.914
23.21750.29420.01232.4328-1.18662.9587-0.06650.32590.14960.1014-0.0914-0.1061-0.35630.1940.1579-0.0546-0.02040.03030.05620.0355-0.0535-9.2140.43455.036
32.26630.14140.23392.4233-0.24142.59520.0156-0.09360.05050.2756-0.0242-0.0147-0.1015-0.06280.0086-0.02130.0240.06240.0575-0.0421-0.006220.62930.2583.346
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A410 - 575
2X-RAY DIFFRACTION2B408 - 575
3X-RAY DIFFRACTION3C411 - 574

+
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