[English] 日本語
Yorodumi
- PDB-4on9: DECH box helicase domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4on9
TitleDECH box helicase domain
ComponentsProbable ATP-dependent RNA helicase DDX58
KeywordsHYDROLASE / Pattern recognition receptor / cytosol / ATPase / DECH box domain / RNA
Function / homology
Function and homology information


regulation of type III interferon production / RIG-I signaling pathway / positive regulation of myeloid dendritic cell cytokine production / OAS antiviral response / detection of virus / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / positive regulation of response to cytokine stimulus / positive regulation of granulocyte macrophage colony-stimulating factor production / pattern recognition receptor activity / TRAF6 mediated IRF7 activation ...regulation of type III interferon production / RIG-I signaling pathway / positive regulation of myeloid dendritic cell cytokine production / OAS antiviral response / detection of virus / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / positive regulation of response to cytokine stimulus / positive regulation of granulocyte macrophage colony-stimulating factor production / pattern recognition receptor activity / TRAF6 mediated IRF7 activation / cytoplasmic pattern recognition receptor signaling pathway / cellular response to exogenous dsRNA / RSV-host interactions / response to exogenous dsRNA / positive regulation of interferon-alpha production / TRAF6 mediated NF-kB activation / bicellular tight junction / positive regulation of defense response to virus by host / antiviral innate immune response / positive regulation of interferon-beta production / regulation of cell migration / positive regulation of interleukin-8 production / Negative regulators of DDX58/IFIH1 signaling / response to virus / DDX58/IFIH1-mediated induction of interferon-alpha/beta / Evasion by RSV of host interferon responses / ISG15 antiviral mechanism / ruffle membrane / positive regulation of interleukin-6 production / SARS-CoV-1 activates/modulates innate immune responses / positive regulation of tumor necrosis factor production / double-stranded RNA binding / Ovarian tumor domain proteases / actin cytoskeleton / TRAF3-dependent IRF activation pathway / gene expression / double-stranded DNA binding / defense response to virus / RNA helicase activity / single-stranded RNA binding / Ub-specific processing proteases / RNA helicase / ribonucleoprotein complex / innate immune response / ubiquitin protein ligase binding / positive regulation of gene expression / GTP binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / zinc ion binding / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
phosphoenolpyruvate carboxylase, domain 3 - #30 / phosphoenolpyruvate carboxylase, domain 3 / RIG-I, CARD domain repeat 2 / RIG-I-like receptor, C-terminal / RIG-I receptor C-terminal domain / RIG-I-like receptor, C-terminal regulatory domain / RIG-I-like receptor, C-terminal domain superfamily / : / C-terminal domain of RIG-I / RIG-I-like receptor (RLR) C-terminal regulatory (CTR) domain profile. ...phosphoenolpyruvate carboxylase, domain 3 - #30 / phosphoenolpyruvate carboxylase, domain 3 / RIG-I, CARD domain repeat 2 / RIG-I-like receptor, C-terminal / RIG-I receptor C-terminal domain / RIG-I-like receptor, C-terminal regulatory domain / RIG-I-like receptor, C-terminal domain superfamily / : / C-terminal domain of RIG-I / RIG-I-like receptor (RLR) C-terminal regulatory (CTR) domain profile. / Caspase recruitment domain / Caspase recruitment domain / Death-like domain superfamily / 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 / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Antiviral innate immune response receptor RIG-I
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å
AuthorsDeimling, T. / Witte, G. / Hopfner, K.P.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2014
Title: Crystal and solution structure of the human RIG-I SF2 domain
Authors: Deimling, T. / Cui, S. / Lammens, K. / Hopfner, K.P. / Witte, G.
History
DepositionJan 28, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 6, 2014Group: Database references
Revision 1.2Mar 11, 2015Group: Database references
Revision 1.3Nov 8, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Probable ATP-dependent RNA helicase DDX58
B: Probable ATP-dependent RNA helicase DDX58
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,6297
Polymers132,2092
Non-polymers4205
Water64936
1
A: Probable ATP-dependent RNA helicase DDX58
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,2973
Polymers66,1051
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Probable ATP-dependent RNA helicase DDX58
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,3324
Polymers66,1051
Non-polymers2283
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5710 Å2
ΔGint-80 kcal/mol
Surface area48940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.910, 112.990, 124.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Probable ATP-dependent RNA helicase DDX58 / DEAD box protein 58 / RIG-I-like receptor 1 / RLR-1 / Retinoic acid-inducible gene 1 protein / RIG- ...DEAD box protein 58 / RIG-I-like receptor 1 / RLR-1 / Retinoic acid-inducible gene 1 protein / RIG-1 / Retinoic acid-inducible gene I protein / RIG-I


Mass: 66104.695 Da / Num. of mol.: 2 / Fragment: UNP residues 230-793
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDX58 / Production host: Escherichia coli (E. coli) / References: UniProt: O95786, RNA helicase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.63 Å3/Da / Density % sol: 53.16 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 1:1 RIG-I SF2 (60mg/ml) : reservoir solution (100mM HEPES pH=6.8, 100mM ammonium sulfate, 6.7%(v/v) Isopropanol, 9%(v/v) PEG4000), 4days, VAPOR DIFFUSION, HANGING DROP, temperature 288K

-
Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99987 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 10, 2011
RadiationMonochromator: Fixed-exit LN2 cooled Double Crystal Monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 2.71→50 Å / Num. all: 38663 / Num. obs: 38281 / % possible obs: 99 % / Observed criterion σ(I): 2
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.71-2.87198.4
2.87-3.07199.8
3.07-3.31199.9
3.31-3.63199.4
3.63-4.05198.7
4.05-4.67199
4.67-5.71199
5.71-8.02198.9

-
Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TBK

3tbk


Resolution: 2.71→49.057 Å / SU ML: 0.36 / σ(F): 1.99 / Phase error: 29.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2575 1890 4.94 %4.94 %
Rwork0.219 ---
obs0.2209 38264 99.04 %-
all-38663 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.71→49.057 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8126 0 21 36 8183
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068286
X-RAY DIFFRACTIONf_angle_d0.90711164
X-RAY DIFFRACTIONf_dihedral_angle_d19.0843135
X-RAY DIFFRACTIONf_chiral_restr0.0351259
X-RAY DIFFRACTIONf_plane_restr0.0041421
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.71-2.77390.36811210.3152251198
2.7739-2.84890.3821300.3258399
2.8489-2.93270.32451340.2969255799
2.9327-3.02740.34331350.28812573100
3.0274-3.13550.33481370.28542603100
3.1355-3.26110.38721360.26582593100
3.2611-3.40940.2591390.24192609100
3.4094-3.58910.2911340.2247256099
3.5891-3.81390.23741370.2128260099
3.8139-4.10830.24381340.1929258699
4.1083-4.52140.21831370.1724260999
4.5214-5.17510.23611370.1731261799
5.1751-6.51770.26451380.2333266099
6.5177-49.06480.20991410.2114271397

+
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