[English] 日本語
Yorodumi
- PDB-3jrv: Structure of poxvirus K7 protein in complex with RNA helicase DDX3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3jrv
TitleStructure of poxvirus K7 protein in complex with RNA helicase DDX3
Components
  • ATP-dependent RNA helicase DDX3X
  • Protein K7
KeywordsVIRAL PROTEIN/PROTEIN BINDING / poxvirus protein K7 / DEAD-box RNA Helicase DDX3 / viral immune evasion / innate immunity / VIRAL PROTEIN-PROTEIN BINDING complex
Function / homology
Function and homology information


positive regulation of toll-like receptor 8 signaling pathway / positive regulation of toll-like receptor 7 signaling pathway / CTPase activity / positive regulation of translation in response to endoplasmic reticulum stress / gamete generation / eukaryotic initiation factor 4E binding / RNA strand annealing activity / protein localization to cytoplasmic stress granule / positive regulation of chemokine (C-C motif) ligand 5 production / positive regulation of mitochondrial translation ...positive regulation of toll-like receptor 8 signaling pathway / positive regulation of toll-like receptor 7 signaling pathway / CTPase activity / positive regulation of translation in response to endoplasmic reticulum stress / gamete generation / eukaryotic initiation factor 4E binding / RNA strand annealing activity / protein localization to cytoplasmic stress granule / positive regulation of chemokine (C-C motif) ligand 5 production / positive regulation of mitochondrial translation / cellular response to arsenic-containing substance / NLRP3 inflammasome complex / positive regulation of protein K63-linked ubiquitination / poly(A) binding / canonical inflammasome complex / gamma-tubulin binding / P granule / negative regulation of non-canonical NF-kappaB signal transduction / transcription factor binding / cellular response to osmotic stress / extrinsic apoptotic signaling pathway via death domain receptors / symbiont-mediated suppression of host TRAF-mediated signal transduction / negative regulation of intrinsic apoptotic signaling pathway / ribosomal small subunit binding / cytoplasmic pattern recognition receptor signaling pathway / Wnt signaling pathway / RNA stem-loop binding / cell leading edge / lipid homeostasis / positive regulation of interferon-alpha production / positive regulation of NLRP3 inflammasome complex assembly / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of translational initiation / negative regulation of protein-containing complex assembly / positive regulation of G1/S transition of mitotic cell cycle / positive regulation of viral genome replication / Dengue virus activates/modulates innate and adaptive immune responses / intrinsic apoptotic signaling pathway / positive regulation of type I interferon production / signaling adaptor activity / positive regulation of interferon-beta production / translation initiation factor binding / protein serine/threonine kinase activator activity / stress granule assembly / chromosome segregation / cytosolic ribosome assembly / cellular response to virus / positive regulation of translation / translational initiation / negative regulation of cell growth / positive regulation of non-canonical NF-kappaB signal transduction / protein sequestering activity / response to virus / cytoplasmic stress granule / mRNA 5'-UTR binding / positive regulation of canonical Wnt signaling pathway / positive regulation of cell growth / lamellipodium / cell differentiation / ribonucleoside triphosphate phosphatase activity / secretory granule lumen / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / ficolin-1-rich granule lumen / innate immune response / symbiont-mediated suppression of host NF-kappaB cascade / DNA helicase activity / RNA helicase activity / intracellular signal transduction / negative regulation of translation / positive regulation of apoptotic process / RNA helicase / cadherin binding / negative regulation of gene expression / mRNA binding / centrosome / positive regulation of gene expression / GTPase activity / negative regulation of apoptotic process / Neutrophil degranulation / host cell cytoplasm / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / mitochondrion / DNA binding / RNA binding / extracellular exosome / nucleoplasm / ATP binding / extracellular region / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Orthopoxvirus, Protein K7 / dsDNA poxvirus / Poxvirus Bcl-2-like / Poxvirus domain superfamily / Poxvirus Bcl-2-like proteins / Apoptosis Regulator Bcl-x / 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. ...Orthopoxvirus, Protein K7 / dsDNA poxvirus / Poxvirus Bcl-2-like / Poxvirus domain superfamily / Poxvirus Bcl-2-like proteins / Apoptosis Regulator Bcl-x / 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 nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ATP-dependent RNA helicase DDX3X / Protein K7
Similarity search - Component
Biological speciesVaccinia virus WR
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsOda, S. / Khan, R.A.
CitationJournal: Structure / Year: 2009
Title: Structural basis for targeting of human RNA helicase DDX3 by poxvirus protein K7
Authors: Oda, S. / Schroder, M. / Khan, A.R.
History
DepositionSep 9, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 18, 2012Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein K7
B: Protein K7
C: ATP-dependent RNA helicase DDX3X
D: ATP-dependent RNA helicase DDX3X
E: ATP-dependent RNA helicase DDX3X


Theoretical massNumber of molelcules
Total (without water)41,8285
Polymers41,8285
Non-polymers00
Water4,630257
1
A: Protein K7
C: ATP-dependent RNA helicase DDX3X


Theoretical massNumber of molelcules
Total (without water)19,8352
Polymers19,8352
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint-6 kcal/mol
Surface area7680 Å2
MethodPISA
2
B: Protein K7
D: ATP-dependent RNA helicase DDX3X


Theoretical massNumber of molelcules
Total (without water)19,8352
Polymers19,8352
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-6 kcal/mol
Surface area7760 Å2
MethodPISA
3
E: ATP-dependent RNA helicase DDX3X


  • defined by author&software
  • 2.16 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)2,1581
Polymers2,1581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.889, 69.529, 65.626
Angle α, β, γ (deg.)90.000, 122.170, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Protein K7


Mass: 17676.480 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus WR / Strain: Western Reserve / Plasmid: pET15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P68466
#2: Protein/peptide ATP-dependent RNA helicase DDX3X / DEAD box protein 3 / X-chromosomal / Helicase-like protein 2 / HLP2 / DEAD box / X isoform


Mass: 2158.251 Da / Num. of mol.: 3 / Fragment: DDX3, UNP residues 71-90 / Source method: obtained synthetically / Details: solid-phase peptide synthesis of chains C, D and E
References: UniProt: O00571, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.25
Details: 100mM sodium citrate, 15.0% (w/v) PEG 3350, pH 5.25, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.978 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 25, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.6→55.6 Å / Num. all: 45578 / Num. obs: 44187 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 16.9 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 35.4
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.373 / Mean I/σ(I) obs: 3.4 / Num. unique all: 3840 / % possible all: 84.9

-
Phasing

PhasingMethod: SAD

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
REFMAC5.5.0070refinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
SHELXEmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.6→55.55 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.952 / Occupancy max: 1 / Occupancy min: 0.1 / SU B: 2.821 / SU ML: 0.045 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.101 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.19 2162 5.1 %RANDOM
Rwork0.141 ---
obs0.143 42627 93.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 54.62 Å2 / Biso mean: 18.284 Å2 / Biso min: 4.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å2-0.01 Å2
2--0.15 Å2-0 Å2
3----0.22 Å2
Refine analyzeLuzzati coordinate error obs: 0.159 Å
Refinement stepCycle: LAST / Resolution: 1.6→55.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2505 0 0 257 2762
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222596
X-RAY DIFFRACTIONr_angle_refined_deg1.491.9383505
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8255315
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.73424.662133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.80415469
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9791511
X-RAY DIFFRACTIONr_chiral_restr0.1170.2387
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021957
X-RAY DIFFRACTIONr_mcbond_it2.7771.51543
X-RAY DIFFRACTIONr_mcangle_it4.16822500
X-RAY DIFFRACTIONr_scbond_it5.73231053
X-RAY DIFFRACTIONr_scangle_it8.0384.51000
X-RAY DIFFRACTIONr_rigid_bond_restr3.55732596
X-RAY DIFFRACTIONr_sphericity_free13.6033257
X-RAY DIFFRACTIONr_sphericity_bonded8.57132542
LS refinement shellResolution: 1.602→1.644 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 134 -
Rwork0.22 2297 -
all-2431 -
obs--72.12 %

+
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