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- PDB-3jrv: Structure of poxvirus K7 protein in complex with RNA helicase DDX3 -

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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


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 / gamete generation / positive regulation of mitochondrial translation ...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 / gamete generation / positive regulation of mitochondrial translation / 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 / positive regulation of NLRP3 inflammasome complex assembly / transcription factor binding / lipid homeostasis / cell leading edge / negative regulation of intrinsic apoptotic signaling pathway / 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 / DNA helicase activity / translation initiation factor binding / signaling adaptor activity / stress granule assembly / intrinsic apoptotic signaling pathway / protein sequestering activity / positive regulation of interferon-beta production / ribonucleoside triphosphate phosphatase activity / protein serine/threonine kinase activator activity / cytosolic ribosome assembly / positive regulation of translation / chromosome segregation / translational initiation / positive regulation of non-canonical NF-kappaB signal transduction / negative regulation of cell growth / response to virus / cellular response to virus / Wnt signaling pathway / mRNA 5'-UTR binding / RNA stem-loop binding / cytoplasmic stress granule / positive regulation of canonical Wnt signaling pathway / lamellipodium / positive regulation of cell growth / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / secretory granule lumen / symbiont-mediated suppression of host NF-kappaB cascade / ficolin-1-rich granule lumen / cell differentiation / host cell cytoplasm / RNA helicase activity / negative regulation of translation / intracellular signal transduction / RNA helicase / cadherin binding / positive regulation of apoptotic process / innate immune response / negative regulation of gene expression / 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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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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: 2.1 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

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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

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Phasing

PhasingMethod: SAD

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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 %

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