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- PDB-8szr: Dog DHX9 bound to ADP -

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Basic information

Entry
Database: PDB / ID: 8szr
TitleDog DHX9 bound to ADP
ComponentsRNA helicaseHelicase
KeywordsHYDROLASE / DExH-box / RHA
Function / homology
Function and homology information


: / single-stranded 3'-5' DNA helicase activity / positive regulation of viral translation / 3'-5' DNA/RNA helicase activity / CRD-mediated mRNA stability complex / regulatory region RNA binding / positive regulation of miRNA-mediated gene silencing / : / positive regulation of RNA export from nucleus / DNA-templated viral transcription ...: / single-stranded 3'-5' DNA helicase activity / positive regulation of viral translation / 3'-5' DNA/RNA helicase activity / CRD-mediated mRNA stability complex / regulatory region RNA binding / positive regulation of miRNA-mediated gene silencing / : / positive regulation of RNA export from nucleus / DNA-templated viral transcription / positive regulation of viral transcription / RISC complex binding / triplex DNA binding / positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / global gene silencing by mRNA cleavage / : / CRD-mediated mRNA stabilization / protein localization to cytoplasmic stress granule / G-quadruplex DNA unwinding / nucleoside triphosphate diphosphatase activity / nuclear stress granule / 3'-5' RNA helicase activity / perichromatin fibrils / RNA secondary structure unwinding / alternative mRNA splicing, via spliceosome / RISC-loading complex / regulation of mRNA processing / RISC complex assembly / positive regulation of cytoplasmic translation / importin-alpha family protein binding / siRNA binding / positive regulation of response to cytokine stimulus / RNA stem-loop binding / RISC complex / sequence-specific mRNA binding / RNA polymerase II complex binding / cellular response to exogenous dsRNA / DNA replication origin binding / positive regulation of interferon-alpha production / positive regulation of DNA repair / positive regulation of interferon-beta production / positive regulation of DNA replication / promoter-specific chromatin binding / DNA-templated transcription termination / cytoplasmic ribonucleoprotein granule / chromatin DNA binding / positive regulation of interleukin-6 production / positive regulation of fibroblast proliferation / actin cytoskeleton / positive regulation of tumor necrosis factor production / single-stranded DNA binding / double-stranded RNA binding / cellular response to tumor necrosis factor / positive regulation of NF-kappaB transcription factor activity / RNA polymerase II-specific DNA-binding transcription factor binding / single-stranded RNA binding / transcription coactivator activity / nuclear body / RNA helicase / RNA polymerase II cis-regulatory region sequence-specific DNA binding / centrosome / nucleolus / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / ATP binding / cytosol
Similarity search - Function
DHX9, first double-stranded RNA binding domain / DHX9, second double-stranded RNA binding domain / DHX9, DEXH-box helicase domain / DEAD-box helicase, OB fold / Oligonucleotide/oligosaccharide-binding (OB)-fold / Helicase-associated domain / Helicase associated domain (HA2), winged-helix / Helicase associated domain (HA2) Add an annotation / Double-stranded RNA binding motif / Double-stranded RNA binding motif ...DHX9, first double-stranded RNA binding domain / DHX9, second double-stranded RNA binding domain / DHX9, DEXH-box helicase domain / DEAD-box helicase, OB fold / Oligonucleotide/oligosaccharide-binding (OB)-fold / Helicase-associated domain / Helicase associated domain (HA2), winged-helix / Helicase associated domain (HA2) Add an annotation / Double-stranded RNA binding motif / Double-stranded RNA binding motif / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / 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
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / RNA helicase
Similarity search - Component
Biological speciesCanis lupus familiaris (dog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.97 Å
AuthorsLee, Y.-T. / Sickmier, E.A. / Grigoriu, S. / Boriack-Sjodin, P.A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2023
Title: Crystal structures of the DExH-box RNA helicase DHX9.
Authors: Lee, Y.T. / Sickmier, E.A. / Grigoriu, S. / Castro, J. / Boriack-Sjodin, P.A.
History
DepositionMay 30, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 8, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA helicase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,5209
Polymers114,4921
Non-polymers1,0288
Water905
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.290, 85.290, 352.100
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein RNA helicase / Helicase


Mass: 114492.352 Da / Num. of mol.: 1 / Fragment: residues 151-1151
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canis lupus familiaris (dog) / Gene: DHX9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A8C0M1F0
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.8 Å3/Da / Density % sol: 56.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 200 mM Lithium sulfate, 100 mM MES pH 6, 20% (w/v) PEG 4000; 5 mM ADP and 50 mM magnesium chloride in protein solution

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95364 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95364 Å / Relative weight: 1
ReflectionResolution: 2.97→48.35 Å / Num. obs: 27977 / % possible obs: 100 % / Redundancy: 26.3 % / CC1/2: 1 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.013 / Rrim(I) all: 0.067 / Χ2: 0.97 / Net I/σ(I): 33 / Num. measured all: 734995
Reflection shellResolution: 2.97→3.15 Å / % possible obs: 99.9 % / Redundancy: 25.7 % / Rmerge(I) obs: 1.301 / Num. measured all: 113359 / Num. unique obs: 4412 / CC1/2: 0.902 / Rpim(I) all: 0.259 / Rrim(I) all: 1.327 / Χ2: 0.88 / Net I/σ(I) obs: 3.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.97→48.35 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.926 / SU B: 23.384 / SU ML: 0.417 / Cross valid method: THROUGHOUT / ESU R Free: 0.453
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2958 1377 4.922 %RANDOM
Rwork0.2434 26598 --
all0.246 ---
obs-27975 99.911 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 120.335 Å2
Baniso -1Baniso -2Baniso -3
1-2.644 Å20 Å2-0 Å2
2--2.644 Å20 Å2
3----5.288 Å2
Refinement stepCycle: LAST / Resolution: 2.97→48.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6785 0 58 5 6848
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0126992
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166680
X-RAY DIFFRACTIONr_angle_refined_deg0.8141.6479493
X-RAY DIFFRACTIONr_angle_other_deg0.2861.56315397
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1535853
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.018546
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.00551
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.639101212
X-RAY DIFFRACTIONr_dihedral_angle_6_deg10.67810317
X-RAY DIFFRACTIONr_chiral_restr0.040.21081
X-RAY DIFFRACTIONr_chiral_restr_other0.0080.21
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.028078
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021559
X-RAY DIFFRACTIONr_nbd_refined0.1960.21588
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1810.26697
X-RAY DIFFRACTIONr_nbtor_refined0.1710.23450
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0730.23583
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2143
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0050.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1510.28
X-RAY DIFFRACTIONr_nbd_other0.160.248
X-RAY DIFFRACTIONr_mcbond_it5.32311.9693421
X-RAY DIFFRACTIONr_mcbond_other5.32211.9693421
X-RAY DIFFRACTIONr_mcangle_it8.68321.5274271
X-RAY DIFFRACTIONr_mcangle_other8.68221.5284272
X-RAY DIFFRACTIONr_scbond_it4.60312.4423571
X-RAY DIFFRACTIONr_scbond_other4.57912.4293544
X-RAY DIFFRACTIONr_scangle_it7.79422.795222
X-RAY DIFFRACTIONr_scangle_other7.78622.7675187
X-RAY DIFFRACTIONr_lrange_it12.294111.9787777
X-RAY DIFFRACTIONr_lrange_other12.275111.9837775
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.97-3.0470.477950.3681927X-RAY DIFFRACTION99.4589
3.047-3.130.402960.3511843X-RAY DIFFRACTION99.9485
3.13-3.220.382950.3471794X-RAY DIFFRACTION100
3.22-3.3190.3721010.3461769X-RAY DIFFRACTION100
3.319-3.4270.37780.3061742X-RAY DIFFRACTION100
3.427-3.5470.342840.2921680X-RAY DIFFRACTION100
3.547-3.680.35800.2941596X-RAY DIFFRACTION100
3.68-3.8290.376840.2871541X-RAY DIFFRACTION100
3.829-3.9990.344770.2621497X-RAY DIFFRACTION100
3.999-4.1920.3840.2511416X-RAY DIFFRACTION100
4.192-4.4170.308740.2371384X-RAY DIFFRACTION100
4.417-4.6830.248660.2191304X-RAY DIFFRACTION100
4.683-5.0030.291650.2151233X-RAY DIFFRACTION100
5.003-5.3990.296590.2291148X-RAY DIFFRACTION100
5.399-5.9070.341610.2641061X-RAY DIFFRACTION100
5.907-6.5920.382430.2431002X-RAY DIFFRACTION100
6.592-7.5880.265480.208869X-RAY DIFFRACTION100
7.588-9.2370.187410.157761X-RAY DIFFRACTION100
9.237-12.8310.182280.162621X-RAY DIFFRACTION99.8462
12.831-48.350.281180.31410X-RAY DIFFRACTION99.7669

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