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- PDB-8szp: Human DHX9 bound to ADP -

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Basic information

Entry
Database: PDB / ID: 8szp
TitleHuman DHX9 bound to ADP
ComponentsATP-dependent RNA helicase A
KeywordsHYDROLASE / DExH-box / RHA
Function / homology
Function and homology information


: / 3'-5' DNA/RNA helicase activity / CRD-mediated mRNA stability complex / regulation of cytoplasmic translation / regulatory region RNA binding / positive regulation of RNA export from nucleus / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / DNA-templated viral transcription / positive regulation of viral transcription / CRD-mediated mRNA stabilization ...: / 3'-5' DNA/RNA helicase activity / CRD-mediated mRNA stability complex / regulation of cytoplasmic translation / regulatory region RNA binding / positive regulation of RNA export from nucleus / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / DNA-templated viral transcription / positive regulation of viral transcription / CRD-mediated mRNA stabilization / positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity / triplex DNA binding / RISC complex binding / protein localization to cytoplasmic stress granule / nucleoside triphosphate diphosphatase activity / nuclear stress granule / G-quadruplex DNA unwinding / 3'-5' RNA helicase activity / perichromatin fibrils / positive regulation of interleukin-18 production / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / alternative mRNA splicing, via spliceosome / RNA secondary structure unwinding / RISC-loading complex / miRNA-mediated post-transcriptional gene silencing / regulation of mRNA processing / RISC complex assembly / positive regulation of cytoplasmic translation / single-stranded 3'-5' DNA helicase activity / regulation of defense response to virus by host / importin-alpha family protein binding / RIP-mediated NFkB activation via ZBP1 / siRNA binding / positive regulation of response to cytokine stimulus / positive regulation of innate immune response / sequence-specific mRNA binding / RISC complex / RNA polymerase binding / DNA duplex unwinding / cellular response to exogenous dsRNA / pyroptotic inflammatory response / RNA polymerase II complex binding / 3'-5' DNA helicase activity / DNA replication origin binding / mRNA transport / positive regulation of interferon-alpha production / DNA helicase activity / positive regulation of DNA repair / positive regulation of interferon-beta production / ribonucleoside triphosphate phosphatase activity / mRNA Splicing - Major Pathway / positive regulation of DNA replication / promoter-specific chromatin binding / DNA-templated transcription termination / transcription coregulator activity / PKR-mediated signaling / chromatin DNA binding / cytoplasmic ribonucleoprotein granule / positive regulation of inflammatory response / osteoblast differentiation / RNA stem-loop binding / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / double-stranded RNA binding / positive regulation of fibroblast proliferation / rhythmic process / actin cytoskeleton / ribosome binding / cellular response to tumor necrosis factor / positive regulation of NF-kappaB transcription factor activity / single-stranded DNA binding / protein-containing complex assembly / double-stranded DNA binding / DNA replication / RNA polymerase II-specific DNA-binding transcription factor binding / RNA helicase activity / transcription coactivator activity / single-stranded RNA binding / nuclear body / RNA helicase / ribonucleoprotein complex / inflammatory response / RNA polymerase II cis-regulatory region sequence-specific DNA binding / innate immune response / centrosome / mRNA binding / nucleolus / regulation of transcription by RNA polymerase II / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / nucleoplasm / ATP binding / membrane / nucleus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
DHX9, first double-stranded RNA binding domain / DHX9, second double-stranded RNA binding domain / DHX9, DEXH-box helicase domain / : / Helicase associated domain (HA2), ratchet-like / 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 ...DHX9, first double-stranded RNA binding domain / DHX9, second double-stranded RNA binding domain / DHX9, DEXH-box helicase domain / : / Helicase associated domain (HA2), ratchet-like / 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 / ATP-dependent RNA helicase A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 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: ATP-dependent RNA helicase A
B: ATP-dependent RNA helicase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)231,51530
Polymers228,6802
Non-polymers2,83528
Water2,414134
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A: ATP-dependent RNA helicase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,65013
Polymers114,3401
Non-polymers1,31012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ATP-dependent RNA helicase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,86517
Polymers114,3401
Non-polymers1,52416
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.100, 122.260, 349.180
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein ATP-dependent RNA helicase A / DEAH box protein 9 / DExH-box helicase 9 / Leukophysin / LKP / Nuclear DNA helicase II / NDH II / ...DEAH box protein 9 / DExH-box helicase 9 / Leukophysin / LKP / Nuclear DNA helicase II / NDH II / RNA helicase A


Mass: 114340.164 Da / Num. of mol.: 2 / Fragment: residues 150-1150
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DHX9, DDX9, LKP, NDH2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q08211, RNA helicase

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Non-polymers , 5 types, 162 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.78 Å3/Da / Density % sol: 55.74 %
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: Diamond / Beamline: I03 / Wavelength: 0.97624 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97624 Å / Relative weight: 1
ReflectionResolution: 2.62→61.13 Å / Num. obs: 76541 / % possible obs: 99.7 % / Redundancy: 12.8 % / CC1/2: 1 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.018 / Rrim(I) all: 0.064 / Χ2: 0.98 / Net I/σ(I): 21.8 / Num. measured all: 980269
Reflection shellResolution: 2.62→2.67 Å / % possible obs: 99.4 % / Redundancy: 14 % / Rmerge(I) obs: 1.398 / Num. measured all: 63231 / Num. unique obs: 4516 / CC1/2: 0.815 / Rpim(I) all: 0.382 / Rrim(I) all: 1.45 / Χ2: 0.92 / Net I/σ(I) obs: 2.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
Aimlessdata scaling
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.62→59.621 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.92 / WRfactor Rfree: 0.266 / WRfactor Rwork: 0.212 / SU B: 13.739 / SU ML: 0.278 / Average fsc free: 0.9349 / Average fsc work: 0.956 / Cross valid method: THROUGHOUT / ESU R: 0.527 / ESU R Free: 0.319
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2736 3769 4.927 %RANDOM
Rwork0.2194 72729 --
all0.222 ---
obs-76498 99.552 %-
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: 87.946 Å2
Baniso -1Baniso -2Baniso -3
1-5.65 Å20 Å2-0 Å2
2---3.047 Å2-0 Å2
3----2.602 Å2
Refinement stepCycle: LAST / Resolution: 2.62→59.621 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13583 0 165 134 13882
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01214044
X-RAY DIFFRACTIONr_bond_other_d0.0010.01613484
X-RAY DIFFRACTIONr_angle_refined_deg0.8771.64819047
X-RAY DIFFRACTIONr_angle_other_deg0.2961.56331070
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.12351712
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.177595
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.01252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.486102431
X-RAY DIFFRACTIONr_dihedral_angle_6_deg12.62310634
X-RAY DIFFRACTIONr_chiral_restr0.0420.22175
X-RAY DIFFRACTIONr_chiral_restr_other0.0260.22
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0216193
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023129
X-RAY DIFFRACTIONr_nbd_refined0.2030.22963
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1820.212727
X-RAY DIFFRACTIONr_nbtor_refined0.1730.26851
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0730.27232
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2293
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0470.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0670.211
X-RAY DIFFRACTIONr_nbd_other0.1090.251
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0810.28
X-RAY DIFFRACTIONr_mcbond_it4.2518.7196857
X-RAY DIFFRACTIONr_mcbond_other4.2468.726857
X-RAY DIFFRACTIONr_mcangle_it6.77815.6748560
X-RAY DIFFRACTIONr_mcangle_other6.77815.6748561
X-RAY DIFFRACTIONr_scbond_it4.0149.2487187
X-RAY DIFFRACTIONr_scbond_other4.0149.2487188
X-RAY DIFFRACTIONr_scangle_it6.63116.85110485
X-RAY DIFFRACTIONr_scangle_other6.63116.8510486
X-RAY DIFFRACTIONr_lrange_it9.92479.99915292
X-RAY DIFFRACTIONr_lrange_other9.92580.0115282
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.62-2.6880.3782830.34852670.34956040.9010.92199.03640.305
2.688-2.7610.3822570.34352140.34555120.8940.92799.25620.3
2.761-2.8410.3542530.30650700.30953640.9250.94299.23560.261
2.841-2.9290.3442550.30448340.30651210.9140.94299.37510.262
2.929-3.0240.3172420.28747390.28950060.9230.94899.50060.248
3.024-3.130.3082460.27745950.27948690.9330.95199.42490.239
3.13-3.2480.3462330.28144320.28446890.9190.9599.48820.251
3.248-3.380.3272560.27142640.27445400.930.95499.55950.247
3.38-3.530.3232260.24740930.25143320.9350.96299.69990.226
3.53-3.7020.2831780.24740010.24941890.9510.96399.76130.231
3.702-3.9010.2732090.2337090.23239310.9560.96799.66930.219
3.901-4.1370.2651690.20535750.20837510.9590.97599.81340.199
4.137-4.4210.2521810.19133570.19535450.9570.97799.80250.189
4.421-4.7730.2221430.17531590.17833060.9710.98199.8790.181
4.773-5.2250.2641660.18128700.18530390.9620.98199.90130.191
5.225-5.8360.3051250.21826480.22227770.9540.97699.8560.223
5.836-6.7280.2451280.20923410.21124700.9660.97899.95950.216
6.728-8.2140.212890.15620180.15821080.9740.98599.95260.176
8.214-11.5080.158760.13715880.13816650.9880.98999.93990.159
11.508-59.6210.341540.2659550.26910150.8860.93499.40890.288

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