[English] 日本語
Yorodumi
- PDB-8szp: Human DHX9 bound to ADP -

+
Open data


ID or keywords:

Loading...

-
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


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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
1
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

-
Components

-
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

-
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

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
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