[English] 日本語
Yorodumi
- PDB-8dpe: Crystal structure of ATP-dependent RNA helicase DDX42 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8dpe
TitleCrystal structure of ATP-dependent RNA helicase DDX42
ComponentsATP-dependent RNA helicase DDX42
KeywordsSPLICING / HYDROLASE / DDX42 / splicing factor / RNA helicase
Function / homology
Function and homology information


U2-type prespliceosome assembly / U2-type prespliceosome / mRNA Splicing - Minor Pathway / Cajal body / mRNA Splicing - Major Pathway / protein localization / regulation of apoptotic process / RNA helicase activity / RNA helicase / nuclear speck ...U2-type prespliceosome assembly / U2-type prespliceosome / mRNA Splicing - Minor Pathway / Cajal body / mRNA Splicing - Major Pathway / protein localization / regulation of apoptotic process / RNA helicase activity / RNA helicase / nuclear speck / ATP hydrolysis activity / RNA binding / nucleoplasm / ATP binding / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
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 / 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-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 / 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
ATP-dependent RNA helicase DDX42
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.531 Å
AuthorsLarsen, N.A. / Tsai, J.
Funding support United States, 1items
OrganizationGrant numberCountry
Not funded United States
CitationJournal: To Be Published
Title: Crystal structure of ATP-dependent RNA helicase DDX42
Authors: Larsen, N.A.
History
DepositionJul 15, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ATP-dependent RNA helicase DDX42


Theoretical massNumber of molelcules
Total (without water)49,8751
Polymers49,8751
Non-polymers00
Water6,359353
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area20870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.917, 73.268, 134.041
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein ATP-dependent RNA helicase DDX42 / DEAD box protein 42 / RNA helicase-like protein / RHELP / RNA helicase-related protein / RNAHP / ...DEAD box protein 42 / RNA helicase-like protein / RHELP / RNA helicase-related protein / RNAHP / SF3b DEAD box protein / Splicing factor 3B-associated 125 kDa protein / SF3b125


Mass: 49874.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDX42 / Production host: Escherichia coli (E. coli) / References: UniProt: Q86XP3, RNA helicase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 353 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.78 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: 1 uL 8 mg/mL DDX42 (in 25 mM Tris, pH 7.5, 300 mM sodium chloride, 1 mM TCEP) + 1 uL reservoir solution (6-10% PEG8000, 0.1 M Tris, pH 8.5-9.0)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Mar 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.53→50 Å / Num. obs: 63581 / % possible obs: 98.4 % / Redundancy: 6.1 % / Biso Wilson estimate: 20.09 Å2 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.025 / Rrim(I) all: 0.062 / Χ2: 1.058 / Net I/σ(I): 8.7 / Num. measured all: 384934
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.53-1.585.40.83861240.6840.3860.9261.04496.2
1.58-1.6560.64661830.8180.2830.7061.07597.4
1.65-1.726.10.47962410.8990.2080.5231.07997.9
1.72-1.816.20.3162800.9570.1340.3391.08698.4
1.81-1.936.20.19663210.9830.0840.2131.09598.5
1.93-2.086.20.11962860.9910.0510.131.08598.3
2.08-2.296.20.07963750.9960.0340.0861.0798.9
2.29-2.626.20.06364330.9970.0270.0691.01999.3
2.62-3.36.10.04865290.9980.0210.0521.01399.5
3.3-505.90.02968090.9980.0130.0321.01599.7

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
SCALEPACKdata scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4NHO

4nho


Resolution: 1.531→38.147 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2552 3220 5.07 %
Rwork0.2121 60289 -
obs0.2142 63509 98.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 71.27 Å2 / Biso mean: 25.6866 Å2 / Biso min: 10.17 Å2
Refinement stepCycle: final / Resolution: 1.531→38.147 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3449 0 0 353 3802
Biso mean---31.02 -
Num. residues----436
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073513
X-RAY DIFFRACTIONf_angle_d1.1884747
X-RAY DIFFRACTIONf_chiral_restr0.044524
X-RAY DIFFRACTIONf_plane_restr0.007620
X-RAY DIFFRACTIONf_dihedral_angle_d13.3591317
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5311-1.5540.33181090.2872249495
1.554-1.57830.28941250.2868254196
1.5783-1.60420.33921360.2684257098
1.6042-1.63180.29611520.2645253997
1.6318-1.66150.29841410.2572256297
1.6615-1.69340.27871330.259259898
1.6934-1.7280.2861580.2558254097
1.728-1.76560.27831250.2429260799
1.7656-1.80670.28821470.2486256497
1.8067-1.85180.27481440.2472259398
1.8518-1.90190.28841470.2415257799
1.9019-1.95790.27481290.2269260898
1.9579-2.02110.29931210.22392648100
2.0211-2.09330.27481450.2232261998
2.0933-2.17710.26541420.2231260898
2.1771-2.27620.22231390.2181263799
2.2762-2.39610.26411610.219261499
2.3961-2.54620.25371470.2155266199
2.5462-2.74280.2921440.21732679100
2.7428-3.01870.26731540.21872666100
3.0187-3.45530.24061390.20862705100
3.4553-4.35230.22671360.18092769100
4.3523-38.1470.21351460.17542890100

+
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