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- PDB-7dtj: Crystal structure of the RecA2 domain of RNA helicase CGH-1 in C.... -

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Basic information

Entry
Database: PDB / ID: 7dtj
TitleCrystal structure of the RecA2 domain of RNA helicase CGH-1 in C. elegans
ComponentsATP-dependent RNA helicase cgh-1
KeywordsRNA BINDING PROTEIN / Helicase / RNA binding
Function / homology
Function and homology information


mRNA decay by 5' to 3' exoribonuclease / mRNA metabolic process / ribonucleoprotein granule / intracellular organelle / gamete generation / P-body assembly / P granule / oogenesis / stress granule assembly / determination of adult lifespan ...mRNA decay by 5' to 3' exoribonuclease / mRNA metabolic process / ribonucleoprotein granule / intracellular organelle / gamete generation / P-body assembly / P granule / oogenesis / stress granule assembly / determination of adult lifespan / P-body / cytoplasmic stress granule / spermatogenesis / RNA helicase activity / negative regulation of translation / RNA helicase / ribonucleoprotein complex / mRNA binding / negative regulation of apoptotic process / apoptotic process / ATP hydrolysis activity / ATP binding
Similarity search - Function
DEAD-box subfamily ATP-dependent helicases signature. / RNA helicase, DEAD-box type, Q motif / ATP-dependent RNA helicase DEAD-box, conserved site / 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-box subfamily ATP-dependent helicases signature. / RNA helicase, DEAD-box type, Q motif / ATP-dependent RNA helicase DEAD-box, conserved site / 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
Similarity search - Domain/homology
ATP-dependent RNA helicase cgh-1
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.402 Å
AuthorsZhang, Y. / Lv, M.Q. / Hong, J.J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31970669 China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2021
Title: Structural and biochemical insights into the recognition of RNA helicase CGH-1 by CAR-1 in C. elegans.
Authors: Zhang, Y. / Lv, M. / Li, F. / Li, M. / Zhang, J. / Shi, Y. / Hong, J.
History
DepositionJan 5, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-dependent RNA helicase cgh-1


Theoretical massNumber of molelcules
Total (without water)21,4891
Polymers21,4891
Non-polymers00
Water1629
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.825, 82.825, 60.769
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein ATP-dependent RNA helicase cgh-1 / Conserved germline helicase 1


Mass: 21488.693 Da / Num. of mol.: 1 / Fragment: RecA2 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: cgh-1, C07H6.5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q95YF3, RNA helicase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O

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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: 56.07 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1M Na acetate pH 5.0, 20% PEG 4000, 0.2M Ammonion acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.402→30.886 Å / Num. obs: 9668 / % possible obs: 99.62 % / Redundancy: 16.5 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 31.1
Reflection shellResolution: 2.402→2.488 Å / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 4.167 / Num. unique obs: 950

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Processing

Software
NameVersionClassification
SCALAdata scaling
PHENIX1.16_3549refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WAX

2wax


Resolution: 2.402→30.886 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2545 494 5.11 %
Rwork0.2258 9170 -
obs0.2271 9664 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 123.45 Å2 / Biso mean: 65.1744 Å2 / Biso min: 36.26 Å2
Refinement stepCycle: final / Resolution: 2.402→30.886 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1387 0 0 9 1396
Biso mean---59.39 -
Num. residues----173
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.402-2.64360.29111350.28952253100
2.6436-3.02580.30851130.27722261100
3.0258-3.81110.30591250.24192291100
3.8111-30.8860.2171210.1979236599
Refinement TLS params.Method: refined / Origin x: -35.3133 Å / Origin y: 8.0866 Å / Origin z: 6.4814 Å
111213212223313233
T0.4712 Å2-0.0033 Å2-0.0288 Å2-0.3947 Å20.0389 Å2--0.4682 Å2
L0.6446 °20.1045 °20.0867 °2-1.7565 °20.0743 °2--4.0919 °2
S0.1247 Å °-0.0771 Å °-0.048 Å °-0.1668 Å °-0.0848 Å °-0.0834 Å °-0.2836 Å °0.138 Å °0.0048 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 247 through 419)

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