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- PDB-7dtk: Crystal structure of the RecA1 domain of RNA helicase CGH-1 in C.... -

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Basic information

Entry
Database: PDB / ID: 7dtk
TitleCrystal structure of the RecA1 domain of RNA helicase CGH-1 in C. elegans
ComponentsATP-dependent RNA helicase cgh-1
KeywordsRNA BINDING PROTEIN / ATP binding / D-E-A-D box
Function / homology
Function and homology information


mRNA decay by 5' to 3' exoribonuclease / mRNA metabolic process / messenger ribonucleoprotein complex / 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 / messenger ribonucleoprotein complex / 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 / apoptotic process / negative regulation of apoptotic process / ATP hydrolysis activity / ATP binding
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 cgh-1
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.849 Å
AuthorsHong, J.J. / Lv, M.Q. / Zhang, Y.
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
B: ATP-dependent RNA helicase cgh-1
A: ATP-dependent RNA helicase cgh-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7216
Polymers53,3522
Non-polymers3684
Water3,693205
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint-8 kcal/mol
Surface area19080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.754, 44.091, 54.213
Angle α, β, γ (deg.)95.490, 96.320, 100.770
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 26676.246 Da / Num. of mol.: 2 / Fragment: RecA1 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: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 205 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.86 Å3/Da / Density % sol: 33.76 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 25% PEG 3350, 0.2M Sodium Chloride, 0.1M Hepes pH 7.5

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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: Dec 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.849→35.656 Å / Num. obs: 31650 / % possible obs: 96.38 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 20.404
Reflection shellResolution: 1.849→1.915 Å / Rmerge(I) obs: 0.318 / Mean I/σ(I) obs: 2.95 / Num. unique obs: 3059

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Processing

Software
NameVersionClassification
SCALAdata scaling
PHENIX1.16_3549refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CT4

4ct4


Resolution: 1.849→35.656 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 22.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.206 1546 4.89 %
Rwork0.1721 30045 -
obs0.1738 31591 96.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.96 Å2 / Biso mean: 34.057 Å2 / Biso min: 13.22 Å2
Refinement stepCycle: final / Resolution: 1.849→35.656 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3129 0 24 205 3358
Biso mean--55.47 37.89 -
Num. residues----407
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8494-1.90910.27721240.257263293
1.9091-1.97730.33191300.2385269095
1.9773-2.05650.26521600.203269896
2.0565-2.15010.25021390.2006272696
2.1501-2.26340.23241300.1844272596
2.2634-2.40520.23491510.177274097
2.4052-2.59080.23961370.1873276797
2.5908-2.85150.23681250.1871275897
2.8515-3.26380.21281520.1763276798
3.2638-4.11110.17161380.1516277698
4.1111-35.6560.16171600.1425276698
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.4517-0.05110.8112.72960.65022.1753-0.1138-0.20190.10020.13970.06150.1273-0.1121-0.13220.04460.1120.01970.02110.18580.00470.1721-7.8058-6.3141-14.6651
22.1360.04070.26342.84331.0712.01460.12750.0762-0.0191-0.0796-0.10330.02210.01360.0399-0.00820.1518-0.0121-0.00970.13980.0140.14958.1636.371815.3377
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'B' and resid 42 through 245)B42 - 245
2X-RAY DIFFRACTION2(chain 'A' and resid 43 through 245)A43 - 245

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