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- PDB-4bru: Crystal structure of the yeast Dhh1-Edc3 complex -

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Basic information

Entry
Database: PDB / ID: 4bru
TitleCrystal structure of the yeast Dhh1-Edc3 complex
Components
  • ATP-DEPENDENT RNA HELICASE DHH1
  • ENHANCER OF MRNA-DECAPPING PROTEIN 3
KeywordsHYDROLASE / DECAPPING / TRANSLATIONAL REPRESSION / MRNP REMODEL P-BODY / DEAD-BOX
Function / homology
Function and homology information


regulation of cytoplasmic mRNA processing body assembly / deadenylation-independent decapping of nuclear-transcribed mRNA / mRNA decay by 5' to 3' exoribonuclease / negative regulation of translational elongation / cytoplasmic side of membrane / deadenylation-dependent decapping of nuclear-transcribed mRNA / P-body assembly / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / mRNA transport / stress granule assembly ...regulation of cytoplasmic mRNA processing body assembly / deadenylation-independent decapping of nuclear-transcribed mRNA / mRNA decay by 5' to 3' exoribonuclease / negative regulation of translational elongation / cytoplasmic side of membrane / deadenylation-dependent decapping of nuclear-transcribed mRNA / P-body assembly / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / mRNA transport / stress granule assembly / positive regulation of translation / P-body / mRNA processing / cytoplasmic stress granule / negative regulation of translation / RNA helicase activity / RNA helicase / mRNA binding / chromatin binding / ATP hydrolysis activity / ATP binding / nucleus / cytoplasm
Similarity search - Function
FDF domain / FDF domain / DFDF domain / DFDF domain profile. / FDF / YjeF N-terminal domain superfamily / YjeF-related protein N-terminus / YjeF N-terminal domain / YjeF N-terminal domain profile. / : ...FDF domain / FDF domain / DFDF domain / DFDF domain profile. / FDF / YjeF N-terminal domain superfamily / YjeF-related protein N-terminus / YjeF N-terminal domain / YjeF N-terminal domain profile. / : / DEAD-box subfamily ATP-dependent helicases signature. / Sm domain profile. / 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 nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ATP-dependent RNA helicase DHH1 / Enhancer of mRNA-decapping protein 3
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.245 Å
AuthorsSharif, H. / Ozgur, S. / Sharma, K. / Basquin, C. / Urlaub, H. / Conti, E.
CitationJournal: Nucleic Acids Res. / Year: 2013
Title: Structural Analysis of the Yeast Dhh1-Pat1 Complex Reveals How Dhh1 Engages Pat1, Edc3 and RNA in Mutually Exclusive Interactions
Authors: Sharif, H. / Ozgur, S. / Sharma, K. / Basquin, C. / Urlaub, H. / Conti, E.
History
DepositionJun 5, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP-DEPENDENT RNA HELICASE DHH1
B: ENHANCER OF MRNA-DECAPPING PROTEIN 3


Theoretical massNumber of molelcules
Total (without water)48,1672
Polymers48,1672
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-19.1 kcal/mol
Surface area18510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.831, 105.831, 124.648
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122

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Components

#1: Protein ATP-DEPENDENT RNA HELICASE DHH1 / DEXD/H-BOX HELICASE 1


Mass: 42840.594 Da / Num. of mol.: 1 / Fragment: RESIDUES 46-422 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Strain: S288C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD PLYSS / References: UniProt: P39517, RNA helicase
#2: Protein/peptide ENHANCER OF MRNA-DECAPPING PROTEIN 3


Mass: 5326.702 Da / Num. of mol.: 1 / Fragment: RESIDUES 77-116
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Strain: S288C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD PLYSS / References: UniProt: P39998

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.29 Å3/Da / Density % sol: 62.67 % / Description: NONE
Crystal growDetails: 50 MM MES PH 6.0, 10% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97961
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97961 Å / Relative weight: 1
ReflectionResolution: 3.25→53.7 Å / Num. obs: 11718 / % possible obs: 99.7 % / Redundancy: 17.3 % / Biso Wilson estimate: 111.31 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 23.5
Reflection shellResolution: 3.25→3.36 Å / Redundancy: 16 % / Rmerge(I) obs: 1.24 / Mean I/σ(I) obs: 2.4 / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSINTEGRATEdata reduction
XDSCORRECTdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1S2M

1s2m


Resolution: 3.245→53.704 Å / SU ML: 0.45 / σ(F): 2.02 / Phase error: 26.1 / Stereochemistry target values: ML
Details: RESIDUE CHAIN A 422 NOT MODELED. RESIDUES CHAIN B 77-87 DISORDERED
RfactorNum. reflection% reflection
Rfree0.2457 1078 5.1 %
Rwork0.2085 --
obs0.2105 11712 99.66 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 105.6 Å2
Refinement stepCycle: LAST / Resolution: 3.245→53.704 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3110 0 0 0 3110
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033172
X-RAY DIFFRACTIONf_angle_d0.794302
X-RAY DIFFRACTIONf_dihedral_angle_d11.7321142
X-RAY DIFFRACTIONf_chiral_restr0.052507
X-RAY DIFFRACTIONf_plane_restr0.003552
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2455-3.39320.32131260.29822490X-RAY DIFFRACTION98
3.3932-3.5720.29041370.25942543X-RAY DIFFRACTION100
3.572-3.79580.3061360.23352535X-RAY DIFFRACTION100
3.7958-4.08880.27891390.21642549X-RAY DIFFRACTION100
4.0888-4.50.25261290.17622525X-RAY DIFFRACTION100
4.5-5.15080.22231390.18432550X-RAY DIFFRACTION100
5.1508-6.48760.27281370.24162546X-RAY DIFFRACTION100
6.4876-53.71090.20141350.18782533X-RAY DIFFRACTION100

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