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- PDB-4brw: Crystal structure of the yeast Dhh1-Pat1 complex -

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Basic information

Entry
Database: PDB / ID: 4brw
TitleCrystal structure of the yeast Dhh1-Pat1 complex
Components
  • ATP-DEPENDENT RNA HELICASE DHH1
  • DNA TOPOISOMERASE 2-ASSOCIATED PROTEIN PAT1
KeywordsHYDROLASE / TRANSLATIONAL REPRESSION / MRNP REMODELING / P- BOD
Function / homology
Function and homology information


regulation of cytoplasmic mRNA processing body assembly / mRNA decay by 5' to 3' exoribonuclease / Lsm1-7-Pat1 complex / negative regulation of translational elongation / cytoplasmic side of membrane / deadenylation-dependent decapping of nuclear-transcribed mRNA / formation of translation preinitiation complex / P-body assembly / regulation of translational initiation / mRNA transport ...regulation of cytoplasmic mRNA processing body assembly / mRNA decay by 5' to 3' exoribonuclease / Lsm1-7-Pat1 complex / negative regulation of translational elongation / cytoplasmic side of membrane / deadenylation-dependent decapping of nuclear-transcribed mRNA / formation of translation preinitiation complex / P-body assembly / regulation of translational initiation / mRNA transport / stress granule assembly / negative regulation of translational initiation / positive regulation of translation / P-body / mRNA processing / kinetochore / cytoplasmic stress granule / cytosolic small ribosomal subunit / RNA helicase activity / negative regulation of translation / RNA helicase / cell cycle / cell division / mRNA binding / chromatin binding / ATP hydrolysis activity / RNA binding / ATP binding / nucleus / cytoplasm
Similarity search - Function
mRNA decay factor PAT1 domain / Pat1-like / Topoisomerase II-associated protein PAT1 / 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 ...mRNA decay factor PAT1 domain / Pat1-like / Topoisomerase II-associated protein PAT1 / 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 nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Deadenylation-dependent mRNA-decapping factor PAT1 / ATP-dependent RNA helicase DHH1
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.795 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 / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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: DNA TOPOISOMERASE 2-ASSOCIATED PROTEIN PAT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1094
Polymers50,7532
Non-polymers3562
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-26 kcal/mol
Surface area19100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.635, 105.635, 122.068
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 DNA TOPOISOMERASE 2-ASSOCIATED PROTEIN PAT1 / DECAPPING ACTIVATOR AND TRANSLATIONAL REPRESSOR PAT1 / TOPOISOMERASE II-ASSOCIATED PROTEIN PAT1 / ...DECAPPING ACTIVATOR AND TRANSLATIONAL REPRESSOR PAT1 / TOPOISOMERASE II-ASSOCIATED PROTEIN PAT1 / MRNA TURNOVER PROTEIN 1


Mass: 7912.046 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN RESIDUES 5-79
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: P25644, RNA helicase
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.21 Å3/Da / Density % sol: 61.74 % / Description: NONE
Crystal growDetails: 50 MM TRIS PH 8.0, 4% MPD, 200 MM NACL, 25% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97139
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 25, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97139 Å / Relative weight: 1
ReflectionResolution: 2.8→79.88 Å / Num. obs: 17668 / % possible obs: 99.6 % / Redundancy: 8.6 % / Biso Wilson estimate: 73.29 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 18.3
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 2.8 / % possible all: 97.1

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Processing

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

1s2m


Resolution: 2.795→48.474 Å / SU ML: 0.41 / σ(F): 1.37 / Phase error: 25.94 / Stereochemistry target values: ML / Details: DISORDERED CHAIN B RESIDUES 5-24, 55-79
RfactorNum. reflection% reflection
Rfree0.2471 1622 5 %
Rwork0.2042 --
obs0.2063 17636 99.52 %
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.3 Å2
Refinement stepCycle: LAST / Resolution: 2.795→48.474 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3185 0 24 4 3213
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033265
X-RAY DIFFRACTIONf_angle_d0.7434414
X-RAY DIFFRACTIONf_dihedral_angle_d13.0281204
X-RAY DIFFRACTIONf_chiral_restr0.053510
X-RAY DIFFRACTIONf_plane_restr0.003567
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7951-2.87740.30541320.28782439X-RAY DIFFRACTION95
2.8774-2.97020.34481340.2882555X-RAY DIFFRACTION100
2.9702-3.07640.33771350.2752594X-RAY DIFFRACTION100
3.0764-3.19950.30841340.2582623X-RAY DIFFRACTION100
3.1995-3.34510.28381360.25832546X-RAY DIFFRACTION100
3.3451-3.52140.29231390.22672617X-RAY DIFFRACTION100
3.5214-3.7420.27461380.21122568X-RAY DIFFRACTION100
3.742-4.03080.24261360.19142602X-RAY DIFFRACTION100
4.0308-4.43620.19821330.17062585X-RAY DIFFRACTION100
4.4362-5.07750.22561360.16852588X-RAY DIFFRACTION100
5.0775-6.39480.22291330.21252574X-RAY DIFFRACTION100
6.3948-48.48160.21891360.18162605X-RAY DIFFRACTION100

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