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- PDB-1q67: Crystal structure of Dcp1p -

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Basic information

Entry
Database: PDB / ID: 1q67
TitleCrystal structure of Dcp1p
ComponentsDecapping protein involved in mRNA degradation-Dcp1p
KeywordsTRANSCRIPTION / beta sandwich
Function / homology
Function and homology information


RNA decapping complex / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / deadenylation-independent decapping of nuclear-transcribed mRNA / mRNA decay by 5' to 3' exoribonuclease / cytoplasmic side of membrane / deadenylation-dependent decapping of nuclear-transcribed mRNA / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / enzyme activator activity / P-body ...RNA decapping complex / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / deadenylation-independent decapping of nuclear-transcribed mRNA / mRNA decay by 5' to 3' exoribonuclease / cytoplasmic side of membrane / deadenylation-dependent decapping of nuclear-transcribed mRNA / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / enzyme activator activity / P-body / mRNA processing / mRNA binding / nucleus / cytoplasm
Similarity search - Function
mRNA-decapping enzyme subunit 1 / Dcp1-like decapping family / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
mRNA-decapping enzyme subunit 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsShe, M. / Decker, C.J. / Liu, Y. / Chen, N. / Parker, R. / Song, H.
Citation
Journal: Nat.Struct.Mol.Biol. / Year: 2004
Title: Crystal structure of Dcp1p and its functional implications in mRNA decapping
Authors: She, M. / Decker, C.J. / Sundramurthy, K. / Liu, Y. / Chen, N. / Parker, R. / Song, H.
#1: Journal: Nature / Year: 1996
Title: An essential component of the decapping enzyme required for normal rates of mRNA turnover
Authors: Beelman, C.A. / Stevens, A. / Caponigro, G. / LaGrandeur, T.E. / Hatfield, L. / Fortner, D.M. / Parker, R.
History
DepositionAug 12, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Decapping protein involved in mRNA degradation-Dcp1p
B: Decapping protein involved in mRNA degradation-Dcp1p


Theoretical massNumber of molelcules
Total (without water)52,5892
Polymers52,5892
Non-polymers00
Water2,810156
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)123.550, 123.550, 77.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

#1: Protein Decapping protein involved in mRNA degradation-Dcp1p /


Mass: 26294.357 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: DCP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12517
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 3.26 Å3/Da / Density % sol: 62.3 %
Crystal growDetails: VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
pH: 7.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
112 mg/mlprotein1drop
220 mMTris-HCl1droppH7.6
3100 mM1dropNaCl
42 mM1dropMgCl2
52 mMdithiothreitol1drop
60.76 Mammonium sulfate1reservoir
71.50 M1reservoirNaCl
85 mMdithiothreitol1reservoir
90.1 MTris-HCl1reservoirpH8.5
106 mMEDTA1reservoir
112 %(v/v)isopropanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9798
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 34251 / % possible obs: 97.9 % / Redundancy: 8.4 % / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 8.3
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.536 / Mean I/σ(I) obs: 1.1 / Rsym value: 0.536 / % possible all: 97.9
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 50 Å / Num. measured all: 286716
Reflection shell
*PLUS
Rmerge(I) obs: 0.371 / Mean I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
CNS1refinement
RefinementMethod to determine structure: SAD / Resolution: 2.3→20 Å / Cross valid method: FREE R / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflection
Rfree0.268 1496 -
Rwork0.227 --
obs0.227 30056 97.8 %
all-30747 -
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2570 0 0 156 2726
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.3

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