|Entry||Database: PDB / ID: 1q67|
|Title||Crystal structure of Dcp1p|
|Components||Decapping protein involved in mRNA degradation-Dcp1p|
|Keywords||TRANSCRIPTION / beta sandwich|
|Function / homology|
Function and homology information
Dcp1-Dcp2 complex / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Butyrate Response Factor 1 (BRF1) 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 / positive regulation of catalytic activity / enzyme activator activity ...Dcp1-Dcp2 complex / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Butyrate Response Factor 1 (BRF1) 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 / positive regulation of catalytic activity / enzyme activator activity / P-body / mRNA processing / mRNA binding / nucleus / cytoplasm
Similarity search - Function
Dcp1-like decapping family / mRNA-decapping enzyme subunit 1 / 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 species||Saccharomyces cerevisiae (baker's yeast)|
|Method||X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å|
|Authors||She, M. / Decker, C.J. / Liu, Y. / Chen, N. / Parker, R. / Song, H.|
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.
|Structure viewer||Molecule: |
Downloads & links
A: Decapping protein involved in mRNA degradation-Dcp1p
B: 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 (baker's yeast)
Gene: DCP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12517
|#2: Water|| ChemComp-HOH / |
|Experiment||Method: X-RAY DIFFRACTION / Number of used crystals: 1|
|Crystal||Density Matthews: 3.26 Å3/Da / Density % sol: 62.3 %|
|Crystal grow||Details: VAPOR DIFFUSION, HANGING DROP|
*PLUSpH: 7.6 / Method: vapor diffusion, hanging drop
|Components of the solutions|
|Diffraction||Mean temperature: 100 K|
|Diffraction source||Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9798|
|Detector||Type: MARRESEARCH / Detector: CCD|
|Radiation||Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray|
|Radiation wavelength||Wavelength: 0.9798 Å / Relative weight: 1|
|Reflection||Resolution: 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 shell||Resolution: 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|
*PLUSHighest resolution: 2.3 Å / Lowest resolution: 50 Å / Num. measured all: 286716
*PLUSRmerge(I) obs: 0.371 / Mean I/σ(I) obs: 1.9
|Refinement||Method to determine structure: SAD / Resolution: 2.3→20 Å / Cross valid method: FREE R / Stereochemistry target values: ENGH & HUBER|
|Refinement step||Cycle: LAST / Resolution: 2.3→20 Å|
|Refine LS restraints|
*PLUSLowest resolution: 20 Å / % reflection Rfree: 10 %
|Refine LS restraints|
*PLUSType: c_angle_deg / Dev ideal: 1.3
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