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- PDB-2wx3: Asymmetric trimer of the human DCP1a C-terminal domain -

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Basic information

Entry
Database: PDB / ID: 2wx3
TitleAsymmetric trimer of the human DCP1a C-terminal domain
ComponentsMRNA-DECAPPING ENZYME 1A
KeywordsSTRUCTURAL PROTEIN / TRIMERIZATION MODULE / MRNA DECAPPING / P-BODY COMPONENT / ASYMMETRIC ASSEMBLY
Function / homology
Function and homology information


mRNA methylguanosine-cap decapping / deadenylation-independent decapping of nuclear-transcribed mRNA / 5'-(N7-methylguanosine 5'-triphospho)-[mRNA] hydrolase / protein localization to cytoplasmic stress granule / mRNA decay by 5' to 3' exoribonuclease / 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / deadenylation-dependent decapping of nuclear-transcribed mRNA / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay ...mRNA methylguanosine-cap decapping / deadenylation-independent decapping of nuclear-transcribed mRNA / 5'-(N7-methylguanosine 5'-triphospho)-[mRNA] hydrolase / protein localization to cytoplasmic stress granule / mRNA decay by 5' to 3' exoribonuclease / 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / deadenylation-dependent decapping of nuclear-transcribed mRNA / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / kinesin binding / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / enzyme activator activity / P-body / cytoplasmic ribonucleoprotein granule / mRNA binding / dendrite / identical protein binding / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Helix Hairpins - #2030 / mRNA-decapping enzyme, C-terminal / mRNA-decapping enzyme C-terminus / mRNA-decapping enzyme subunit 1 / Dcp1-like decapping family / Helix Hairpins / Helix non-globular / Special / PH-like domain superfamily
Similarity search - Domain/homology
mRNA-decapping enzyme 1A
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.31 Å
AuthorsTritschler, F. / Motz, C. / Weichenrieder, O.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Dcp1 Forms Asymmetric Trimers to Assemble Into Active Mrna Decapping Complexes in Metazoa.
Authors: Tritschler, F. / Braun, J.E. / Motz, C. / Igreja, C. / Haas, G. / Truffault, V. / Izaurralde, E. / Weichenrieder, O.
History
DepositionNov 1, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 1, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MRNA-DECAPPING ENZYME 1A
B: MRNA-DECAPPING ENZYME 1A
C: MRNA-DECAPPING ENZYME 1A


Theoretical massNumber of molelcules
Total (without water)17,3783
Polymers17,3783
Non-polymers00
Water97354
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5470 Å2
ΔGint-57.39 kcal/mol
Surface area8010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.750, 64.750, 103.030
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein MRNA-DECAPPING ENZYME 1A


Mass: 5792.622 Da / Num. of mol.: 3 / Fragment: TRIMERIZATION DOMAIN, RESIDUES 539-582
Source method: isolated from a genetically manipulated source
Details: EC3.-.-.- IN UNIPROT DISPUTED BY DEPOSITOR / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PRSFDUET-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / References: UniProt: Q9NPI6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TERMINAL CLONING TAG - GPHMADL

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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: 3.6 Å3/Da / Density % sol: 66 % / Description: NONE
Crystal growpH: 6 / Details: 50MM MES (PH 6.0), 1.2M NA-MALONATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.0688, 0.9792
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 8, 2008 / Details: MIRRORS
RadiationMonochromator: SI(111)MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.06881
20.97921
ReflectionResolution: 2.3→80 Å / Num. obs: 11317 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 44.1 Å2 / Rsym value: 0.08 / Net I/σ(I): 11.9
Reflection shellResolution: 2.31→2.37 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2.5 / Rsym value: 0.56 / % possible all: 95.7

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
XDSdata reduction
XSCALEdata scaling
autoSHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.31→56.08 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.882 / SU B: 5.699 / SU ML: 0.14 / Cross valid method: THROUGHOUT / ESU R: 0.206 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. RESIDUES A575-A582, B532-B534, B577-B582, C532-C535 ARE DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.25232 608 5.4 %RANDOM
Rwork0.20793 ---
obs0.21007 10707 98.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.402 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20.05 Å2-0 Å2
2--0.11 Å2-0 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 2.31→56.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1050 0 0 54 1104
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0211062
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6481.981437
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1955129
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.48726.74443
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.4715210
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1040.2186
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02733
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1191.5658
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.16921073
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.5183404
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.8794.5364
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.31→2.369 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 74 -
Rwork0.247 698 -
obs--95.66 %

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