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- PDB-2qkl: The crystal structure of fission yeast mRNA decapping enzyme Dcp1... -

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Basic information

Entry
Database: PDB / ID: 2qkl
TitleThe crystal structure of fission yeast mRNA decapping enzyme Dcp1-Dcp2 complex
Components
  • SPAC19A8.12 protein
  • SPBC3B9.21 protein
KeywordsHYDROLASE / protein-protein complex
Function / homology
Function and homology information


mRNA phosphatase activator activity / RNA decapping complex / mRNA methylguanosine-cap decapping / 5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase activity / 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity / Hydrolases / deadenylation-dependent decapping of nuclear-transcribed mRNA / mRNA cap binding / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / nuclear-transcribed mRNA catabolic process ...mRNA phosphatase activator activity / RNA decapping complex / mRNA methylguanosine-cap decapping / 5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase activity / 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity / Hydrolases / deadenylation-dependent decapping of nuclear-transcribed mRNA / mRNA cap binding / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / nuclear-transcribed mRNA catabolic process / P-body / mRNA processing / cytoplasmic stress granule / manganese ion binding / single-stranded RNA binding / magnesium ion binding / RNA binding / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Dcp2, box A domain / mRNA-decapping enzyme subunit 1 / Dcp1-like decapping family / mRNA decapping protein 2, Box A domain / mRNA decapping protein 2, Box A domain superfamily / mRNA decapping enzyme 2 , NUDIX hydrolase domain / Dcp2, box A domain / Dcp2, box A domain / NUDIX hydrolase, conserved site / Nudix box signature. ...Dcp2, box A domain / mRNA-decapping enzyme subunit 1 / Dcp1-like decapping family / mRNA decapping protein 2, Box A domain / mRNA decapping protein 2, Box A domain superfamily / mRNA decapping enzyme 2 , NUDIX hydrolase domain / Dcp2, box A domain / Dcp2, box A domain / NUDIX hydrolase, conserved site / Nudix box signature. / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / PH-like domain superfamily / Arc Repressor Mutant, subunit A / Roll / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
LEAD (II) ION / mRNA decapping complex subunit 2 / mRNA-decapping enzyme subunit 1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.33 Å
AuthorsShe, M. / Chen, N. / Song, H.
CitationJournal: Mol.Cell / Year: 2008
Title: Structural basis of dcp2 recognition and activation by dcp1.
Authors: She, M. / Decker, C.J. / Svergun, D.I. / Round, A. / Chen, N. / Muhlrad, D. / Parker, R. / Song, H.
History
DepositionJul 11, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 21, 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: SPBC3B9.21 protein
B: SPAC19A8.12 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5123
Polymers26,3052
Non-polymers2071
Water75742
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.723, 49.665, 115.052
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe asymmetric unit contains one biological unit of Dcp1-Dcp2 complex

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Components

#1: Protein SPBC3B9.21 protein / Dcp1 protein


Mass: 15002.142 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: dcp1 / Plasmid: pGEX-6p-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 star / References: UniProt: Q9P805
#2: Protein SPAC19A8.12 protein


Mass: 11302.781 Da / Num. of mol.: 1 / Fragment: Residues 1-95
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: SPAC19A8.12 / Plasmid: pGEX-6p-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 star / References: UniProt: O13828, EC: 3.6.1.30
#3: Chemical ChemComp-PB / LEAD (II) ION


Mass: 207.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Pb
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 2.32 Å3/Da / Density % sol: 46.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M Ammonium Acetate and 5% PEG3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorDate: Oct 3, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.33→20 Å / Num. all: 12284 / Num. obs: 11066 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.9 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 7.6
Reflection shellResolution: 2.33→2.39 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.345 / Mean I/σ(I) obs: 2.2 / % possible all: 99.5

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
d*TREKdata reduction
d*TREKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.33→20 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.934 / SU B: 14.972 / SU ML: 0.187 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.411 / ESU R Free: 0.257 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.259 563 5.1 %RANDOM
Rwork0.227 ---
obs0.229 10983 99.97 %-
all-12284 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.623 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å20 Å20 Å2
2---0.07 Å20 Å2
3---0.41 Å2
Refinement stepCycle: LAST / Resolution: 2.33→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1769 0 1 42 1812
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221822
X-RAY DIFFRACTIONr_angle_refined_deg1.2581.9292470
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0865208
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.39623.762101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.88515306
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9681513
X-RAY DIFFRACTIONr_chiral_restr0.0850.2268
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021412
X-RAY DIFFRACTIONr_nbd_refined0.1990.2692
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21210
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.255
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2220.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1010.25
X-RAY DIFFRACTIONr_mcbond_it0.4261.51064
X-RAY DIFFRACTIONr_mcangle_it0.83621722
X-RAY DIFFRACTIONr_scbond_it1.3223832
X-RAY DIFFRACTIONr_scangle_it2.1114.5748
LS refinement shellResolution: 2.33→2.39 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 49 -
Rwork0.289 741 -
obs-790 99.75 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.8065-0.0341-0.03661.9185-0.82653.54150.00210.17550.1789-0.0372-0.0110.0249-0.0324-0.03280.0089-0.2041-0.02080.0077-0.1817-0.0052-0.175361.906112.18776.783
23.0263-0.65150.31983.44110.42423.5563-0.0161-0.1384-0.0870.3859-0.01860.010.0934-0.13520.0347-0.0858-0.01890.0168-0.1503-0.006-0.143558.649710.860229.3864
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1271 - 127
2X-RAY DIFFRACTION2BB2 - 912 - 91

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