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

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Basic information

Entry
Database: PDB / ID: 2qkm
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 / : ...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 / 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. / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / NUDIX domain / PH-domain like / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / PH-like domain superfamily / Arc Repressor Mutant, subunit A / Roll / Alpha-Beta Complex / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / mRNA decapping complex subunit 2 / mRNA-decapping enzyme subunit 1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsShe, M. / 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 1.0Apr 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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: SPBC3B9.21 protein
B: SPAC19A8.12 protein
C: SPBC3B9.21 protein
D: SPAC19A8.12 protein
E: SPBC3B9.21 protein
F: SPAC19A8.12 protein
G: SPBC3B9.21 protein
H: SPAC19A8.12 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,80910
Polymers183,7958
Non-polymers1,0142
Water1,946108
1
A: SPBC3B9.21 protein
B: SPAC19A8.12 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4563
Polymers45,9492
Non-polymers5071
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
MethodPISA
2
E: SPBC3B9.21 protein
F: SPAC19A8.12 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4563
Polymers45,9492
Non-polymers5071
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
MethodPISA
3
C: SPBC3B9.21 protein
D: SPAC19A8.12 protein


Theoretical massNumber of molelcules
Total (without water)45,9492
Polymers45,9492
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: SPBC3B9.21 protein
H: SPAC19A8.12 protein


Theoretical massNumber of molelcules
Total (without water)45,9492
Polymers45,9492
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.289, 161.443, 91.386
Angle α, β, γ (deg.)90.00, 97.49, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21E
12B
22F
13C
23G
14D
24H

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARG4AA1 - 1271 - 127
21ARGARG4EE1 - 1271 - 127
12SERSER4BB1 - 2661 - 266
22SERSER4FF1 - 2661 - 266
13GLUGLU4CC1 - 1231 - 123
23GLUGLU4GG1 - 1231 - 123
14ILEILE6DD1 - 2331 - 233
24ILEILE6HH1 - 2331 - 233

NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein
SPBC3B9.21 protein / Dcp1 protein


Mass: 15002.142 Da / Num. of mol.: 4
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, EC: 3.6.1.30
#2: Protein
SPAC19A8.12 protein


Mass: 30946.633 Da / Num. of mol.: 4 / Fragment: residues 1-266
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
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.72 Å3/Da / Density % sol: 54.74 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 8% Ethylene Glycol, 100 mM HEPES pH 7.0, 11.6% MPD, 4.4% PEG 4000 and 10 mM ATP, VAPOR DIFFUSION, HANGING DROP, temperature 285K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 15, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.8→90.54 Å / Num. all: 48289 / Num. obs: 48226 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.13
Reflection shellResolution: 2.8→2.87 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.323 / Mean I/σ(I) obs: 3.3 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 2A6T, 2QKL

2a6t

2qkl


Resolution: 2.8→20 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.867 / SU B: 31.214 / SU ML: 0.302 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.42 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28923 2373 4.9 %RANDOM
Rwork0.23339 ---
obs0.23611 45695 99.88 %-
all-48289 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.918 Å2
Baniso -1Baniso -2Baniso -3
1-5.02 Å20 Å20.82 Å2
2--0.84 Å20 Å2
3----5.65 Å2
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11704 0 62 108 11874
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02212041
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2411.94816283
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5951397
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.25123.915613
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.753152150
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.631585
X-RAY DIFFRACTIONr_chiral_restr0.090.21767
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029090
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2250.25473
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.28081
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2451
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.260.257
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2130.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6331.57261
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.131211493
X-RAY DIFFRACTIONr_scbond_it1.04835446
X-RAY DIFFRACTIONr_scangle_it1.6944.54790
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1034medium positional0.350.5
2B2143medium positional0.490.5
3C1026medium positional0.480.5
4D1540loose positional0.745
1A1034medium thermal0.342
2B2143medium thermal0.422
3C1026medium thermal0.332
4D1540loose thermal2.1310
LS refinement shellResolution: 2.8→2.871 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 154 -
Rwork0.277 3331 -
obs--99.91 %
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)
12.10410.0165-0.20753.69560.31562.10380.0883-0.0715-0.0774-0.04690.0245-0.53380.15160.2153-0.1128-0.06760.040.0129-0.0576-0.0574-0.105812.3221-45.618315.7576
20.6054-0.1781-0.04880.8568-0.47512.9942-0.0209-0.0080.0586-0.00380.0217-0.00520.0533-0.2053-0.0009-0.0802-0.01930.0317-0.0748-0.0272-0.1012-5.9105-34.480539.9733
34.0392-0.533-0.18621.72421.09512.83080.00780.15710.0922-0.30470.0393-0.0676-0.1886-0.0748-0.04710.07180.0487-0.0052-0.08950.0084-0.2625-4.2315-41.0874-8.3299
41.2156-0.1181-2.04890.70790.08915.54160.06530.2245-0.0857-0.1395-0.12310.45510.0565-0.95840.0578-0.2834-0.0036-0.05950.1906-0.01010.0271-29.6247-34.833226.9877
51.91140.37-0.0584.1071-0.6142.30160.03080.03490.2379-0.26920.06770.4294-0.0262-0.2476-0.0985-0.00950.06-0.0295-0.05850.0764-0.1167-16.487412.56512.1639
60.652-0.2225-0.41970.92970.36882.6079-0.0408-0.0598-0.02540.11620.04020.01350.01780.12570.00060.0493-0.00250.0008-0.08560.0276-0.1331-4.82011.139140.1211
73.7504-0.26610.3271.2105-1.21633.0457-0.0690.0345-0.2065-0.3641-0.00240.06970.26760.18450.07140.09770.08670.0956-0.04260.0372-0.24885.7477.3774-6.9353
81.5397-0.71890.84940.80720.12885.8546-0.0446-0.23990.2673-0.01540.0506-0.39060.16570.6235-0.006-0.21420.0033-0.01850.1060.0588-0.087820.28541.48632.6773
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1271 - 127
2X-RAY DIFFRACTION2BB1 - 2661 - 266
3X-RAY DIFFRACTION3CC1 - 1231 - 123
4X-RAY DIFFRACTION4DD1 - 2331 - 233
5X-RAY DIFFRACTION5EE1 - 1271 - 127
6X-RAY DIFFRACTION6FF1 - 2661 - 266
7X-RAY DIFFRACTION7GG1 - 1231 - 123
8X-RAY DIFFRACTION8HH1 - 2351 - 235

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