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- PDB-5j3y: Crystal structure of S. pombe Dcp2:Dcp1 mRNA decapping complex -

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Basic information

Entry
Database: PDB / ID: 5j3y
TitleCrystal structure of S. pombe Dcp2:Dcp1 mRNA decapping complex
Components
  • mRNA decapping complex subunit 2
  • mRNA-decapping enzyme subunit 1
KeywordsHYDROLASE / decapping / mRNA decay / EVH1 / Nudix
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 / cytoplasm / cytosol
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 / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase ...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 / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / 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
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: 3.288 Å
AuthorsValkov, E. / Muthukumar, S. / Chang, C.T. / Jonas, S. / Weichenrieder, O. / Izaurralde, E.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2016
Title: Structure of the Dcp2-Dcp1 mRNA-decapping complex in the activated conformation.
Authors: Valkov, E. / Muthukumar, S. / Chang, C.T. / Jonas, S. / Weichenrieder, O. / Izaurralde, E.
History
DepositionMar 31, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2016Group: Database references
Revision 1.2Jun 15, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 650HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700SHEET 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 subunit 1
B: mRNA decapping complex subunit 2
C: mRNA-decapping enzyme subunit 1
D: mRNA decapping complex subunit 2


Theoretical massNumber of molelcules
Total (without water)87,3884
Polymers87,3884
Non-polymers00
Water00
1
A: mRNA-decapping enzyme subunit 1
B: mRNA decapping complex subunit 2


Theoretical massNumber of molelcules
Total (without water)43,6942
Polymers43,6942
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: mRNA-decapping enzyme subunit 1
D: mRNA decapping complex subunit 2


Theoretical massNumber of molelcules
Total (without water)43,6942
Polymers43,6942
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)124.362, 124.362, 366.978
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein mRNA-decapping enzyme subunit 1


Mass: 15294.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: dcp1, SPBC3B9.21 / Plasmid: pnEApG / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): star / References: UniProt: Q9P805
#2: Protein mRNA decapping complex subunit 2


Mass: 28399.793 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: dcp2, SPAC19A8.12 / Plasmid: pnYC / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): star
References: UniProt: O13828, 5'-(N7-methylguanosine 5'-triphospho)-[mRNA] hydrolase

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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: 4.7 Å3/Da / Density % sol: 74 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 6.5
Details: 0.1 M MES/NaOH (pH 6.5), 0.2 M ammonium sulfate, 30% (w/v) PEG 5000 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 13, 2014 / Details: DYNAMICALLY BENDABLE MIRRORS
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.29→47.4 Å / Num. obs: 26491 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 9.6 % / Biso Wilson estimate: 112 Å2 / CC1/2: 0.995 / Rsym value: 0.136 / Net I/av σ(I): 2.9 / Net I/σ(I): 10.3
Reflection shellResolution: 3.29→3.47 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.859 / Mean I/σ(I) obs: 2.3 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(dev_2283: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QKM

2qkm


Resolution: 3.288→47.444 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2518 1321 5.01 %
Rwork0.2244 --
obs0.2258 26390 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.288→47.444 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6021 0 0 0 6021
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026168
X-RAY DIFFRACTIONf_angle_d0.3998331
X-RAY DIFFRACTIONf_dihedral_angle_d8.6783714
X-RAY DIFFRACTIONf_chiral_restr0.041895
X-RAY DIFFRACTIONf_plane_restr0.0031069
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2877-3.41930.33761380.30862614X-RAY DIFFRACTION96
3.4193-3.57490.31971440.27842737X-RAY DIFFRACTION100
3.5749-3.76330.28791450.24172740X-RAY DIFFRACTION100
3.7633-3.9990.24331440.22942739X-RAY DIFFRACTION100
3.999-4.30760.22961460.2222760X-RAY DIFFRACTION100
4.3076-4.74070.22321450.1962767X-RAY DIFFRACTION100
4.7407-5.42580.2411470.19292818X-RAY DIFFRACTION100
5.4258-6.83270.23881510.25372849X-RAY DIFFRACTION100
6.8327-47.44850.25681610.21523045X-RAY DIFFRACTION100
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)
13.50312.6686-1.0844.55281.16742.1536-0.471-0.30970.4243-0.4306-0.06070.4324-0.23890.95550.43061.49510.39020.01581.16590.18881.164242.50744.82-45.0576
29.5292-0.1511-0.7795.65671.40764.23710.22251.01620.0076-0.3928-0.58921.60920.3509-0.2545-0.0341.31290.41090.05420.6142-0.1981.342826.66620.3484-42.7143
30.4321-1.9798-0.05259.53982.18367.9555-0.342-0.3826-0.3313-0.0341-0.43373.2378-0.3161-1.91640.55871.620.75070.30551.51770.12372.900214.6552-9.8871-34.4254
43.9645-0.7929-1.27788.6401-5.66695.42930.71150.44670.2937-2.3768-0.04890.37830.85530.735-0.4171.65340.37130.18610.5848-0.0781.235328.34953.3822-44.8119
57.6088-2.3832-0.16112.1113-1.27515.2276-0.10320.6426-0.4852-0.2362-1.0192-0.03550.2850.1387-1.50821.09790.40910.11890.5784-0.13931.159525.58421.5941-48.9315
65.24223.7327-1.82484.1457-2.27122.72930.5343-0.18260.1522-1.5215-0.25620.72951.26130.2305-0.17721.29750.3975-0.06210.958-0.25881.49320.4572-0.5612-43.1541
75.15385.42752.82345.82532.18047.2450.38450.8942-0.79721.50341.2039-0.99762.80690.3517-1.73891.14180.08810.15550.7643-0.26341.5513.7618-0.4098-39.3736
87.74265.7124-5.56246.6038-4.76424.1789-1.1539-2.10360.32851.4899-0.231.5456-0.99810.14861.07231.60790.4650.36840.89290.08861.779622.31910.234-32.8078
94.9015-0.1986-0.70694.8265-5.56817.0486-0.4649-1.32890.9229-0.28870.55931.7706-3.88330.8437-0.1242.36630.24440.05851.1644-0.0961.449522.318210.8818-37.4398
108.13383.4364-2.99545.9015-0.15612.09730.1651.34451.0598-1.123-0.37840.13560.66730.43750.08431.65310.55470.07561.0510.27611.043840.1786-9.3936-47.3771
117.832-1.61860.92562.9312.37993.3794-0.3256-0.5917-0.2174-0.1623-0.91590.12620.39410.5321.01091.64880.47150.1551.050.1510.968540.7742-7.5494-32.7421
124.9152.26234.13797.1339-0.39476.2137-0.35080.6351-1.6515-0.43010.0489-0.28730.79871.1773-0.09061.32230.75190.29371.54280.04071.072146.1328-15.0387-42.8497
136.21962.6177-2.78815.73620.34812.7695-0.4747-0.03471.36840.7577-0.3577-1.10440.56322.14270.68161.40060.26740.15831.49420.41561.483853.0952-4.7221-29.8111
143.07641.560.83027.64211.03457.14340.25280.2195-0.0520.6434-0.24821.39650.336-0.7127-0.11081.16560.42160.17481.041-0.13831.247435.2109-33.8734-28.8117
154.8252-4.63880.52374.6546-0.44820.07030.09290.31090.86670.4773-0.2844-0.5714-0.8903-0.2941-0.29261.50.5220.29670.729-0.00071.143442.7671-28.082-30.3691
167.5489-3.79330.83887.11171.15377.83260.017-0.0459-0.34-0.1816-0.60921.47290.22-1.95310.46871.03750.26690.01621.3557-0.23821.703927.0359-38.3648-35.1353
175.47552.29183.65944.1103-2.69428.4839-0.20021.5244-0.1033-1.3541-0.65872.02790.237-0.16020.89221.83950.5208-0.40091.0417-0.33471.325834.82-27.2884-47.3549
189.6687-4.2801-5.08929.93255.31024.2333-0.227-0.12380.0491-1.27430.7092-1.3832-0.73390.4935-0.39581.32840.46-0.05671.0208-0.18550.901347.2381-37.7932-41.9268
195.505-4.7538-6.0589.3144.51959.59-0.6131-0.88210.1903-0.30560.670.9296-1.15950.9842-0.14371.4892-0.4758-0.33231.80470.32431.628456.2604-10.737512.9714
205.2878-0.2131-3.7715.9775-2.0836.93560.5573-0.6587-0.4195-1.4409-1.3326-1.02181.29011.15940.64991.47920.23620.15161.2680.22361.399955.2993-17.8497-5.536
218.0636-2.28666.05089.79855.30189.91861.4824-0.5792-0.21160.6201-0.386-1.10310.21172.564-1.07681.1578-0.3595-0.11471.8320.44151.213663.6932-15.0911-0.7662
228.664-3.76286.78597.57730.92678.1288-0.08350.00830.20961.0649-0.4028-1.5607-0.8311.91480.5131.26990.02330.28111.57520.21661.208459.6361-16.8077-6.6288
237.1073-6.20873.77535.9294-2.89673.1621-1.0564-0.3566-1.95980.54960.58621.16491.35460.9280.26871.57080.43760.30171.18480.42521.223252.5612-13.1065-14.8616
242.98732.0219-2.56937.93143.87138.36380.48960.81490.1766-0.6457-0.5317-0.4372-0.7154-0.4932-0.09371.5870.18690.05371.18480.16161.356754.8768-10.7639-9.1812
255.96862.3374-4.54277.2496-0.93958.74050.3982-1.37170.07620.5552-0.2896-0.2173-0.08071.0139-0.11091.2045-0.08110.02531.38610.17351.149947.9995-24.321612.7865
262.77171.74870.04418.50993.36385.1548-0.4945-1.1832-0.17110.5605-0.22792.5835-1.0112-0.95690.61971.3449-0.07960.0571.10210.04431.210835.4473-18.112720.0158
274.5973-0.8101-1.34987.54662.25266.2541-0.1596-0.127-0.8425-0.5277-0.13940.40391.5943-0.08190.29581.8239-0.12510.22931.00720.16181.326335.0222-44.86545.1686
285.6605-0.49941.16978.99932.58678.60750.0518-0.4435-1.0107-0.26860.3437-0.98081.84940.0972-0.17941.80760.25180.39611.11570.23551.684246.0713-49.01367.0984
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 19 )
2X-RAY DIFFRACTION2chain 'A' and (resid 20 through 38 )
3X-RAY DIFFRACTION3chain 'A' and (resid 39 through 51 )
4X-RAY DIFFRACTION4chain 'A' and (resid 52 through 59 )
5X-RAY DIFFRACTION5chain 'A' and (resid 60 through 70 )
6X-RAY DIFFRACTION6chain 'A' and (resid 71 through 90 )
7X-RAY DIFFRACTION7chain 'A' and (resid 91 through 102 )
8X-RAY DIFFRACTION8chain 'A' and (resid 103 through 110 )
9X-RAY DIFFRACTION9chain 'A' and (resid 111 through 124 )
10X-RAY DIFFRACTION10chain 'B' and (resid 1 through 19 )
11X-RAY DIFFRACTION11chain 'B' and (resid 20 through 47 )
12X-RAY DIFFRACTION12chain 'B' and (resid 48 through 71 )
13X-RAY DIFFRACTION13chain 'B' and (resid 72 through 92 )
14X-RAY DIFFRACTION14chain 'B' and (resid 93 through 160 )
15X-RAY DIFFRACTION15chain 'B' and (resid 161 through 176 )
16X-RAY DIFFRACTION16chain 'B' and (resid 177 through 203 )
17X-RAY DIFFRACTION17chain 'B' and (resid 204 through 222 )
18X-RAY DIFFRACTION18chain 'B' and (resid 223 through 242 )
19X-RAY DIFFRACTION19chain 'C' and (resid 1 through 19 )
20X-RAY DIFFRACTION20chain 'C' and (resid 20 through 59 )
21X-RAY DIFFRACTION21chain 'C' and (resid 60 through 70 )
22X-RAY DIFFRACTION22chain 'C' and (resid 71 through 89 )
23X-RAY DIFFRACTION23chain 'C' and (resid 90 through 97 )
24X-RAY DIFFRACTION24chain 'C' and (resid 98 through 124 )
25X-RAY DIFFRACTION25chain 'D' and (resid 1 through 71 )
26X-RAY DIFFRACTION26chain 'D' and (resid 72 through 92 )
27X-RAY DIFFRACTION27chain 'D' and (resid 93 through 176 )
28X-RAY DIFFRACTION28chain 'D' and (resid 177 through 241 )

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