[English] 日本語
Yorodumi
- PDB-5j3y: Crystal structure of S. pombe Dcp2:Dcp1 mRNA decapping complex -

+
Open data


ID or keywords:

Loading...

-
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 / deadenylation-independent decapping of nuclear-transcribed mRNA / mRNA 5'-diphosphatase activity / 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity / Hydrolases / mRNA cap binding ...mRNA phosphatase activator activity / : / RNA decapping complex / mRNA methylguanosine-cap decapping / 5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase activity / deadenylation-independent decapping of nuclear-transcribed mRNA / mRNA 5'-diphosphatase activity / 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity / Hydrolases / mRNA cap binding / deadenylation-dependent decapping of nuclear-transcribed mRNA / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / P-body / mRNA processing / cytoplasmic stress granule / manganese ion binding / single-stranded RNA binding / mRNA binding / magnesium ion binding / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
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) ...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) / NUDIX domain / PH-domain like / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / PH-like domain superfamily / Roll / Mainly 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.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more