[English] 日本語
Yorodumi
- PDB-5bv3: Yeast Scavenger Decapping Enzyme in complex with m7GDP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5bv3
TitleYeast Scavenger Decapping Enzyme in complex with m7GDP
Componentsm7GpppX diphosphatase
KeywordsHYDROLASE / scavenger decapping enzyme / cap structure / decapping enzyme / substrate inhibition / protein dynamics
Function / homology
Function and homology information


exoribonuclease activator activity / m7G(5')pppN diphosphatase complex / nuclear-transcribed mRNA catabolic process, deadenylation-independent decay / 5'-(N7-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase / 5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase activity / mRNA decay by 3' to 5' exoribonuclease / deadenylation-dependent decapping of nuclear-transcribed mRNA / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / RNA 7-methylguanosine cap binding / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay ...exoribonuclease activator activity / m7G(5')pppN diphosphatase complex / nuclear-transcribed mRNA catabolic process, deadenylation-independent decay / 5'-(N7-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase / 5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase activity / mRNA decay by 3' to 5' exoribonuclease / deadenylation-dependent decapping of nuclear-transcribed mRNA / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / RNA 7-methylguanosine cap binding / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / nuclear-transcribed mRNA catabolic process / response to osmotic stress / cellular response to starvation / response to nutrient / P-body / response to heat / response to oxidative stress / protein heterodimerization activity / perinuclear region of cytoplasm / protein homodimerization activity / mitochondrion / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Scavenger mRNA decapping enzyme, N-terminal domain / Scavenger mRNA decapping enzyme DcpS/DCS2 / Scavenger mRNA decapping enzyme, N-terminal / Scavenger mRNA decapping enzyme (DcpS) N-terminal / Scavenger mRNA decapping enzyme C-term binding / Histidine triad, conserved site / HIT domain signature. / HIT-like / HIT family, subunit A / HIT-like superfamily ...Scavenger mRNA decapping enzyme, N-terminal domain / Scavenger mRNA decapping enzyme DcpS/DCS2 / Scavenger mRNA decapping enzyme, N-terminal / Scavenger mRNA decapping enzyme (DcpS) N-terminal / Scavenger mRNA decapping enzyme C-term binding / Histidine triad, conserved site / HIT domain signature. / HIT-like / HIT family, subunit A / HIT-like superfamily / Phosphorylase Kinase; domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE / m7GpppX diphosphatase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 Å
AuthorsNeu, A. / Neu, U. / Sprangers, R.
Funding support Germany, 1items
OrganizationGrant numberCountry
Germany
CitationJournal: Nat.Chem.Biol. / Year: 2015
Title: An excess of catalytically required motions inhibits the scavenger decapping enzyme.
Authors: Neu, A. / Neu, U. / Fuchs, A.L. / Schlager, B. / Sprangers, R.
History
DepositionJun 4, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2015Group: Database references
Revision 1.2Aug 26, 2015Group: 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 / struct_ncs_dom_lim
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.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: m7GpppX diphosphatase
B: m7GpppX diphosphatase
C: m7GpppX diphosphatase
D: m7GpppX diphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,57617
Polymers160,8444
Non-polymers1,73313
Water2,630146
1
A: m7GpppX diphosphatase
B: m7GpppX diphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,3018
Polymers80,4222
Non-polymers8796
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: m7GpppX diphosphatase
D: m7GpppX diphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,2769
Polymers80,4222
Non-polymers8547
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.990, 104.520, 189.960
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETLYSLYSAA7 - 3442 - 339
21METMETLYSLYSBB7 - 3442 - 339
12METMETILEILEAA7 - 3452 - 340
22METMETILEILECC7 - 3452 - 340
13METMETILEILEAA7 - 3422 - 337
23METMETILEILEDD7 - 3422 - 337
14GLYGLYLYSLYSBB6 - 3441 - 339
24GLYGLYLYSLYSCC6 - 3441 - 339
15GLYGLYILEILEBB6 - 3421 - 337
25GLYGLYILEILEDD6 - 3421 - 337
16GLYGLYILEILECC6 - 3421 - 337
26GLYGLYILEILEDD6 - 3421 - 337

NCS ensembles :
ID
1
2
3
4
5
6

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.367595, -0.929849, 0.015945), (-0.929871, -0.367765, -0.009434), (0.014636, -0.011359, -0.999828)13.37316, 21.33419, 116.020493
3given(1), (1), (1)
4given(0.36545, -0.930654, 0.018135), (-0.930711, -0.365646, -0.008928), (0.014939, -0.013616, -0.999796)13.27253, 21.307501, 116.029846

-
Components

#1: Protein
m7GpppX diphosphatase / / DCS-1 / Hint-related 7meGMP-directed hydrolase 1 / Protein Dcs1p / Scavenger mRNA-decapping enzyme DcpS


Mass: 40210.883 Da / Num. of mol.: 4 / Fragment: Dcs1p, UNP residues 8-350 / Mutation: H268N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: DCS1, YLR270W / Plasmid: pETM-1060 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q06151, 5'-(N7-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase
#2: Chemical ChemComp-M7G / 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE


Mass: 459.243 Da / Num. of mol.: 2 / Fragment: 7-methylguanosine diphosphate / Source method: obtained synthetically / Formula: C11H19N5O11P2
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 100 mM Hepes, 100 mM NaCl, 1.6 M AmSO4 / PH range: 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 27, 2009
RadiationMonochromator: LN2 cooled fixed-exit Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→20 Å / Num. obs: 83079 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 2.31 % / Biso Wilson estimate: 50.217 Å2 / Rmerge F obs: 0.183 / Rmerge(I) obs: 0.079 / Rrim(I) all: 0.089 / Χ2: 0.991 / Net I/σ(I): 12.57 / Num. measured all: 361983
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.25-2.311.1770.7162.3220444613260990.85199.5
2.31-2.3710.5822.7219918596159330.69399.5
2.37-2.440.8940.6173.1223639582858060.70499.6
2.44-2.520.7270.5433.7925789563156220.60999.8
2.52-2.60.5970.454.4625100546554470.50499.7
2.6-2.690.4990.3665.1724446532753190.41199.8
2.69-2.790.3770.2796.4323401510550950.31299.8
2.79-2.90.2820.2137.9322761495649480.23999.8
2.9-3.030.2170.1649.621627474547320.18499.7
3.03-3.180.1580.12111.9720808452545110.13699.7
3.18-3.350.1090.09414.7319662431243000.10599.7
3.35-3.560.0750.07418.0418699411340860.08299.3
3.56-3.80.0530.05722.0617431386438400.06399.4
3.8-4.110.040.04825.7816379361935870.05499.1
4.11-4.50.0310.04129.614892331832780.04698.8
4.5-5.030.0260.03831.7713555303329900.04298.6
5.03-5.810.0270.03930.3712007270726590.04498.2
5.81-7.120.0270.03831.2210097228022250.04397.6
7.12-10.060.0210.03335.877760182017530.03896.3
10.060.0180.03137.6356810698490.03579.4

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XMM

1xmm


Resolution: 2.25→19.89 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.935 / WRfactor Rfree: 0.2305 / WRfactor Rwork: 0.1963 / FOM work R set: 0.7532 / SU B: 18.374 / SU ML: 0.212 / SU R Cruickshank DPI: 0.2745 / SU Rfree: 0.209 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.274 / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2481 4133 5 %RANDOM
Rwork0.2215 ---
obs0.2228 78749 98.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 147.13 Å2 / Biso mean: 54.795 Å2 / Biso min: 25 Å2
Baniso -1Baniso -2Baniso -3
1--5.37 Å2-0 Å2-0 Å2
2--1.63 Å2-0 Å2
3---3.74 Å2
Refinement stepCycle: final / Resolution: 2.25→19.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10329 0 97 146 10572
Biso mean--48.38 43.39 -
Num. residues----1289
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01910681
X-RAY DIFFRACTIONr_bond_other_d0.0060.029954
X-RAY DIFFRACTIONr_angle_refined_deg1.3541.95514534
X-RAY DIFFRACTIONr_angle_other_deg1.2142.99822817
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.93451278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.86224.721502
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.843151786
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4171546
X-RAY DIFFRACTIONr_chiral_restr0.0760.21622
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02111962
X-RAY DIFFRACTIONr_gen_planes_other0.0060.022434
X-RAY DIFFRACTIONr_mcbond_it3.1345.7525151
X-RAY DIFFRACTIONr_mcbond_other3.1345.7525150
X-RAY DIFFRACTIONr_mcangle_it4.2077.2356416
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A165920.14
12B165920.14
21A192580.05
22C192580.05
31A160940.14
32D160940.14
41B164130.14
42C164130.14
51B179250.05
52D179250.05
61C160620.14
62D160620.14
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.411 301 -
Rwork0.391 5709 -
all-6010 -
obs--99.39 %
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)
15.2749-0.0181-0.02840.64620.40472.53840.05780.3989-0.099-0.2761-0.08450.03020.4531-0.26620.02670.6732-0.0405-0.02650.0618-0.0110.014831.5816-12.999232.9962
21.26920.1860.74021.61830.48963.7067-0.08930.13090.0451-0.22870.0776-0.2223-0.26840.38260.01170.5277-0.02870.05330.07220.00620.037841.850111.007231.9202
34.5287-0.0773-0.91261.3459-0.01892.31290.05010.0382-0.3279-0.1034-0.06950.13290.3927-0.63380.01940.6512-0.1165-0.06320.18910.00370.039721.7206-13.096635.5816
40.8672-0.14830.68871.5851-0.01894.09750.0065-0.08340.0211-0.01340.02190.2093-0.258-0.6248-0.02840.46860.05720.00410.16490.00640.030623.724619.174444.487
50.4032-0.6472-0.14223.81430.33012.3137-0.1337-0.13570.0440.48460.1735-0.12490.21130.1858-0.03990.45890.0365-0.04310.2283-0.06940.024836.7362-3.079784.1437
61.5235-0.1916-0.2412.02860.92684.1775-0.13710.0773-0.19250.2058-0.04250.13021.0372-0.42560.17960.7436-0.12510.08990.2251-0.01610.035918.7944-21.455484.7145
70.8625-1.0367-0.12614.286-0.75162.8381-0.02660.07640.19970.09630.0777-0.4004-0.23680.2236-0.05110.3948-0.0144-0.02310.2067-0.05470.076934.20216.059980.9844
80.9104-0.1373-0.1640.79320.82094.377-0.09670.12160.15-0.0643-0.06150.2416-0.0374-0.98640.15820.5222-0.1308-0.01290.6256-0.05910.14435.1766-8.178271.7206
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 126
2X-RAY DIFFRACTION2A127 - 345
3X-RAY DIFFRACTION3B7 - 129
4X-RAY DIFFRACTION4B130 - 344
5X-RAY DIFFRACTION5C7 - 126
6X-RAY DIFFRACTION6C127 - 346
7X-RAY DIFFRACTION7D6 - 127
8X-RAY DIFFRACTION8D128 - 342

+
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://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