[English] 日本語
Yorodumi
- PDB-6y3z: Crystal structure of the Pby1 ATP-grasp enzyme bound to the S. ce... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6y3z
TitleCrystal structure of the Pby1 ATP-grasp enzyme bound to the S. cerevisiae mRNA decapping complex (Dcp1-Dcp2-Edc3)
Components
  • Enhancer of mRNA-decapping protein 3
  • Probable tubulin--tyrosine ligase PBY1
  • m7GpppN-mRNA hydrolase
  • mRNA-decapping enzyme subunit 1
KeywordsHYDROLASE / RNA decay enzyme
Function / homology
Function and homology information


tubulin-tyrosine ligase / RNA decapping complex / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / deadenylation-independent decapping of nuclear-transcribed mRNA / mRNA decay by 5' to 3' exoribonuclease / 5'-(N7-methylguanosine 5'-triphospho)-[mRNA] hydrolase / 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity / cytoplasmic side of membrane / deadenylation-dependent decapping of nuclear-transcribed mRNA ...tubulin-tyrosine ligase / RNA decapping complex / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / deadenylation-independent decapping of nuclear-transcribed mRNA / mRNA decay by 5' to 3' exoribonuclease / 5'-(N7-methylguanosine 5'-triphospho)-[mRNA] hydrolase / 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity / cytoplasmic side of membrane / deadenylation-dependent decapping of nuclear-transcribed mRNA / P-body assembly / tubulin-tyrosine ligase activity / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / enzyme activator activity / positive regulation of transcription initiation by RNA polymerase II / stress granule assembly / P-body / mRNA processing / manganese ion binding / hydrolase activity / mRNA binding / chromatin binding / nucleus / cytoplasm
Similarity search - Function
Probable tubulin-tyrosine ligase / FDF domain / FDF domain / DFDF domain / DFDF domain profile. / FDF / mRNA-decapping enzyme subunit 1 / Dcp1-like decapping family / Survival protein SurE-like phosphatase/nucleotidase / SurE-like phosphatase/nucleotidase superfamily ...Probable tubulin-tyrosine ligase / FDF domain / FDF domain / DFDF domain / DFDF domain profile. / FDF / mRNA-decapping enzyme subunit 1 / Dcp1-like decapping family / Survival protein SurE-like phosphatase/nucleotidase / SurE-like phosphatase/nucleotidase superfamily / Survival protein SurE / YjeF N-terminal domain superfamily / YjeF-related protein N-terminus / YjeF N-terminal domain / YjeF N-terminal domain profile. / 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 / Tubulin-tyrosine ligase/Tubulin polyglutamylase / Tubulin-tyrosine ligase family / TTL domain profile. / : / Sm domain profile. / NUDIX hydrolase, conserved site / Nudix box signature. / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / PH-like domain superfamily
Similarity search - Domain/homology
Probable tubulin--tyrosine ligase PBY1 / Enhancer of mRNA-decapping protein 3 / m7GpppN-mRNA hydrolase / mRNA-decapping enzyme subunit 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.49 Å
AuthorsGraille, M.
Funding support France, 3items
OrganizationGrant numberCountry
ATIP-Avenir France
French National Research AgencyANR-11-BSV800902 France
French National Research AgencyANR-10-LABX-0030-INRT France
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Pby1 is a direct partner of the Dcp2 decapping enzyme.
Authors: Charenton, C. / Gaudon-Plesse, C. / Back, R. / Ulryck, N. / Cosson, L. / Seraphin, B. / Graille, M.
History
DepositionFeb 19, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1May 20, 2020Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 24, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: m7GpppN-mRNA hydrolase
B: mRNA-decapping enzyme subunit 1
C: Enhancer of mRNA-decapping protein 3
P: Probable tubulin--tyrosine ligase PBY1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,0215
Polymers116,9974
Non-polymers241
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4530 Å2
ΔGint-24 kcal/mol
Surface area36020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.210, 90.600, 194.240
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein m7GpppN-mRNA hydrolase / / Protein PSU1 / mRNA-decapping enzyme subunit 2


Mass: 32946.887 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: DCP2, PSU1, YNL118C, N1917
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P53550, 5'-(N7-methylguanosine 5'-triphospho)-[mRNA] hydrolase
#2: Protein mRNA-decapping enzyme subunit 1


Mass: 26705.814 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: DCP1, YOL149W
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q12517
#3: Protein Enhancer of mRNA-decapping protein 3


Mass: 7448.622 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: EDC3, LSM16, YEL015W
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P39998
#4: Protein Probable tubulin--tyrosine ligase PBY1 / P-body-associated protein 1


Mass: 49895.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: PBY1, YBR094W, YBR0821
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P38254, tubulin-tyrosine ligase
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.07 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.05 M calcium acetate; 0.1 M sodium cacodylate pH6; 25% MPD

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97626 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 3.49→48.5 Å / Num. obs: 16546 / % possible obs: 99.5 % / Redundancy: 10.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.034 / Rsym value: 0.107 / Net I/σ(I): 9.6
Reflection shellResolution: 3.49→3.55 Å / Rmerge(I) obs: 1.409 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 828 / CC1/2: 0.07 / Rpim(I) all: 0.479 / Rsym value: 1.494

-
Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4K6E, 6Y3P, 5LOP

4k6e

6y3p

5lop


Resolution: 3.49→48.5 Å / Cor.coef. Fo:Fc: 0.899 / Cor.coef. Fo:Fc free: 0.876 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.638
RfactorNum. reflection% reflectionSelection details
Rfree0.321 766 4.63 %RANDOM
Rwork0.246 ---
obs0.25 16539 99.5 %-
Displacement parametersBiso max: 300 Å2 / Biso mean: 193.18 Å2 / Biso min: 83.52 Å2
Baniso -1Baniso -2Baniso -3
1-14.7068 Å20 Å20 Å2
2---16.5042 Å20 Å2
3---1.7973 Å2
Refine analyzeLuzzati coordinate error obs: 0.54 Å
Refinement stepCycle: final / Resolution: 3.49→48.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5569 0 1 0 5570
Biso mean--128.98 --
Num. residues----672
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2038SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes176HARMONIC2
X-RAY DIFFRACTIONt_gen_planes781HARMONIC5
X-RAY DIFFRACTIONt_it5682HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion728SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6605SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5682HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg7660HARMONIC21.27
X-RAY DIFFRACTIONt_omega_torsion2.92
X-RAY DIFFRACTIONt_other_torsion27.31
LS refinement shellResolution: 3.49→3.73 Å / Rfactor Rfree error: 0 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.273 124 4.29 %
Rwork0.229 2767 -
all0.231 2891 -
obs--98.2 %
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)
14.0178-0.914-3.92940.5938-1.01435.6324-0.04710.43920.4969-0.246-0.0657-1.08850.96740.25230.11280.18470.20180.304-0.2654-0.2910.150924.6037-6.632420.9765
27.15534.9102-0.5069.037-3.944711.4522-0.014-0.49680.01810.2210.1444-0.4870.19310.0968-0.13050.6078-0.12880.304-0.0401-0.304-0.512427.8621-20.3561-13.4558
33.77332.60282.16168.64611.30963.61140.29830.12790.20460.7459-0.36850.17750.59580.17810.07030.17240.0517-0.0581-0.4735-0.0424-0.36843.35970.182648.6714
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A14 - 266
2X-RAY DIFFRACTION2{ C|* }C2 - 64
3X-RAY DIFFRACTION3{ P|* }P335 - 751

+
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