[English] 日本語
Yorodumi
- PDB-5lmf: Structure of C-terminal domain from S. cerevisiae Pat1 decapping ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5lmf
TitleStructure of C-terminal domain from S. cerevisiae Pat1 decapping activator bound to Dcp2 HLM3 peptide (region 484-500)
Components
  • DNA topoisomerase 2-associated protein PAT1
  • mRNA decapping protein 2
KeywordsRNA BINDING PROTEIN / Protein peptide complex / ISOMERASE
Function / homology
Function and homology information


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 / Lsm1-7-Pat1 complex / 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 ...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 / Lsm1-7-Pat1 complex / 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 / formation of translation preinitiation complex / P-body assembly / regulation of translational initiation / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / positive regulation of transcription initiation by RNA polymerase II / stress granule assembly / negative regulation of translational initiation / P-body / kinetochore / mRNA processing / cytoplasmic stress granule / cytosolic small ribosomal subunit / manganese ion binding / hydrolase activity / cell cycle / cell division / mRNA binding / chromatin binding / RNA binding / nucleus / cytoplasm
Similarity search - Function
mRNA decay factor PAT1 domain / Pat1-like / Topoisomerase II-associated protein PAT1 / 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. ...mRNA decay factor PAT1 domain / Pat1-like / Topoisomerase II-associated protein PAT1 / 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. / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily
Similarity search - Domain/homology
mRNA decapping protein 2 / DNA topoisomerase 2-associated protein PAT1 / m7GpppN-mRNA hydrolase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsCharenton, C. / Gaudon-Plesse, C. / Fourati, Z. / Taverniti, V. / Back, R. / Kolesnikova, O. / Seraphin, B. / Graille, M.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: A unique surface on Pat1 C-terminal domain directly interacts with Dcp2 decapping enzyme and Xrn1 5'-3' mRNA exonuclease in yeast.
Authors: Charenton, C. / Gaudon-Plesse, C. / Fourati, Z. / Taverniti, V. / Back, R. / Kolesnikova, O. / Seraphin, B. / Graille, M.
History
DepositionJul 30, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Nov 8, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed
Revision 1.3Nov 15, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Sep 26, 2018Group: Data collection / Derived calculations / Structure summary
Category: pdbx_struct_special_symmetry / struct / Item: _struct.title
Revision 1.5Jan 10, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA topoisomerase 2-associated protein PAT1
B: DNA topoisomerase 2-associated protein PAT1
C: mRNA decapping protein 2
D: mRNA decapping protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,89916
Polymers88,2454
Non-polymers65412
Water2,576143
1
A: DNA topoisomerase 2-associated protein PAT1
D: mRNA decapping protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3697
Polymers44,1232
Non-polymers2465
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-10 kcal/mol
Surface area17110 Å2
MethodPISA
2
B: DNA topoisomerase 2-associated protein PAT1
C: mRNA decapping protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5309
Polymers44,1232
Non-polymers4087
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-4 kcal/mol
Surface area17860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.360, 122.920, 126.970
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-1001-

MG

-
Components

-
Protein / Protein/peptide , 2 types, 4 molecules ABCD

#1: Protein DNA topoisomerase 2-associated protein PAT1 / Decapping activator and translational repressor PAT1 / Topoisomerase II-associated protein PAT1 / ...Decapping activator and translational repressor PAT1 / Topoisomerase II-associated protein PAT1 / mRNA turnover protein 1


Mass: 42282.438 Da / Num. of mol.: 2 / Fragment: UNP residues 437-795 / Mutation: Q706A/L713A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PAT1, MRT1, YCR077C, YCR77C / Production host: Escherichia coli (E. coli) / References: UniProt: P25644
#2: Protein/peptide mRNA decapping protein 2 / Dcp2 decapping factor


Mass: 1840.106 Da / Num. of mol.: 2 / Fragment: UNP residues 483-499 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: B3LNX5, UniProt: P53550*PLUS

-
Non-polymers , 4 types, 155 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 2.48 Å3/Da / Density % sol: 50.32 %
Crystal growTemperature: 297.15 K / Method: vapor diffusion, hanging drop / Details: 0.2 M MgCl2 ; 20% PEG3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 41458 / % possible obs: 99.6 % / Redundancy: 3 % / Rsym value: 0.102 / Net I/σ(I): 7.5
Reflection shellResolution: 2.15→2.27 Å / Mean I/σ(I) obs: 0.94 / CC1/2: 0.459 / % possible all: 93.9

-
Processing

Software
NameVersionClassification
BUSTER-TNT2.10.2refinement
PDB_EXTRACT3.2data extraction
XSCALEdata scaling
MOLREPphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OGP

4ogp


Resolution: 2.15→31.48 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.911 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.249 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.244 / SU Rfree Blow DPI: 0.192 / SU Rfree Cruickshank DPI: 0.196
RfactorNum. reflection% reflectionSelection details
Rfree0.246 2062 5 %RANDOM
Rwork0.212 ---
obs0.213 41247 97.9 %-
Displacement parametersBiso max: 152.71 Å2 / Biso mean: 60.67 Å2 / Biso min: 32.57 Å2
Baniso -1Baniso -2Baniso -3
1-13.3984 Å20 Å20 Å2
2--5.4051 Å20 Å2
3----18.8035 Å2
Refine analyzeLuzzati coordinate error obs: 0.39 Å
Refinement stepCycle: final / Resolution: 2.15→31.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5409 0 39 143 5591
Biso mean--61.61 50.57 -
Num. residues----664
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2037SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes163HARMONIC2
X-RAY DIFFRACTIONt_gen_planes744HARMONIC5
X-RAY DIFFRACTIONt_it5518HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion758SEMIHARMONIC5
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_contact6602SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5518HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg7419HARMONIC21.07
X-RAY DIFFRACTIONt_omega_torsion2.36
X-RAY DIFFRACTIONt_other_torsion19.54
LS refinement shellResolution: 2.15→2.21 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 149 5 %
Rwork0.29 2833 -
all-2982 -
obs--97.68 %
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)
10.8134-0.45160.29061.0921-0.32090.49420.0156-0.0831-0.0486-0.01090.01140.1277-0.0279-0.0835-0.0271-0.1628-0.0011-0.007-0.15510.02860.086512.816723.044636.4588
20.705-0.46210.20941.8971-0.12880.57860.0678-0.0013-0.0602-0.1732-0.11570.28260.09520.03890.0479-0.1904-0.0032-0.0334-0.2083-0.01160.07826.61957.778832.5149
30.4356-1.19160.3241.70570.28561.3442-0.0059-0.0086-0.00020.081-0.0324-0.01630.05880.05020.03820.0350.0717-0.0484-0.16190.01380.107838.4124-8.11753.9925
42.417-0.6627-0.95180.34460.69570.31460.0290.04870.0057-0.0583-0.0130.0393-0.06630.0893-0.016-0.07770.0617-0.0878-0.054-0.03020.11661.160239.262914.7615
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A472 - 796
2X-RAY DIFFRACTION2{ B|* }B473 - 796
3X-RAY DIFFRACTION3{ C|* }C484 - 500
4X-RAY DIFFRACTION4{ D|* }D484 - 500

+
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