[English] 日本語
Yorodumi
- PDB-5lon: Structure of /K. lactis/ Dcp1-Dcp2 decapping complex. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5lon
TitleStructure of /K. lactis/ Dcp1-Dcp2 decapping complex.
Components
  • KLLA0E01827p
  • KLLA0F23980p
KeywordsRNA BINDING PROTEIN / RNA decay / multiprotein complex
Function / homology
Function and homology information


5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity / intracellular organelle / deadenylation-dependent decapping of nuclear-transcribed mRNA / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / enzyme activator activity / manganese ion binding / RNA binding / cytoplasm
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
KLLA0F23980p / KLLA0E01827p
Similarity search - Component
Biological speciesKluyveromyces lactis NRRL Y-1140 (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsCharenton, C. / Taverniti, V. / Gaudon-Plesse, C. / Back, R. / Seraphin, B. / Graille, M.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-11-BSV800902 France
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2016
Title: Structure of the active form of Dcp1-Dcp2 decapping enzyme bound to m(7)GDP and its Edc3 activator.
Authors: Charenton, C. / Taverniti, V. / Gaudon-Plesse, C. / Back, R. / Seraphin, B. / Graille, M.
History
DepositionAug 9, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Database references
Revision 1.2Nov 16, 2016Group: Database references
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: KLLA0F23980p
B: KLLA0E01827p


Theoretical massNumber of molelcules
Total (without water)54,5652
Polymers54,5652
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-17 kcal/mol
Surface area20720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)216.685, 216.685, 216.685
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number211
Space group name H-MI432

-
Components

#1: Protein KLLA0F23980p


Mass: 32634.709 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis NRRL Y-1140 (yeast)
Gene: KLLA0_F23980g / Production host: Escherichia coli (E. coli) / Variant (production host): Codon+ / References: UniProt: Q6CIU1
#2: Protein KLLA0E01827p


Mass: 21929.830 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis NRRL Y-1140 (yeast)
Gene: KLLA0_E01827g / Production host: Escherichia coli (E. coli) / Variant (production host): Codon+ / References: UniProt: Q6CPV9

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4 Å3/Da / Density % sol: 69.24 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2M ammonium sulfate ; 0.1M tri- sodium citrate pH 5.6 ; 15% (w/v) PEG 4000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.5→48.45 Å / Num. obs: 11272 / % possible obs: 99.9 % / Redundancy: 78.7 % / Biso Wilson estimate: 114.82 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.04 / Rsym value: 0.257 / Net I/σ(I): 18.7
Reflection shellResolution: 3.5→3.83 Å / Redundancy: 78.7 % / Rmerge(I) obs: 0.612 / Mean I/σ(I) obs: 2 / CC1/2: 0.442 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LOP

5lop


Resolution: 3.5→48.45 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.866 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.577
RfactorNum. reflection% reflectionSelection details
Rfree0.312 543 4.82 %RANDOM
Rwork0.25 ---
obs0.253 11272 100 %-
Displacement parametersBiso mean: 210.55 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.64 Å
Refinement stepCycle: LAST / Resolution: 3.5→48.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3239 0 5 0 3244
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013319HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.184494HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1168SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes91HARMONIC2
X-RAY DIFFRACTIONt_gen_planes456HARMONIC5
X-RAY DIFFRACTIONt_it3319HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.56
X-RAY DIFFRACTIONt_other_torsion25.26
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion427SEMIHARMONIC5
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_contact3667SEMIHARMONIC4
LS refinement shellResolution: 3.5→3.83 Å / Rfactor Rfree error: 0 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.325 129 4.93 %
Rwork0.271 2486 -
all0.274 2615 -
obs--100 %
Refinement TLS params.

L22: 0 °2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°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)
12.2663-1.1656-1.192-0.13786.98050.094-0.0979-1.08850.1162-0.2764-0.05241.0885-0.44480.18240.4936-0.13740.304-0.3494-0.03190.6079-81.08215.4393-46.1654
21.3562.66671.8906-0.08790.69110.2649-0.2585-0.1227-0.0363-0.29340.2957-0.046-0.18380.02850.08730.01440.23950.08-0.0180.3755-57.310524.6888-39.3108
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

+
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