[English] 日本語
Yorodumi
- PDB-2wx3: Asymmetric trimer of the human DCP1a C-terminal domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2wx3
TitleAsymmetric trimer of the human DCP1a C-terminal domain
ComponentsMRNA-DECAPPING ENZYME 1A
KeywordsSTRUCTURAL PROTEIN / TRIMERIZATION MODULE / MRNA DECAPPING / P-BODY COMPONENT / ASYMMETRIC ASSEMBLY
Function / homology
Function and homology information


mRNA methylguanosine-cap decapping / deadenylation-independent decapping of nuclear-transcribed mRNA / 5'-(N7-methylguanosine 5'-triphospho)-[mRNA] hydrolase / protein localization to cytoplasmic stress granule / mRNA decay by 5' to 3' exoribonuclease / 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / deadenylation-dependent decapping of nuclear-transcribed mRNA / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay ...mRNA methylguanosine-cap decapping / deadenylation-independent decapping of nuclear-transcribed mRNA / 5'-(N7-methylguanosine 5'-triphospho)-[mRNA] hydrolase / protein localization to cytoplasmic stress granule / mRNA decay by 5' to 3' exoribonuclease / 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / deadenylation-dependent decapping of nuclear-transcribed mRNA / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / kinesin binding / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / enzyme activator activity / P-body / cytoplasmic ribonucleoprotein granule / mRNA binding / dendrite / identical protein binding / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
Helix Hairpins - #2030 / mRNA-decapping enzyme, C-terminal / mRNA-decapping enzyme C-terminus / mRNA-decapping enzyme subunit 1 / Dcp1-like decapping family / Helix Hairpins / Helix non-globular / Special / PH-like domain superfamily
Similarity search - Domain/homology
mRNA-decapping enzyme 1A
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.31 Å
AuthorsTritschler, F. / Motz, C. / Weichenrieder, O.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Dcp1 Forms Asymmetric Trimers to Assemble Into Active Mrna Decapping Complexes in Metazoa.
Authors: Tritschler, F. / Braun, J.E. / Motz, C. / Igreja, C. / Haas, G. / Truffault, V. / Izaurralde, E. / Weichenrieder, O.
History
DepositionNov 1, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 1, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MRNA-DECAPPING ENZYME 1A
B: MRNA-DECAPPING ENZYME 1A
C: MRNA-DECAPPING ENZYME 1A


Theoretical massNumber of molelcules
Total (without water)17,3783
Polymers17,3783
Non-polymers00
Water97354
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5470 Å2
ΔGint-57.39 kcal/mol
Surface area8010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.750, 64.750, 103.030
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein MRNA-DECAPPING ENZYME 1A


Mass: 5792.622 Da / Num. of mol.: 3 / Fragment: TRIMERIZATION DOMAIN, RESIDUES 539-582
Source method: isolated from a genetically manipulated source
Details: EC3.-.-.- IN UNIPROT DISPUTED BY DEPOSITOR / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PRSFDUET-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / References: UniProt: Q9NPI6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TERMINAL CLONING TAG - GPHMADL

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.6 Å3/Da / Density % sol: 66 % / Description: NONE
Crystal growpH: 6 / Details: 50MM MES (PH 6.0), 1.2M NA-MALONATE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.0688, 0.9792
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 8, 2008 / Details: MIRRORS
RadiationMonochromator: SI(111)MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.06881
20.97921
ReflectionResolution: 2.3→80 Å / Num. obs: 11317 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 44.1 Å2 / Rsym value: 0.08 / Net I/σ(I): 11.9
Reflection shellResolution: 2.31→2.37 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2.5 / Rsym value: 0.56 / % possible all: 95.7

-
Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
XDSdata reduction
XSCALEdata scaling
autoSHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.31→56.08 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.882 / SU B: 5.699 / SU ML: 0.14 / Cross valid method: THROUGHOUT / ESU R: 0.206 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. RESIDUES A575-A582, B532-B534, B577-B582, C532-C535 ARE DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.25232 608 5.4 %RANDOM
Rwork0.20793 ---
obs0.21007 10707 98.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.402 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20.05 Å2-0 Å2
2--0.11 Å2-0 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 2.31→56.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1050 0 0 54 1104
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0211062
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6481.981437
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1955129
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.48726.74443
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.4715210
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1040.2186
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02733
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1191.5658
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.16921073
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.5183404
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.8794.5364
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.31→2.369 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 74 -
Rwork0.247 698 -
obs--95.66 %

+
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