[English] 日本語
Yorodumi
- PDB-6dg0: MEC-8 C-terminal RRM domain bound to AGCACA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6dg0
TitleMEC-8 C-terminal RRM domain bound to AGCACA
Components
  • DNA (5'-D(*AP*GP*CP*AP*CP*A)-3')
  • Mec-8 protein
KeywordsRNA BINDING PROTEIN/DNA / RNA recognition motif / splicing factor / RNA-binding / RNA BINDING PROTEIN / RNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


nematode larval development / muscle organ morphogenesis / hemidesmosome assembly / mechanosensory behavior / embryo development ending in birth or egg hatching / neuron development / mRNA binding / RNA binding / nucleus
Similarity search - Function
Protein couch potato, RNA recognition motif / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
DNA / Mec-8 protein / Mec-8 protein
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.457 Å
AuthorsMackereth, C.D. / Soufari, H.
CitationJournal: To Be Published
Title: Structure of MEC-8 RRM2 in complex with AGCACA
Authors: Soufari, H. / Mackereth, C.D.
History
DepositionMay 16, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: 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: Mec-8 protein
B: Mec-8 protein
C: DNA (5'-D(*AP*GP*CP*AP*CP*A)-3')
D: DNA (5'-D(*AP*GP*CP*AP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)22,7704
Polymers22,7704
Non-polymers00
Water1,838102
1
A: Mec-8 protein
D: DNA (5'-D(*AP*GP*CP*AP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)11,3852
Polymers11,3852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mec-8 protein
C: DNA (5'-D(*AP*GP*CP*AP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)11,3852
Polymers11,3852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.075, 68.714, 57.531
Angle α, β, γ (deg.)90.00, 122.40, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-213-

HOH

21B-217-

HOH

31B-225-

HOH

41B-238-

HOH

51B-241-

HOH

-
Components

#1: Protein Mec-8 protein


Mass: 9582.746 Da / Num. of mol.: 2 / Mutation: C227A,C266A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: mec-8 / Plasmid: pET-GB1a / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / Variant (production host): pLysY / References: UniProt: Q22039, UniProt: G5ECJ4*PLUS
#2: DNA chain DNA (5'-D(*AP*GP*CP*AP*CP*A)-3')


Mass: 1802.233 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Caenorhabditis elegans (invertebrata)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 2.73 Å3/Da / Density % sol: 54.98 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 1mM MES ph6.5, PEG 8000 25%

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jan 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.457→28.082 Å / Num. obs: 8221 / % possible obs: 94.1 % / Redundancy: 1.8 % / Biso Wilson estimate: 31.75 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.05359 / Rrim(I) all: 0.07579 / Net I/σ(I): 9.64
Reflection shellResolution: 2.457→2.544 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.2121 / Mean I/σ(I) obs: 2.56 / Num. unique obs: 658 / CC1/2: 0.932 / % possible all: 76.33

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1URN

1urn


Resolution: 2.457→28.082 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2871 413 5.02 %
Rwork0.235 --
obs0.2376 8221 94.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.457→28.082 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1278 240 0 102 1620
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031571
X-RAY DIFFRACTIONf_angle_d0.7792161
X-RAY DIFFRACTIONf_dihedral_angle_d17.758573
X-RAY DIFFRACTIONf_chiral_restr0.032244
X-RAY DIFFRACTIONf_plane_restr0.002243
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4567-2.81190.37641330.29132426X-RAY DIFFRACTION89
2.8119-3.54150.35191410.26152732X-RAY DIFFRACTION99
3.5415-28.08350.22841390.20242650X-RAY DIFFRACTION95

+
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