[English] 日本語
Yorodumi
- PDB-3vem: Structural basis of transcriptional gene silencing mediated by Ar... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3vem
TitleStructural basis of transcriptional gene silencing mediated by Arabidopsis MOM1
ComponentsHelicase protein MOM1
KeywordsTRANSCRIPTION / Coiled-coil / hendecad / transcriptional gene silencing / siRNA / nucleus / chromatin
Function / homology
Function and homology information


: / heterochromatin formation => GO:0031507 / regulatory ncRNA-mediated gene silencing / negative regulation of gene expression, epigenetic / helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / 2 iron, 2 sulfur cluster binding / defense response to bacterium / protein homodimerization activity / ATP binding ...: / heterochromatin formation => GO:0031507 / regulatory ncRNA-mediated gene silencing / negative regulation of gene expression, epigenetic / helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / 2 iron, 2 sulfur cluster binding / defense response to bacterium / protein homodimerization activity / ATP binding / metal ion binding / nucleus
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1310 / MOM1 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Helicase protein MOM1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.2 Å
AuthorsNishikura, T. / Petty, T.J. / Halazonetis, T. / Paszkowski, J. / Thore, S.
CitationJournal: PLOS GENET. / Year: 2012
Title: Structural Basis of Transcriptional Gene Silencing Mediated by Arabidopsis MOM1.
Authors: Nishimura, T. / Molinard, G. / Petty, T.J. / Broger, L. / Gabus, C. / Halazonetis, T.D. / Thore, S. / Paszkowski, J.
History
DepositionJan 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Helicase protein MOM1
B: Helicase protein MOM1
C: Helicase protein MOM1
D: Helicase protein MOM1


Theoretical massNumber of molelcules
Total (without water)53,0414
Polymers53,0414
Non-polymers00
Water0
1
A: Helicase protein MOM1
B: Helicase protein MOM1


Theoretical massNumber of molelcules
Total (without water)26,5202
Polymers26,5202
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-38 kcal/mol
Surface area12630 Å2
MethodPISA
2
C: Helicase protein MOM1
D: Helicase protein MOM1


Theoretical massNumber of molelcules
Total (without water)26,5202
Polymers26,5202
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint-38 kcal/mol
Surface area12530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.640, 85.640, 292.740
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein
Helicase protein MOM1 / / Protein MAINTENANCE OF METHYLATION / Protein MORPHEUS MOLECULE 1


Mass: 13260.241 Da / Num. of mol.: 4 / Fragment: Conserved MOM1 Motif 2 (CMM2)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: MOM1, MOM, At1g08060, T6D22.14 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9M658

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5.84 Å3/Da / Density % sol: 78.95 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris, 0.3 M magnesium formate dihydrate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.2→15 Å / Num. obs: 21107 / % possible obs: 99.58 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHARPphasing
PHENIX(phenix.refine: 1.6.1_353)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 3.2→14.959 Å / SU ML: 0.47 / σ(F): 2 / Phase error: 32.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2932 1055 5 %RANDOM
Rwork0.2584 ---
obs0.2601 21107 99.58 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 81.944 Å2 / ksol: 0.305 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--15.0553 Å2-0 Å20 Å2
2---15.0553 Å20 Å2
3---30.1106 Å2
Refinement stepCycle: LAST / Resolution: 3.2→14.959 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2761 0 0 0 2761
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012799
X-RAY DIFFRACTIONf_angle_d1.2633720
X-RAY DIFFRACTIONf_dihedral_angle_d20.4081127
X-RAY DIFFRACTIONf_chiral_restr0.088402
X-RAY DIFFRACTIONf_plane_restr0.004481
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.3440.37441260.3682391X-RAY DIFFRACTION98
3.344-3.51810.3571310.30532489X-RAY DIFFRACTION100
3.5181-3.73530.3051320.27982503X-RAY DIFFRACTION100
3.7353-4.01860.34421290.26362472X-RAY DIFFRACTION100
4.0186-4.41350.3311310.24022486X-RAY DIFFRACTION100
4.4135-5.03080.27031320.21272524X-RAY DIFFRACTION100
5.0308-6.260.36461340.30962543X-RAY DIFFRACTION100
6.26-14.95940.22181400.21892644X-RAY DIFFRACTION99

+
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