[English] 日本語
Yorodumi
- PDB-6w6f: Structural and catalytic roles of human 18S rRNA methyltransferas... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6w6f
TitleStructural and catalytic roles of human 18S rRNA methyltransferases DIMT1 in ribosome assembly and translation
ComponentsProbable dimethyladenosine transferase
KeywordsRNA BINDING PROTEIN / RNA modification enzyme
Function / homology
Function and homology information


18S rRNA (adenine1779-N6/adenine1780-N6)-dimethyltransferase / 18S rRNA (adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase activity / rRNA (adenine-N6,N6-)-dimethyltransferase activity / positive regulation of rRNA processing / rRNA modification in the nucleus and cytosol / rRNA methylation / small-subunit processome / ribosomal small subunit biogenesis / nucleolus / RNA binding ...18S rRNA (adenine1779-N6/adenine1780-N6)-dimethyltransferase / 18S rRNA (adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase activity / rRNA (adenine-N6,N6-)-dimethyltransferase activity / positive regulation of rRNA processing / rRNA modification in the nucleus and cytosol / rRNA methylation / small-subunit processome / ribosomal small subunit biogenesis / nucleolus / RNA binding / nucleoplasm / cytosol
Similarity search - Function
Helicase, Ruva Protein; domain 3 - #480 / Ribosomal RNA adenine dimethylase / Ribosomal RNA adenine methylase transferase, conserved site / Ribosomal RNA adenine methylase transferase, N-terminal / Ribosomal RNA adenine dimethylases signature. / Ribosomal RNA adenine dimethylases / Ribosomal RNA adenine methyltransferase KsgA/Erm / Ribosomal RNA adenine dimethylase / rRNA adenine N(6)-methyltransferase family profile. / Helicase, Ruva Protein; domain 3 ...Helicase, Ruva Protein; domain 3 - #480 / Ribosomal RNA adenine dimethylase / Ribosomal RNA adenine methylase transferase, conserved site / Ribosomal RNA adenine methylase transferase, N-terminal / Ribosomal RNA adenine dimethylases signature. / Ribosomal RNA adenine dimethylases / Ribosomal RNA adenine methyltransferase KsgA/Erm / Ribosomal RNA adenine dimethylase / rRNA adenine N(6)-methyltransferase family profile. / Helicase, Ruva Protein; domain 3 / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Probable dimethyladenosine transferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsShen, H. / Stoute, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R35GM133721-01 United States
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Structural and catalytic roles of the human 18SrRNA methyltransferases DIMT1 in ribosome assembly and translation.
Authors: Shen, H. / Stoute, J. / Liu, K.F.
History
DepositionMar 16, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Sep 2, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Oct 18, 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: Probable dimethyladenosine transferase
B: Probable dimethyladenosine transferase


Theoretical massNumber of molelcules
Total (without water)70,5852
Polymers70,5852
Non-polymers00
Water43224
1
A: Probable dimethyladenosine transferase


Theoretical massNumber of molelcules
Total (without water)35,2921
Polymers35,2921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Probable dimethyladenosine transferase


Theoretical massNumber of molelcules
Total (without water)35,2921
Polymers35,2921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.204, 96.504, 150.019
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein Probable dimethyladenosine transferase / DIM1 dimethyladenosine transferase 1 homolog / DIM1 dimethyladenosine transferase 1-like / Probable ...DIM1 dimethyladenosine transferase 1 homolog / DIM1 dimethyladenosine transferase 1-like / Probable 18S rRNA (adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase / Probable 18S rRNA dimethylase / Probable S-adenosylmethionine-6-N' / N'-adenosyl(rRNA) dimethyltransferase


Mass: 35292.434 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DIMT1, DIMT1L, HUSSY-05 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12
References: UniProt: Q9UNQ2, 18S rRNA (adenine1779-N6/adenine1780-N6)-dimethyltransferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 3.09 Å3/Da / Density % sol: 60.16 %
Crystal growTemperature: 285 K / Method: evaporation
Details: 0.2 M Ammonium sulfate, 0.1 M Tris pH 48.5, 20% PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X17B1 / Wavelength: 0.92 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 14517 / % possible obs: 96.7 % / Redundancy: 13.2 % / Biso Wilson estimate: 45 Å2 / CC1/2: 0.986 / Net I/σ(I): 7.5
Reflection shellResolution: 3.2→3.26 Å / Num. unique obs: 732 / CC1/2: 0.934

-
Processing

Software
NameVersionClassification
REFMAC1.16_3549refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6W6C

6w6c


Resolution: 3.2→48.35 Å / SU ML: 0.4264 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 22.242
RfactorNum. reflection% reflection
Rfree0.2292 760 5.24 %
Rwork0.1729 --
obs0.1759 14517 96.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 28.4 Å2
Refinement stepCycle: LAST / Resolution: 3.2→48.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4418 0 0 24 4442
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014514
X-RAY DIFFRACTIONf_angle_d1.07026112
X-RAY DIFFRACTIONf_chiral_restr0.0561710
X-RAY DIFFRACTIONf_plane_restr0.0062782
X-RAY DIFFRACTIONf_dihedral_angle_d10.58452790
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.450.33291620.22972781X-RAY DIFFRACTION99.93
3.45-3.80.25671430.18872803X-RAY DIFFRACTION99.97
3.8-4.340.20161780.15782776X-RAY DIFFRACTION99.8
4.34-5.470.18031440.14122813X-RAY DIFFRACTION98.34
5.47-100.23181330.17262584X-RAY DIFFRACTION86.42
Refinement TLS params.Method: refined / Origin x: 1.53652884532 Å / Origin y: -5.57243786412 Å / Origin z: 36.6249919112 Å
111213212223313233
T0.0844557595257 Å20.000173161766305 Å20.0141496091764 Å2-0.0663264152218 Å2-0.01763612379 Å2--0.0827658829602 Å2
L0.0529427820655 °20.00980966687198 °2-0.0315472081636 °2-0.0766082052762 °2-0.0199028595445 °2--0.0421978372727 °2
S-0.0383781619583 Å °-0.0129198051684 Å °0.0117079326667 Å °-0.0213618568668 Å °0.0523590302371 Å °-0.0717179888212 Å °0.0106831918933 Å °0.00401046759223 Å °0.00416328524821 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 313
2X-RAY DIFFRACTION1allB1 - 313

+
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