[English] 日本語
Yorodumi
- PDB-6w6c: Structural and catalytic roles of human 18S rRNA methyltransferas... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6w6c
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 methylation / rRNA modification in the nucleus and cytosol / 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 methylation / rRNA modification in the nucleus and cytosol / 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: 2.38 Å
AuthorsShen, H. / Stoute, J.
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
Water4,378243
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)60.076, 95.397, 150.910
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 (E. coli)
References: UniProt: Q9UNQ2, 18S rRNA (adenine1779-N6/adenine1780-N6)-dimethyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 3.06 Å3/Da / Density % sol: 59.85 %
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 EIGER2 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: 2.38→50 Å / Num. obs: 35302 / % possible obs: 99.9 % / Redundancy: 13 % / Biso Wilson estimate: 35.77 Å2 / CC1/2: 0.991 / CC star: 0.998 / Net I/σ(I): 16
Reflection shellResolution: 2.38→2.42 Å / Num. unique obs: 1716 / CC1/2: 0.838 / CC star: 0.955

-
Processing

Software
NameVersionClassification
REFMAC1.17.1_3660refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1zq9

1zq9


Resolution: 2.38→48.18 Å / SU ML: 0.3016 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.4159
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2431 1787 5.06 %
Rwork0.1825 33515 -
obs0.1856 35302 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.81 Å2
Refinement stepCycle: LAST / Resolution: 2.38→48.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4426 0 0 243 4669
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00884522
X-RAY DIFFRACTIONf_angle_d0.95946122
X-RAY DIFFRACTIONf_chiral_restr0.0539710
X-RAY DIFFRACTIONf_plane_restr0.0066784
X-RAY DIFFRACTIONf_dihedral_angle_d22.824594
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.38-2.450.28721290.2082485X-RAY DIFFRACTION98.31
2.45-2.520.31081290.2162541X-RAY DIFFRACTION100
2.52-2.60.26581190.20632561X-RAY DIFFRACTION100
2.6-2.70.27791420.20722544X-RAY DIFFRACTION100
2.7-2.80.30171330.21022545X-RAY DIFFRACTION100
2.8-2.930.26971480.2082525X-RAY DIFFRACTION100
2.93-3.090.26161500.20642582X-RAY DIFFRACTION100
3.09-3.280.26851370.20292548X-RAY DIFFRACTION100
3.28-3.530.24781250.19332623X-RAY DIFFRACTION100
3.53-3.890.22881470.17272548X-RAY DIFFRACTION100
3.89-4.450.21541200.14922626X-RAY DIFFRACTION99.96
4.45-5.60.20951560.14932629X-RAY DIFFRACTION100
5.61-48.180.21561520.182758X-RAY DIFFRACTION99.69
Refinement TLS params.Method: refined / Origin x: 1.43288178868 Å / Origin y: -3.76225836322 Å / Origin z: 37.2524032905 Å
111213212223313233
T0.234649122758 Å20.0248327508204 Å20.0175774495175 Å2-0.22748101756 Å20.0186209519014 Å2--0.245727178311 Å2
L0.529396874825 °20.230574443283 °20.146478680295 °2-0.851075026266 °20.357152317608 °2--0.705086608023 °2
S-0.0044704157349 Å °0.00353544812595 Å °-0.0331958230323 Å °-0.0820582300843 Å °0.0083062268387 Å °-0.00380872464632 Å °0.00146407935148 Å °-0.0107261684145 Å °0.00504089005585 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://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