[English] 日本語
Yorodumi
- PDB-7mjw: Methylated MiaB in the complex with 5'-deoxyadenosine, methionine... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7mjw
TitleMethylated MiaB in the complex with 5'-deoxyadenosine, methionine and RNA
Components
  • RNA (5'-R(*GP*GP*AP*CP*UP*GP*AP*AP*(MIA)P*AP*UP*CP*C)-3')
  • tRNA-2-methylthio-N(6)-dimethylallyladenosine synthase
KeywordsTRANSFERASE/RNA / tRNA-2-methylthio-N(6)-dimethylallyladenosine synthase / TRANSFERASE / TRANSFERASE-RNA complex
Function / homology
Function and homology information


tRNA-2-methylthio-N(6)-dimethylallyladenosine(37) synthase activity / tRNA-2-methylthio-N6-dimethylallyladenosine synthase / 3 iron, 4 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / metal ion binding / cytosol
Similarity search - Function
tRNA-2-methylthio-N(6)-dimethylallyladenosine synthase MiaB / Methylthiotransferase / Methylthiotransferase, N-terminal / Methylthiotransferase, N-terminal domain superfamily / Uncharacterized protein family UPF0004 / Methylthiotransferase N-terminal domain profile. / Methylthiotransferase, conserved site / Methylthiotransferase radical SAM domain signature. / TRAM domain / Radical SAM, alpha/beta horseshoe ...tRNA-2-methylthio-N(6)-dimethylallyladenosine synthase MiaB / Methylthiotransferase / Methylthiotransferase, N-terminal / Methylthiotransferase, N-terminal domain superfamily / Uncharacterized protein family UPF0004 / Methylthiotransferase N-terminal domain profile. / Methylthiotransferase, conserved site / Methylthiotransferase radical SAM domain signature. / TRAM domain / Radical SAM, alpha/beta horseshoe / TRAM domain / TRAM domain profile. / Elp3/MiaB/NifB / Elongator protein 3, MiaB family, Radical SAM / Radical SAM superfamily / Radical SAM core domain profile. / Radical SAM
Similarity search - Domain/homology
5'-DEOXYADENOSINE / METHIONINE / IRON/SULFUR CLUSTER / FE3-S4 methylated cluster / RNA / RNA (> 10) / tRNA-2-methylthio-N(6)-dimethylallyladenosine synthase
Similarity search - Component
Biological speciesBacteroides uniformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsEsakova, O.A. / Grove, T.L. / Yennawar, N.H. / Arcinas, A.J. / Wang, B. / Krebs, C. / Almo, S.C. / Booker, S.J.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)NIH (GM-122595 to S.J.B) United States
National Science Foundation (NSF, United States)NSF (MCB-1716686 to S.J.B.) United States
Howard Hughes Medical Institute (HHMI)Squire J. Booker United States
CitationJournal: Nature / Year: 2021
Title: Structural basis for tRNA methylthiolation by the radical SAM enzyme MiaB.
Authors: Esakova, O.A. / Grove, T.L. / Yennawar, N.H. / Arcinas, A.J. / Wang, B. / Krebs, C. / Almo, S.C. / Booker, S.J.
History
DepositionApr 20, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 29, 2021Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 6, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: tRNA-2-methylthio-N(6)-dimethylallyladenosine synthase
M: RNA (5'-R(*GP*GP*AP*CP*UP*GP*AP*AP*(MIA)P*AP*UP*CP*C)-3')
B: tRNA-2-methylthio-N(6)-dimethylallyladenosine synthase
G: RNA (5'-R(*GP*GP*AP*CP*UP*GP*AP*AP*(MIA)P*AP*UP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,21515
Polymers111,0164
Non-polymers2,19911
Water21,7441207
1
A: tRNA-2-methylthio-N(6)-dimethylallyladenosine synthase
M: RNA (5'-R(*GP*GP*AP*CP*UP*GP*AP*AP*(MIA)P*AP*UP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5957
Polymers55,5082
Non-polymers1,0875
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-36 kcal/mol
Surface area19370 Å2
MethodPISA
2
B: tRNA-2-methylthio-N(6)-dimethylallyladenosine synthase
G: RNA (5'-R(*GP*GP*AP*CP*UP*GP*AP*AP*(MIA)P*AP*UP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6208
Polymers55,5082
Non-polymers1,1126
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3860 Å2
ΔGint-45 kcal/mol
Surface area18500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.900, 97.413, 80.738
Angle α, β, γ (deg.)90.000, 108.080, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein / RNA chain , 2 types, 4 molecules ABMG

#1: Protein tRNA-2-methylthio-N(6)-dimethylallyladenosine synthase / (Dimethylallyl)adenosine tRNA methylthiotransferase MiaB / tRNA-i(6)A37 methylthiotransferase


Mass: 51275.305 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides uniformis (bacteria)
Gene: miaB_2, miaB, DW795_02470, DW831_10175, DWW14_18715, DWX44_14905, DXC07_08890, DXC80_15965, DXD90_15595, ERS417307_03809, GAP41_19630, GAP48_15545, GAP55_16410, GAQ44_15640
Production host: Escherichia coli (E. coli)
References: UniProt: A0A174NUT3, tRNA-2-methylthio-N6-dimethylallyladenosine synthase
#2: RNA chain RNA (5'-R(*GP*GP*AP*CP*UP*GP*AP*AP*(MIA)P*AP*UP*CP*C)-3')


Mass: 4232.682 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Bacteroides uniformis (bacteria)

-
Non-polymers , 6 types, 1218 molecules

#3: Chemical ChemComp-ZKP / FE3-S4 methylated cluster


Mass: 310.830 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH3Fe3S4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MET / METHIONINE


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H11NO2S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-5AD / 5'-DEOXYADENOSINE


Mass: 251.242 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1207 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 46.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 100 mM sodium cacodylate pH 5.5, 13% PEG 4000, 1,2-butanediol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0033 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0033 Å / Relative weight: 1
ReflectionResolution: 1.35→50 Å / Num. obs: 308607 / % possible obs: 99.9 % / Redundancy: 5.5 % / Biso Wilson estimate: 12.98 Å2 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.03 / Rrim(I) all: 0.071 / Χ2: 0.888 / Net I/σ(I): 9.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.4-1.435.30.882110740.7160.4170.9770.70999.9
1.43-1.455.40.734111040.770.3450.8130.77499.9
1.45-1.495.40.569110710.8490.2670.630.8100
1.49-1.525.40.453111240.8910.2120.5010.787100
1.52-1.565.50.368110530.9150.1720.4060.869100
1.56-1.65.50.282111420.9540.1310.3110.791100
1.6-1.655.50.232111280.9680.1080.2560.837100
1.65-1.75.60.188110330.9770.0870.2080.831100
1.7-1.765.60.153111490.9820.0710.1690.869100
1.76-1.835.60.117111130.9890.0540.1290.844100
1.83-1.925.60.102111010.9870.0470.1130.944100
1.92-2.025.60.084111180.9920.0380.0921.078100
2.02-2.145.70.075111250.9910.0340.0821.283100
2.14-2.315.70.065111730.9940.030.0721.318100
2.31-2.545.70.05111170.9960.0230.0551.041100
2.54-2.915.70.042111730.9970.0190.0460.936100
2.91-3.665.70.035111980.9980.0160.0390.869100
3.66-505.50.03112900.9980.0140.0340.63299.7

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QGQ

2qgq


Resolution: 1.4→39.08 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 16.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1737 3070 0.99 %
Rwork0.1494 305537 -
obs0.1497 308607 78.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 53.51 Å2 / Biso mean: 19.6576 Å2 / Biso min: 7.55 Å2
Refinement stepCycle: final / Resolution: 1.4→39.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6932 562 89 1207 8790
Biso mean--11.28 29.74 -
Num. residues----908
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0188026
X-RAY DIFFRACTIONf_angle_d1.84811025
X-RAY DIFFRACTIONf_dihedral_angle_d20.4253179
X-RAY DIFFRACTIONf_chiral_restr0.1651264
X-RAY DIFFRACTIONf_plane_restr0.0151329
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4-1.420.238590.26355876593533
1.42-1.450.2959740.24717411748542
1.45-1.470.2347860.22498573865948
1.47-1.50.2283900.21448956904650
1.5-1.530.2298890.19838988907751
1.53-1.560.2024950.18469290938553
1.56-1.590.20651020.1684100461014857
1.59-1.630.18511090.1581110821119163
1.63-1.670.19021320.1511125571268971
1.67-1.710.16011420.1464138871402979
1.71-1.760.18741560.1428154271558387
1.76-1.820.16511640.1502166861685095
1.82-1.890.19941760.1517176261780299
1.89-1.960.19521790.15441766717846100
1.96-2.050.22251750.14921769517870100
2.05-2.160.1631780.14751770717885100
2.16-2.290.1661770.14811769817875100
2.29-2.470.17041790.15091766017839100
2.47-2.720.15171770.15461767617853100
2.72-3.110.1771760.15461772117897100
3.11-3.920.18371750.13911766317838100
3.92-39.080.13751800.13061764517825100
Refinement TLS params.Method: refined / Origin x: 6.8375 Å / Origin y: 20.714 Å / Origin z: 49.8641 Å
111213212223313233
T0.0861 Å20.0075 Å20.0164 Å2-0.0796 Å20.0166 Å2--0.1208 Å2
L0.0789 °20.0289 °20.1373 °2-0.2349 °20.3519 °2--1.1413 °2
S-0.0058 Å °0.0312 Å °0.0345 Å °-0.0333 Å °0.0003 Å °0.003 Å °-0.0876 Å °-0.0021 Å °0.0057 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA17 - 501
2X-RAY DIFFRACTION1allA601
3X-RAY DIFFRACTION1allA701 - 801
4X-RAY DIFFRACTION1allM29 - 41
5X-RAY DIFFRACTION1allB17 - 501
6X-RAY DIFFRACTION1allB601
7X-RAY DIFFRACTION1allB701 - 801
8X-RAY DIFFRACTION1allG29 - 41
9X-RAY DIFFRACTION1allS3 - 1251
10X-RAY DIFFRACTION1allH1 - 4

+
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