[English] 日本語
Yorodumi
- EMDB-62860: CryoEM structure of class Ib Ribonucleotide reductase from Mycoba... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-62860
TitleCryoEM structure of class Ib Ribonucleotide reductase from Mycobacterium thermoresistibile, conformer D
Map data
Sample
  • Complex: Binary complex of RNR
    • Protein or peptide: Ribonucleoside-diphosphate reductase subunit beta
    • Protein or peptide: Ribonucleoside-diphosphate reductase
  • Ligand: MANGANESE (II) ION
KeywordsEnzyme complex / supply Dexoyribonucleotides for replication and repair / asymmetric complex / REPLICATION
Biological speciesMycolicibacterium thermoresistibile ATCC 19527 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsYadav LR / Mande SC / Vinothkumar KR / Kumar J
Funding support India, 2 items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)Centre of Excellence Grant (BT/PR15450/COE/34/46/2016) India
Department of Biotechnology (DBT, India)DBT/PR12422/MED/31/287/2014 India
CitationJournal: To Be Published
Title: Dynamics of Class Ib ribonucleotide reductase complex revealed by CryoEM
Authors: Yadav LR / Mande SC / Vinothkumar KR / Kumar J
History
DepositionDec 24, 2024-
Header (metadata) releaseJul 1, 2026-
Map releaseJul 1, 2026-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_62860.png

Downloads & links

-
Map

FileDownload / File: emd_62860.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 288 pix.
= 306.72 Å		1.07 Å/pix.
x 288 pix.
= 306.72 Å		1.07 Å/pix.
x 288 pix.
= 306.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.065 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.11
Minimum - Maximum-1.1420288 - 1.9825737
Average (Standard dev.)0.000409024 (±0.04012465)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 306.72003 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: #1

Fileemd_62860_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_62860_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_62860_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Binary complex of RNR

EntireName: Binary complex of RNR
Components
  • Complex: Binary complex of RNR
    • Protein or peptide: Ribonucleoside-diphosphate reductase subunit beta
    • Protein or peptide: Ribonucleoside-diphosphate reductase
  • Ligand: MANGANESE (II) ION

-
Supramolecule #1: Binary complex of RNR

SupramoleculeName: Binary complex of RNR / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 / Details: Heterotetrameric asymmetric complex of RNR
Source (natural)Organism: Mycolicibacterium thermoresistibile ATCC 19527 (bacteria)

-
Macromolecule #1: Ribonucleoside-diphosphate reductase subunit beta

MacromoleculeName: Ribonucleoside-diphosphate reductase subunit beta / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: ribonucleoside-diphosphate reductase
Source (natural)Organism: Mycolicibacterium thermoresistibile ATCC 19527 (bacteria)
Molecular weightTheoretical: 36.487891 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKLVNRVSAI NWNRLEDDKD AEVWHRLTGN FWLPEKVPVS NDIPSWNTLT DTEKQLTMRV FTGLTLLDTI QGTVGAVSLI PDALTPHEE AVLTNIAFME SVHAKSYSNI FSTLCSTAEI DDAFRWSEEN PNLQRKAEIV MQYYRGDEPL KRKVASTLLE S FLFYSGFY ...String:
MKLVNRVSAI NWNRLEDDKD AEVWHRLTGN FWLPEKVPVS NDIPSWNTLT DTEKQLTMRV FTGLTLLDTI QGTVGAVSLI PDALTPHEE AVLTNIAFME SVHAKSYSNI FSTLCSTAEI DDAFRWSEEN PNLQRKAEIV MQYYRGDEPL KRKVASTLLE S FLFYSGFY LPMYWSSRAK LTNTADMIRL IIRDEAVHGY YIGYKYQRGL AMVEPAKQKE LKDYTYDLLF ELYDNEVEYT QD LYDDVGL TEDVKKFLRY NANKALMNLG YEALFPKDET DVNPAILSAL APNADENHDF FSGSGSSYVI GKAVVTEDED W

UniProtKB: Ribonucleoside-diphosphate reductase subunit beta

-
Macromolecule #2: Ribonucleoside-diphosphate reductase

MacromoleculeName: Ribonucleoside-diphosphate reductase / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: ribonucleoside-diphosphate reductase
Source (natural)Organism: Mycolicibacterium thermoresistibile ATCC 19527 (bacteria)
Molecular weightTheoretical: 76.554211 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: DGKIQFDKDK QAAREFFLQH VNQNTVFFHD YDEKLDYLIE NDYYEPEVLD QYSRDFVKSL LDRAYAKKFR FPTFLGAFKY YTSYTLKTF DGKRYLERFE DRVVMVALTL AAGDVELAEK LVDEIMDGRF QPATPTFLNS GKKQRGEPVS CFLLRIEDNM E SIGRAINS ...String:
DGKIQFDKDK QAAREFFLQH VNQNTVFFHD YDEKLDYLIE NDYYEPEVLD QYSRDFVKSL LDRAYAKKFR FPTFLGAFKY YTSYTLKTF DGKRYLERFE DRVVMVALTL AAGDVELAEK LVDEIMDGRF QPATPTFLNS GKKQRGEPVS CFLLRIEDNM E SIGRAINS ALQLSKRGGG VALLLSNVRE FGAPIKNIEN QSSGVIPIMK LLEDSFSYAN QLGARQGAGA VYLHAHHPDI YR FLDTKRE NADEKIRIKT LSLGVVIPDI TFELAKKNED MYLFSPYDVE RVYGVPFADI SVTEKYYEMV DNPRIRKSKI NAR EFFQTL AELQFESGYP YIMFEDTVNR SNPIEGKVTH SNLCSEILQV STPSEFNDDL SYKVVGKDIS CNLGSLNIAK AMDS PDFGQ TVEVAIRALT AVSDQTRIDS VPSIVRGNDE SHSIGLGQMN LHGYLGRERI FYGSEEAIDF TNMYFYTVCY HAVRA SNRI AIERGKHFVG FEKSKYATGE FFDKYTDQVW EPKTDKVREL FAKANIHIPT QEDWRRLKES VQKHGIYNAY LQAVPP TGS ISYINHSTSS IHPIASKIEI RKEGKIGRVY YPAPYMTNDN LEYFQDAYEI GYEKIIDTYA AATQHVDQGL SLTLFFK DT ATTRDVNKAQ IYAWRKGIKT LYYIR

UniProtKB: Ribonucleoside-diphosphate reductase

-
Macromolecule #3: MANGANESE (II) ION

MacromoleculeName: MANGANESE (II) ION / type: ligand / ID: 3 / Number of copies: 4 / Formula: MN
Molecular weightTheoretical: 54.938 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1.25 mg/mL
BufferpH: 8 / Details: 25mM Tris pH8, 150mM NaCl
GridModel: Quantifoil R0.6/1 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 291 K / Instrument: FEI VITROBOT MARK IV
Detailssampled crosslinked with glutaraldehyde

-
Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsPhase plate: OTHER / Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Number grids imaged: 1 / Number real images: 831 / Average exposure time: 8.0 sec. / Average electron dose: 47.36 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 300000
CTF correctionSoftware - Name: cryoSPARC (ver. v3.3.2) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

2bq1


Details: 1UZR was used for beta subunit
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v3.3.2) / Number images used: 112390
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. v3.3.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v3.3.2)
Final 3D classificationSoftware - Name: cryoSPARC (ver. v3.3.2)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial model
PDB IDChain

2bq1

source_name: PDB, initial_model_type: experimental model

1uzr

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9l6o:
CryoEM structure of class Ib Ribonucleotide reductase from Mycobacterium thermoresistibile, conformer D

+
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