[English] 日本語
Yorodumi
- EMDB-70545: Structure of Mycobacterium smegmatis EtfD -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-70545
TitleStructure of Mycobacterium smegmatis EtfD
Map dataCryoEM map of Mycobacterium smegmatis EtfD (sharpened)
Sample
  • Complex: Structure of Mycobacterium smegmatis EtfD
    • Protein or peptide: Iron-sulfur-binding reductase
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: MENAQUINONE-9
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: Non-cubane [4Fe-4S]-cluster
  • Ligand: 1,3,5,7-tetrathia-2$l^{2},4$l^{4},6$l^{2}-triferraspiro[3.3]heptane
Keywordsoxidoreductase / membrane protein / electron transport chain / beta oxidation
Function / homology
Function and homology information


4 iron, 4 sulfur cluster binding / oxidoreductase activity / metal ion binding / plasma membrane
Similarity search - Function
4Fe-4S dicluster domain / : / Cysteine-rich domain / Cysteine-rich domain / Alpha-helical ferredoxin / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain
Similarity search - Domain/homology
Iron-sulfur-binding reductase
Similarity search - Component
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsCourbon GM / Rubinstein JL
Funding support Canada, 1 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT191893 Canada
CitationJournal: To Be Published
Title: Mycobacterial EtfD contains an unusual linear [3Fe-4S] cluster and enables beta oxidation to drive proton pumping by the electron transport chain
Authors: Courbon GM / Rubinstein JL
History
DepositionMay 8, 2025-
Header (metadata) releaseMay 21, 2025-
Map releaseMay 21, 2025-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_70545.png

Downloads & links

-
Map

FileDownload / File: emd_70545.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM map of Mycobacterium smegmatis EtfD (sharpened)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.02 Å/pix.
x 320 pix.
= 327.68 Å		1.02 Å/pix.
x 320 pix.
= 327.68 Å		1.02 Å/pix.
x 320 pix.
= 327.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.024 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.16
Minimum - Maximum-1.0467362 - 1.7700719
Average (Standard dev.)-0.000009377364 (±0.019762378)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 327.68002 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: CryoEM map of Mycobacterium smegmatis EtfD (unsharpened)

Fileemd_70545_additional_1.map
AnnotationCryoEM map of Mycobacterium smegmatis EtfD (unsharpened)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: CryoEM map of Mycobacterium smegmatis EtfD (Half B)

Fileemd_70545_half_map_1.map
AnnotationCryoEM map of Mycobacterium smegmatis EtfD (Half B)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: CryoEM map of Mycobacterium smegmatis EtfD (Half A)

Fileemd_70545_half_map_2.map
AnnotationCryoEM map of Mycobacterium smegmatis EtfD (Half A)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Structure of Mycobacterium smegmatis EtfD

EntireName: Structure of Mycobacterium smegmatis EtfD
Components
  • Complex: Structure of Mycobacterium smegmatis EtfD
    • Protein or peptide: Iron-sulfur-binding reductase
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: MENAQUINONE-9
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: Non-cubane [4Fe-4S]-cluster
  • Ligand: 1,3,5,7-tetrathia-2$l^{2},4$l^{4},6$l^{2}-triferraspiro[3.3]heptane

-
Supramolecule #1: Structure of Mycobacterium smegmatis EtfD

SupramoleculeName: Structure of Mycobacterium smegmatis EtfD / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)

-
Macromolecule #1: Iron-sulfur-binding reductase

MacromoleculeName: Iron-sulfur-binding reductase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 111.045625 KDa
SequenceString: MAHTLEVSRL IIGLLMTAIV LVFAAKRVLW LTKLIRSGQK TLDENGRKND LQKRITTQIT EVFGQTRLLR WSVPGIAHFF TMWGFFVLA SVYLEAYGVL FDPEFHIPFI GRWPVLGFLQ DFFAVAVLLG IIVFAIIRVV REPKKIGRDS RFYGSHTGGA W EILFMIFL ...String:
MAHTLEVSRL IIGLLMTAIV LVFAAKRVLW LTKLIRSGQK TLDENGRKND LQKRITTQIT EVFGQTRLLR WSVPGIAHFF TMWGFFVLA SVYLEAYGVL FDPEFHIPFI GRWPVLGFLQ DFFAVAVLLG IIVFAIIRVV REPKKIGRDS RFYGSHTGGA W EILFMIFL VIATYALFRG AAVNTLGERF PYQSGAFFSD FMAWILRPLG ATANMWIETV ALMGHIGVML VFLLIVLHSK HL HIGLAPI NVTFKRLPNG LGPLLPMESN GEYIDFEDPA EDAVFGKGKI EDFTWKGYLD FTTCTECGRC QSQCPAWNTG KPL SPKLVI MNLRDHMFAK APYILGEKPS PLESTPEGGL GEKARGEKHE QKHAHDHVPE SGFERILGSG PEQALRPLVG TEEQ GGVID PDVLWSCTNC GACVEQCPVD IEHIDHIVDM RRYQVMVESE FPGELGVLFK NLETKGNPWG QNAKDRTNWI DEVDF DVPV YGEDVDSFDG FEYLFWVGCA GAYEDRAKKT TKAVAELLAT AGVKFLVLGT GETCTGDSAR RSGNEFLFQQ LAAQNV ETI NELFEGVETV DRKIVVTCPH CFNTIGREYP QLGANYSVVH HTQLLNRLVR DKKLVPVKSV SEQNGQPVTY HDPCFLG RH NKVYEAPREL VEASGVTLKE MPRHADRGLC CGAGGARMWM EEHIGKRVNV ERTEEAMDTA STIATGCPFC RVMITDGV D DVAASRNVEK AEVLDVAQLL LNSLDTSKVT LPEKGTAAKE SEKRAAARAE AEAKAEAAAP PVEEAAPEAE APAAPAAGG AEAKPVTGLG MAGAAKRPGA KKAAPAAEAS AAPAAAPAPA KGLGLAGGAK RPGAKKAAAP AAEAPAAPAS DAPPVKGLGL AGGAKRPGA KKTAAAAPAE KPAATEAPEA SATPAAPAAP VKGLGLAAGA KRPGAKKTAA APAEKPAAAE TEAPAPAETA A PAEPAKPE PPVVGLGIAA GARRPGAKKA AAKPAAAPAP AAEKPAEQAA EPEKPAEKPA EPEKPEPPVV GLGIKPGAKR PG KR

UniProtKB: Iron-sulfur-binding reductase

-
Macromolecule #2: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 2 / Number of copies: 1 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

ChemComp-LMT:
DODECYL-BETA-D-MALTOSIDE / detergent*YM

-
Macromolecule #3: MENAQUINONE-9

MacromoleculeName: MENAQUINONE-9 / type: ligand / ID: 3 / Number of copies: 1 / Formula: MQ9
Molecular weightTheoretical: 785.233 Da
Chemical component information

ChemComp-MQ9:
MENAQUINONE-9

-
Macromolecule #4: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 4 / Number of copies: 1 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

-
Macromolecule #5: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 5 / Number of copies: 2 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

-
Macromolecule #6: Non-cubane [4Fe-4S]-cluster

MacromoleculeName: Non-cubane [4Fe-4S]-cluster / type: ligand / ID: 6 / Number of copies: 1 / Formula: 9S8
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-9S8:
Non-cubane [4Fe-4S]-cluster

-
Macromolecule #7: 1,3,5,7-tetrathia-2$l^{2},4$l^{4},6$l^{2}-triferraspiro[3.3]heptane

MacromoleculeName: 1,3,5,7-tetrathia-2$l^{2},4$l^{4},6$l^{2}-triferraspiro[3.3]heptane
type: ligand / ID: 7 / Number of copies: 1 / Formula: A1CBX
Molecular weightTheoretical: 295.795 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 70.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.4 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 48053
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
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