[English] 日本語
Yorodumi
- EMDB-42164: The CryoEM structure of the high affinity Carbon monoxide dehydro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-42164
TitleThe CryoEM structure of the high affinity Carbon monoxide dehydrogenase from Mycobacterium smegmatis
Map dataPrimary Map
Sample
  • Complex: MoCu Carbon monoxide Dehydrogenase (MoCu-CODH)
    • Protein or peptide: Carbon monoxide dehydrogenase medium chain
    • Protein or peptide: [2Fe-2S] binding domain protein
  • Protein or peptide: Carbon monoxide dehydrogenase (Large chain), CoxL
  • Ligand: CU(I)-S-MO(IV)(=O)OH CLUSTER
  • Ligand: PTERIN CYTOSINE DINUCLEOTIDE
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: water
KeywordsCarbon monoxide dehydrogenase / MoCu / Mycobacterium smegmatis / High affinity / trace gas scavenging / OXIDOREDUCTASE
Function / homology
Function and homology information


carbon-monoxide dehydrogenase (acceptor) / anaerobic carbon-monoxide dehydrogenase activity / molybdenum ion binding / FAD binding / 2 iron, 2 sulfur cluster binding / oxidoreductase activity / iron ion binding / copper ion binding / metal ion binding
Similarity search - Function
Carbon-monoxide dehydrogenase, large subunit / : / : / CO dehydrogenase flavoprotein C-terminal domain / Molybdopterin dehydrogenase, FAD-binding / CO dehydrogenase flavoprotein, C-terminal / CO dehydrogenase flavoprotein, C-terminal domain superfamily / FAD binding domain in molybdopterin dehydrogenase / CO dehydrogenase flavoprotein C-terminal domain / Aldehyde oxidase/xanthine dehydrogenase ...Carbon-monoxide dehydrogenase, large subunit / : / : / CO dehydrogenase flavoprotein C-terminal domain / Molybdopterin dehydrogenase, FAD-binding / CO dehydrogenase flavoprotein, C-terminal / CO dehydrogenase flavoprotein, C-terminal domain superfamily / FAD binding domain in molybdopterin dehydrogenase / CO dehydrogenase flavoprotein C-terminal domain / Aldehyde oxidase/xanthine dehydrogenase / Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain / Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead / [2Fe-2S]-binding / Aldehyde oxidase/xanthine dehydrogenase, first molybdopterin binding domain / Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead superfamily / [2Fe-2S]-binding domain superfamily / Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain superfamily / Aldehyde oxidase/xanthine dehydrogenase, second molybdopterin binding domain / [2Fe-2S] binding domain / Molybdopterin cofactor-binding domain / Molybdopterin cofactor-binding domain / Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain / FAD-binding, type PCMH, subdomain 1 / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily
Similarity search - Domain/homology
Carbon monoxide dehydrogenase medium chain / [2Fe-2S] binding domain protein / Carbon monoxide dehydrogenase (Large chain), CoxL
Similarity search - Component
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.85 Å
AuthorsGrinter R / Venugopal H / Greening C / Gillett D
Funding support Australia, 1 items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP200103074 Australia
CitationJournal: Nat Chem Biol / Year: 2025
Title: Quinone extraction drives atmospheric carbon monoxide oxidation in bacteria.
Authors: Ashleigh Kropp / David L Gillett / Hari Venugopal / Miguel A Gonzálvez / James P Lingford / Surbhi Jain / Christopher K Barlow / Jie Zhang / Chris Greening / Rhys Grinter /
Abstract: Diverse bacteria and archaea use atmospheric CO as an energy source for long-term survival. Bacteria use [MoCu]-CO dehydrogenases (Mo-CODH) to convert atmospheric CO to carbon dioxide, transferring ...Diverse bacteria and archaea use atmospheric CO as an energy source for long-term survival. Bacteria use [MoCu]-CO dehydrogenases (Mo-CODH) to convert atmospheric CO to carbon dioxide, transferring the obtained electrons to the aerobic respiratory chain. However, it is unknown how these enzymes oxidize CO at low concentrations and interact with the respiratory chain. Here, we use cryo-electron microscopy and structural modeling to show how Mo-CODH (CoxSML) from Mycobacterium smegmatis interacts with its partner, the membrane-bound menaquinone-binding protein CoxG. We provide electrochemical, biochemical and genetic evidence that Mo-CODH transfers CO-derived electrons to the aerobic respiratory chain through CoxG. Lastly, we show that Mo-CODH and CoxG genetically and structurally associate in diverse bacteria and archaea. These findings reveal the basis of the biogeochemically and ecologically important process of atmospheric CO oxidation, while demonstrating that long-range quinone transport is a general mechanism of energy conservation, which convergently evolved on multiple occasions.
History
DepositionOct 2, 2023-
Header (metadata) releaseOct 16, 2024-
Map releaseOct 16, 2024-
UpdateJul 9, 2025-
Current statusJul 9, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_42164.png

Downloads & links

-
Map

FileDownload / File: emd_42164.map.gz / Format: CCP4 / Size: 129.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPrimary Map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 324 pix.
= 265.68 Å		0.82 Å/pix.
x 324 pix.
= 265.68 Å		0.82 Å/pix.
x 324 pix.
= 265.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.23
Minimum - Maximum-5.0479937 - 17.120714
Average (Standard dev.)0.0012077261 (±0.22044414)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions324324324
Spacing324324324
CellA=B=C: 265.68 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: Half map 1

Fileemd_42164_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map 2

Fileemd_42164_half_map_2.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : MoCu Carbon monoxide Dehydrogenase (MoCu-CODH)

EntireName: MoCu Carbon monoxide Dehydrogenase (MoCu-CODH)
Components
  • Complex: MoCu Carbon monoxide Dehydrogenase (MoCu-CODH)
    • Protein or peptide: Carbon monoxide dehydrogenase medium chain
    • Protein or peptide: [2Fe-2S] binding domain protein
  • Protein or peptide: Carbon monoxide dehydrogenase (Large chain), CoxL
  • Ligand: CU(I)-S-MO(IV)(=O)OH CLUSTER
  • Ligand: PTERIN CYTOSINE DINUCLEOTIDE
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: water

-
Supramolecule #1: MoCu Carbon monoxide Dehydrogenase (MoCu-CODH)

SupramoleculeName: MoCu Carbon monoxide Dehydrogenase (MoCu-CODH) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2-#3
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 270 KDa

-
Macromolecule #1: Carbon monoxide dehydrogenase (Large chain), CoxL

MacromoleculeName: Carbon monoxide dehydrogenase (Large chain), CoxL / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 85.957844 KDa
SequenceString: MTTLENPVER PEDTAVNDAK PCGHGRMLRK EDPRFIRGRG NYVDDVKLPG MLHLAILRSP YAHATINSID VTAAQAHPKV KAVVTGADL AAKGLAWMPT LSNDVQAVLA TDKVRFQGQE VAFVVAEDRY SARDALELID VDYEPLDPVI DARHALDPGA P VIRTDLDG ...String:
MTTLENPVER PEDTAVNDAK PCGHGRMLRK EDPRFIRGRG NYVDDVKLPG MLHLAILRSP YAHATINSID VTAAQAHPKV KAVVTGADL AAKGLAWMPT LSNDVQAVLA TDKVRFQGQE VAFVVAEDRY SARDALELID VDYEPLDPVI DARHALDPGA P VIRTDLDG KTDNHCFDWE TGDAAATDAV FAKADVVVKQ EMVYPRVHPA PMETCGAVAD LDPVTRKLTL WSTTQAPHAH RT LYALVAG LPEHKIRVIS PDIGGGFGNK VPIYPGYVCA IVGSLLLGKP VKWMEDRSEN LTSTGFARDY IMVGEIAATR DGK ILAIRS NVLADHGAFN GTAAPVKYPA GFFGVFTGSY DIEAAYCHMT AVYTNKAPGG VAYACSFRIT EAVYFVERLV DCLA YELKM DPAQLRLQNL LKAEQFPYTS KTGWVYDSGD YEKTMRLAME MVDYEGLRAE QAEKRKRGEL MGIGMSFFTE AVGAG PRKD MDILGLGMAD GCELRVHPTG KAVVRLSVQS QGQGHETTFA QIVAEELGIP PEDIDVVHGD TDQTPFGLGT YGSRST PVS GAAAALVARK VRDKAKIIAA GMLEASIADL EWDKGSFHIK GDPSASVTIA DIAMRAHGAG DLPEGLEGGL DAQICYN PS NLTYPYGAYF CVVDIDPGTA VVKVRRFVAV DDCGTRINPM IIEGQIHGGL VDGIGMALME MIAFDEDGNC LGGSLMDY L IPTAMEVPHF ETGHTVTPSP HHPIGAKGIG ESATVGSPPA VVNAVVDALA PYGVRHADMP LTPSRVWEAM QGRATPPI

UniProtKB: Carbon monoxide dehydrogenase (Large chain), CoxL

-
Macromolecule #2: Carbon monoxide dehydrogenase medium chain

MacromoleculeName: Carbon monoxide dehydrogenase medium chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 31.710051 KDa
SequenceString: MQVPGPFEYE RATSVDHAVG LLDRLGEDAR IVAGGHSLLP MMKLRIANPE YLVDINDLAV ELGYVITDPT LVRIGAMARH RQVLESDPL AAVCPIFRDA ERVIADPVVR NRGTLGGSLC QADPAEDLTT VCTILGAVCL ARGPGGEREI GIDDFLVGPY E TALAHNEM ...String:
MQVPGPFEYE RATSVDHAVG LLDRLGEDAR IVAGGHSLLP MMKLRIANPE YLVDINDLAV ELGYVITDPT LVRIGAMARH RQVLESDPL AAVCPIFRDA ERVIADPVVR NRGTLGGSLC QADPAEDLTT VCTILGAVCL ARGPGGEREI GIDDFLVGPY E TALAHNEM LVEVRIPVRH RTSSAYAKVE RRVGDWAVTA AGAQVTLDGD SIVAARVGLT AVNPDPDALR ALADDLIGKP AT EETFAAA GELAVQACEP VTDTRGSADY KRHLARELTI RTMRTAVERV RTAPAPEGN

UniProtKB: Carbon monoxide dehydrogenase medium chain

-
Macromolecule #3: [2Fe-2S] binding domain protein

MacromoleculeName: [2Fe-2S] binding domain protein / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 17.14857 KDa
SequenceString:
MQVTMTVNGE AVTADVEPRM LLVHFLRDQL GLTGTHWGCD TSNCGTCVVE VDGEPVKSCT MLAAMASGHS VNTVEGMEVD GKLDPVQEG FMQCHGLQCG FCTPGMMITA RALLRQNPDP TEEEIREAIS GQICRCTGYT TIVRSVQWAA RHAREEAKA

UniProtKB: [2Fe-2S] binding domain protein

-
Macromolecule #4: CU(I)-S-MO(IV)(=O)OH CLUSTER

MacromoleculeName: CU(I)-S-MO(IV)(=O)OH CLUSTER / type: ligand / ID: 4 / Number of copies: 2 / Formula: CUN
Molecular weightTheoretical: 224.558 Da
Chemical component information

ChemComp-CUN:
CU(I)-S-MO(IV)(=O)OH CLUSTER

-
Macromolecule #5: PTERIN CYTOSINE DINUCLEOTIDE

MacromoleculeName: PTERIN CYTOSINE DINUCLEOTIDE / type: ligand / ID: 5 / Number of copies: 2 / Formula: MCN
Molecular weightTheoretical: 696.501 Da
Chemical component information

ChemComp-MCN:
PTERIN CYTOSINE DINUCLEOTIDE

-
Macromolecule #6: FLAVIN-ADENINE DINUCLEOTIDE

MacromoleculeName: FLAVIN-ADENINE DINUCLEOTIDE / type: ligand / ID: 6 / Number of copies: 2 / Formula: FAD
Molecular weightTheoretical: 785.55 Da
Chemical component information

ChemComp-FAD:
FLAVIN-ADENINE DINUCLEOTIDE / FAD*YM

-
Macromolecule #7: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 7 / Number of copies: 4 / Formula: FES
Molecular weightTheoretical: 175.82 Da
Chemical component information

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER

-
Macromolecule #8: water

MacromoleculeName: water / type: ligand / ID: 8 / Number of copies: 899 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.9 / Component:
ConcentrationNameFormula
0.05 MTris
0.2 MNaCl
GridModel: Quantifoil R2/4 / Material: GOLD / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.001 kPa
VitrificationCryogen name: PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 4508 / Average electron dose: 66.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: DARK FIELD / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.3 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 3.1.2) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: EXACT BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 1.85 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.1.2) / Number images used: 290597
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 3.1.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.1.2)
Final 3D classificationNumber classes: 1 / Software - Name: cryoSPARC (ver. 3.1.2)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: Cross-correlation coefficient
Output model

PDB-8uem:
The CryoEM structure of the high affinity Carbon monoxide dehydrogenase from Mycobacterium smegmatis

+
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