[English] 日本語
Yorodumi
- PDB-9wcx: Cryo-EM structure of the Mycobacterium abscessus cytochrome bcc:a... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9wcx
TitleCryo-EM structure of the Mycobacterium abscessus cytochrome bcc:aa3 supercomplex
Components
  • (Cytochrome bc1 complex cytochrome ...) x 2
  • (Cytochrome c oxidase subunit ...) x 2
  • Cytochrome bc1 complex Rieske iron-sulfur subunit
  • Cytochrome c oxidase polypeptide 4
  • DUF5130 domain-containing protein
  • Lipoprotein lpqE
  • Probable cytochrome c oxidase subunit 3
  • Prokaryotic respiratory supercomplex associate factor 1
  • Superoxide dismutase [Cu-Zn]
  • cytochrome-c oxidase
KeywordsOXIDOREDUCTASE / Apo structure of Supercomplex
Function / homology
Function and homology information


aerobic electron transport chain / cytochrome-c oxidase / oxidative phosphorylation / quinol-cytochrome-c reductase / quinol-cytochrome-c reductase activity / cytochrome-c oxidase activity / superoxide dismutase / superoxide dismutase activity / electron transport coupled proton transport / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen ...aerobic electron transport chain / cytochrome-c oxidase / oxidative phosphorylation / quinol-cytochrome-c reductase / quinol-cytochrome-c reductase activity / cytochrome-c oxidase activity / superoxide dismutase / superoxide dismutase activity / electron transport coupled proton transport / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / ATP synthesis coupled electron transport / respiratory electron transport chain / monooxygenase activity / electron transport chain / 2 iron, 2 sulfur cluster binding / oxidoreductase activity / iron ion binding / copper ion binding / heme binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
: / Copper chaperone PCuAC superfamily / Protein of unknown function DUF5130 / Domain of unknown function (DUF5130) / Copper chaperone PCuAC / Putative lipoprotein LpqE-like / Cytochrome bc1 complex, cytochrome c subunit / Cytochrome c oxidase subunit IV, actinobacteria / QcrA subunit, N-terminal / Cytochrome c oxidase subunit IV ...: / Copper chaperone PCuAC superfamily / Protein of unknown function DUF5130 / Domain of unknown function (DUF5130) / Copper chaperone PCuAC / Putative lipoprotein LpqE-like / Cytochrome bc1 complex, cytochrome c subunit / Cytochrome c oxidase subunit IV, actinobacteria / QcrA subunit, N-terminal / Cytochrome c oxidase subunit IV / QcrA subunit N-terminal region / Cytochrome b(N-terminal)/b6/petB / Cytochrome c oxidase, subunit I bacterial type / : / Cytochrome C oxidase, cbb3-type, subunit III / Superoxide dismutase, copper/zinc, binding site / Copper/Zinc superoxide dismutase signature 2. / Cytochrome c oxidase subunit III / Cytochrome c oxidase subunit III-like / Cytochrome c oxidase, subunit III, 4-helical bundle / Cytochrome c oxidase subunit III / Heme-copper oxidase subunit III family profile. / Superoxide dismutase, copper/zinc binding domain / Copper/zinc superoxide dismutase (SODC) / Cytochrome c oxidase subunit III-like superfamily / Superoxide dismutase-like, copper/zinc binding domain superfamily / Cytochrome c/quinol oxidase subunit II / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / Cytochrome C oxidase subunit II, transmembrane domain superfamily / Cytochrome c oxidase, subunit I, copper-binding site / Heme-copper oxidase catalytic subunit, copper B binding region signature. / Cytochrome c oxidase-like, subunit I domain / Cytochrome oxidase subunit I profile. / Cytochrome C oxidase subunit II, periplasmic domain / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome oxidase subunit II copper A binding domain profile. / Cytochrome c oxidase subunit I / Cytochrome c oxidase-like, subunit I superfamily / Cytochrome C and Quinol oxidase polypeptide I / Cytochrome c / Cytochrome b/b6, N-terminal / Cytochrome b/b6-like domain superfamily / Cytochrome b/b6 N-terminal region profile. / Di-haem cytochrome, transmembrane / Rieske iron-sulphur protein / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Cupredoxin / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Chem-9XX / Chem-9Y0 / Chem-9YF / CARDIOLIPIN / COPPER (II) ION / FE2/S2 (INORGANIC) CLUSTER / HEME-A / HEME C / PROTOPORPHYRIN IX CONTAINING FE / MENAQUINONE-9 ...Chem-9XX / Chem-9Y0 / Chem-9YF / CARDIOLIPIN / COPPER (II) ION / FE2/S2 (INORGANIC) CLUSTER / HEME-A / HEME C / PROTOPORPHYRIN IX CONTAINING FE / MENAQUINONE-9 / OXYGEN MOLECULE / PALMITIC ACID / Cytochrome c oxidase subunit 1 / Lipoprotein lpqE / Superoxide dismutase [Cu-Zn] / Uncharacterized protein / DUF5130 domain-containing protein / cytochrome-c oxidase / Cytochrome c oxidase polypeptide 4 / Cytochrome bc1 complex cytochrome b subunit / Cytochrome bc1 complex Rieske iron-sulfur subunit / Cytochrome bc1 complex cytochrome c subunit / Probable cytochrome c oxidase subunit 3
Similarity search - Component
Biological speciesMycobacteroides abscessus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.66 Å
AuthorsMathiyazakan, V. / Gruber, G.
Funding support Singapore, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Singapore)NRF-CRP27-2021-0002 Singapore
CitationJournal: Nat Commun / Year: 2026
Title: The Mycobacterium abscessus cytochrome bcc:aa oxidase structure paves the way for an agent targeting subunit QcrB.
Authors: Vikneswaran Mathiyazakan / Emilia Xin Yi Tan / Garrett Moraski / Sandip Basak / Wuan-Geok Saw / Kevin Pethe / Gerhard Grüber /
Abstract: The cytochrome bcc:aa oxidase is the target of telacebec, a clinically advanced drug developed for Mycobacterium tuberculosis. However, telacebec is inactive against Mycobacterium abscessus, an ...The cytochrome bcc:aa oxidase is the target of telacebec, a clinically advanced drug developed for Mycobacterium tuberculosis. However, telacebec is inactive against Mycobacterium abscessus, an opportunistic pathogen increasingly linked to chronic pulmonary infections and notoriously known for intrinsic resistance to numerous antibiotics. Here, we report the 2.6 Å cryo-electron microscopy structure of the M. abscessus bcc:aa cytochrome oxidase supercomplex, revealing key pathways and the evolution of the mycobacterial QcrB menaquinol-binding cavity. Structure-guided mutagenesis identified polymorphisms that modulate telacebec binding and potency in both M. abscessus and Mycobacterium smegmatis. Leveraging these insights, we designed ND-011458, a QcrB inhibitor with potent activity against M. abscessus and being bactericidal in combination with Clofazimine. The 2.26 Å inhibitor-bound structure elucidates its binding mode and provides a framework for the design of next-generation inhibitors for M. abscessus pulmonary diseases.
History
DepositionAug 18, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 1, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
G: Prokaryotic respiratory supercomplex associate factor 1
I: Cytochrome c oxidase subunit 1
J: Cytochrome c oxidase subunit CtaJ
L: Cytochrome c oxidase subunit 1
U: Cytochrome bc1 complex cytochrome c subunit
V: Cytochrome bc1 complex Rieske iron-sulfur subunit
X: Superoxide dismutase [Cu-Zn]
a: Superoxide dismutase [Cu-Zn]
b: Prokaryotic respiratory supercomplex associate factor 1
d: cytochrome-c oxidase
e: cytochrome-c oxidase
f: Probable cytochrome c oxidase subunit 3
g: Probable cytochrome c oxidase subunit 3
h: Cytochrome c oxidase subunit CtaJ
i: Cytochrome bc1 complex cytochrome b subunit
j: Cytochrome bc1 complex cytochrome b subunit
k: DUF5130 domain-containing protein
l: DUF5130 domain-containing protein
m: Cytochrome c oxidase polypeptide 4
n: Cytochrome c oxidase polypeptide 4
o: Cytochrome bc1 complex cytochrome c subunit
p: Cytochrome bc1 complex Rieske iron-sulfur subunit
q: Lipoprotein lpqE
r: Lipoprotein lpqE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)773,41394
Polymers717,61724
Non-polymers55,79670
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

-
Protein , 8 types, 16 molecules GbVpXadefgklmnqr

#1: Protein Prokaryotic respiratory supercomplex associate factor 1


Mass: 10679.506 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: A0A1U1LTV7 / Source: (natural) Mycobacteroides abscessus (bacteria)
#5: Protein Cytochrome bc1 complex Rieske iron-sulfur subunit / Cytochrome bc1 reductase complex subunit QcrA / Rieske iron-sulfur protein


Mass: 43008.285 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mycobacteroides abscessus (bacteria) / References: UniProt: B1MNZ8
#6: Protein Superoxide dismutase [Cu-Zn]


Mass: 23842.414 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mycobacteroides abscessus (bacteria) / References: UniProt: B1MIN6, superoxide dismutase
#7: Protein cytochrome-c oxidase / Cytochrome aa3 subunit 2


Mass: 38750.297 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mycobacteroides abscessus (bacteria) / References: UniProt: B1MNZ2, cytochrome-c oxidase
#8: Protein Probable cytochrome c oxidase subunit 3 / Cytochrome aa3 subunit 3 / Cytochrome c oxidase polypeptide III


Mass: 22538.057 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mycobacteroides abscessus (bacteria) / References: UniProt: B1MP00, cytochrome-c oxidase
#10: Protein DUF5130 domain-containing protein


Mass: 18192.475 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mycobacteroides abscessus (bacteria) / References: UniProt: B1MMU2
#11: Protein Cytochrome c oxidase polypeptide 4 / Cytochrome aa3 subunit 4 / Cytochrome c oxidase polypeptide IV


Mass: 15068.367 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mycobacteroides abscessus (bacteria) / References: UniProt: B1MNZ3, cytochrome-c oxidase
#12: Protein Lipoprotein lpqE


Mass: 23241.809 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mycobacteroides abscessus (bacteria) / References: UniProt: B1MGY1

-
Cytochrome c oxidase subunit ... , 2 types, 4 molecules ILJh

#2: Protein Cytochrome c oxidase subunit 1


Mass: 62692.160 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mycobacteroides abscessus (bacteria) / References: UniProt: B1MDZ6, cytochrome-c oxidase
#3: Protein Cytochrome c oxidase subunit CtaJ


Mass: 9157.419 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mycobacteroides abscessus (bacteria) / References: UniProt: B1MMU1

-
Cytochrome bc1 complex cytochrome ... , 2 types, 4 molecules Uoij

#4: Protein Cytochrome bc1 complex cytochrome c subunit


Mass: 31176.285 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mycobacteroides abscessus (bacteria) / References: UniProt: B1MNZ9, quinol-cytochrome-c reductase
#9: Protein Cytochrome bc1 complex cytochrome b subunit / Cytochrome bc1 reductase complex subunit QcrB / Ubiquinol--cytochrome c reductase cytochrome b subunit


Mass: 60461.324 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mycobacteroides abscessus (bacteria) / References: UniProt: B1MNZ7, quinol-cytochrome-c reductase

-
Non-polymers , 13 types, 144 molecules

#13: Chemical
ChemComp-9XX / (2S)-1-(hexadecanoyloxy)propan-2-yl (10S)-10-methyloctadecanoate / (S)-1-(palmitoyloxy)propan-2-yl (S)-10-methyloctadecanoate


Mass: 594.992 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C38H74O4 / Feature type: SUBJECT OF INVESTIGATION
#14: Chemical
ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL


Mass: 1464.043 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C81H156O17P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#15: Chemical
ChemComp-9Y0 / (2R)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)propyl (E)-octadec-9-enoate


Mass: 717.996 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C39H76NO8P / Feature type: SUBJECT OF INVESTIGATION
#16: Chemical
ChemComp-HEA / HEME-A


Mass: 852.837 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C49H56FeN4O6 / Feature type: SUBJECT OF INVESTIGATION
#17: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#18: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H32O2 / Feature type: SUBJECT OF INVESTIGATION
#19: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2 / Feature type: SUBJECT OF INVESTIGATION
#20: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#21: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#22: Chemical
ChemComp-9YF / (2R)-2-(hexadecanoyloxy)-3-{[(S)-hydroxy{[(1R,2R,3R,4R,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propyl (9S)-9-methyloctadecanoate


Mass: 853.112 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C44H85O13P / Feature type: SUBJECT OF INVESTIGATION
#23: Chemical
ChemComp-MQ9 / MENAQUINONE-9


Mass: 785.233 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C56H80O2 / Feature type: SUBJECT OF INVESTIGATION
#24: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#25: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Mycobacterium abscessus cytochrome bcc:aa3 supercomplex
Type: COMPLEX / Entity ID: #1-#12 / Source: NATURAL
Molecular weightValue: 760 kDa/nm / Experimental value: NO
Source (natural)Organism: Mycobacteroides abscessus (bacteria)
Buffer solutionpH: 7.4
SpecimenConc.: 13 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal magnification: 130000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 700 nm
Image recordingElectron dose: 56 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

EM software
IDNameVersionCategory
1cryoSPARC4particle selection
9PHENIX1.20.1_4487model refinement
13cryoSPARC43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.66 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 194219 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
RefinementHighest resolution: 2.66 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

+
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