9F61 | pdb_00009f61

Structure of the Chlamydomonas reinhardtii respiratory complex IV from respiratory supercomplex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.55 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

In-cell architecture of the mitochondrial respiratory chain.

Waltz, F.Righetto, R.D.Lamm, L.Salinas-Giege, T.Kelley, R.Zhang, X.Obr, M.Khavnekar, S.Kotecha, A.Engel, B.D.

(2025) Science 387: 1296-1301

  • DOI: https://doi.org/10.1126/science.ads8738
  • Primary Citation of Related Structures:  
    9F5X, 9F5Y, 9F5Z, 9F60, 9F61, 9F62

  • PubMed Abstract: 

    Mitochondria regenerate adenosine triphosphate (ATP) through oxidative phosphorylation. This process is carried out by five membrane-bound complexes collectively known as the respiratory chain, working in concert to transfer electrons and pump protons. The precise organization of these complexes in native cells is debated. We used in situ cryo-electron tomography to visualize the native structures and organization of several major mitochondrial complexes in Chlamydomonas reinhardtii cells. ATP synthases and respiratory complexes segregate into curved and flat crista membrane domains, respectively. Respiratory complexes I, III, and IV assemble into a respirasome supercomplex, from which we determined a native 5-angstrom (Å) resolution structure showing binding of electron carrier cytochrome c . Combined with single-particle cryo-electron microscopy at 2.4-Å resolution, we model how the respiratory complexes organize inside native mitochondria.


  • Organizational Affiliation
    • Biozentrum, University of Basel, Basel, Switzerland.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 1A [auth 3A]505Chlamydomonas reinhardtiiMutation(s): 0 
EC: 7.1.1.9
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase polypeptide IIB [auth 3B]284Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
cytochrome-c oxidaseC [auth 3C]153Chlamydomonas reinhardtiiMutation(s): 0 
EC: 7.1.1.9
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 3D [auth 3D]382Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cox5bE [auth 3E]175Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cox5cF [auth 3F]96Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Cox6aG [auth 3G]125Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Cox6bH [auth 3H]148Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Cox7cI [auth 3I]101Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunitJ [auth 3J]105Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Cox7aK [auth 3K]58Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
CoxInL [auth 3L]87Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
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Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEA
Query on HEA

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M [auth 3A],
N [auth 3A]
HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
PC7
Query on PC7

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Q [auth 3A](7S)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE
C42 H85 N O8 P
PZNPLUBHRSSFHT-FAIXQHPJSA-O
PGT
Query on PGT

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R [auth 3A](1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
C40 H79 O10 P
KBPVYRBBONZJHF-AMAPPZPBSA-N
PTY
Query on PTY

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T [auth 3D],
V [auth 3F]
PHOSPHATIDYLETHANOLAMINE
C40 H80 N O8 P
NJGIRBISCGPRPF-KXQOOQHDSA-N
3PH
Query on 3PH

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U [auth 3D],
W [auth 3I]
1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
C39 H77 O8 P
YFWHNAWEOZTIPI-DIPNUNPCSA-N
CUA
Query on CUA

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S [auth 3C]DINUCLEAR COPPER ION
Cu2
ALKZAGKDWUSJED-UHFFFAOYSA-N
CU
Query on CU

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O [auth 3A]COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
MG
Query on MG

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P [auth 3A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.55 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:
RECONSTRUCTIONcryoSPARC

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Alexander von Humboldt FoundationGermany--
Swiss National Science FoundationSwitzerland210561

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-12
    Type: Initial release
  • Version 1.1: 2025-04-02
    Changes: Data collection, Database references