9F5Z | pdb_00009f5z

Structure of the Chlamydomonas reinhardtii respiratory complex III from respiratory supercomplex

PDB DOI: https://doi.org/10.2210/pdb9F5Z/pdb
EM Map EMD-50204: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Chlamydomonas reinhardtii
Mutation(s): No

Deposited: 2024-04-30 Released: 2025-03-12
Deposition Author(s): Waltz, F., Righetto, R., Kotecha, A., Engel, B.D.
Funding Organization(s): Alexander von Humboldt Foundation, Swiss National Science Foundation

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.39 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

PubMed: 40112058 Search on PubMed
DOI: https://doi.org/10.1126/science.ads8738
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 533.14 kDa
Atom Count: 34,454
Modeled Residue Count: 4,196
Deposited Residue Count: 4,642
Unique protein chains: 10

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b	A [auth 1A], B [auth 1B]	381	Chlamydomonas reinhardtii	Mutation(s): 0
UniProt
Find proteins for P23662 (Chlamydomonas reinhardtii) Explore P23662 Go to UniProtKB: P23662
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P23662
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Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit Rieske, mitochondrial	C [auth 1C], D [auth 1D]	262	Chlamydomonas reinhardtii	Mutation(s): 0 EC: 7.1.1.8
UniProt
Find proteins for Q8HEB4 (Chlamydomonas reinhardtii) Explore Q8HEB4 Go to UniProtKB: Q8HEB4
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8HEB4
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Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c1	E [auth 1E], F [auth 1F]	314	Chlamydomonas reinhardtii	Mutation(s): 0 EC: 1.10.2.2
UniProt
Find proteins for Q9FQ96 (Chlamydomonas reinhardtii) Explore Q9FQ96 Go to UniProtKB: Q9FQ96
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UniProt Group	Q9FQ96
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Complex III subunit 9	G [auth 1G], H [auth 1H]	60	Chlamydomonas reinhardtii	Mutation(s): 0
UniProt
Find proteins for A8JC51 (Chlamydomonas reinhardtii) Explore A8JC51 Go to UniProtKB: A8JC51
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A8JC51
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit 6	I [auth 1I], J [auth 1J]	69	Chlamydomonas reinhardtii	Mutation(s): 0
UniProt
Find proteins for A8J8N9 (Chlamydomonas reinhardtii) Explore A8J8N9 Go to UniProtKB: A8J8N9
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A8J8N9
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial ubiquinol-cytochrome c oxidoreductase subunit 8	K [auth 1K], L [auth 1L]	73	Chlamydomonas reinhardtii	Mutation(s): 0 EC: 1.10.2.2
UniProt
Find proteins for A8J7I9 (Chlamydomonas reinhardtii) Explore A8J7I9 Go to UniProtKB: A8J7I9
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UniProt Group	A8J7I9
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
MPP-Beta	M [auth 1M], N [auth 1N]	495	Chlamydomonas reinhardtii	Mutation(s): 0 EC: 3.4.24.64
UniProt
Find proteins for A8J5P7 (Chlamydomonas reinhardtii) Explore A8J5P7 Go to UniProtKB: A8J5P7
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UniProt Group	A8J5P7
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial ubiquinol-cytochrome c oxidoreductase subunit 10	O [auth 1O], P [auth 1P]	59	Chlamydomonas reinhardtii	Mutation(s): 0 EC: 1.10.2.2
UniProt
Find proteins for A8J4K5 (Chlamydomonas reinhardtii) Explore A8J4K5 Go to UniProtKB: A8J4K5
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UniProt Group	A8J4K5
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-MPP	Q [auth 1Q], S [auth 1S]	485	Chlamydomonas reinhardtii	Mutation(s): 0
UniProt
Find proteins for A8IKI9 (Chlamydomonas reinhardtii) Explore A8IKI9 Go to UniProtKB: A8IKI9
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UniProt Group	A8IKI9
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit 7	R [auth 1R], T [auth 1T]	123	Chlamydomonas reinhardtii	Mutation(s): 0
UniProt
Find proteins for A8HX89 (Chlamydomonas reinhardtii) Explore A8HX89 Go to UniProtKB: A8HX89
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A8HX89
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Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CDL Query on CDL Download:Ideal Coordinates CCD File SDF format, chain EA [auth 1B] SDF format, chain HA [auth 1B] SDF format, chain RA [auth 1K] SDF format, chain UA [auth 1L] SDF format, chain VA [auth 1M] SDF format, chain Y [auth 1A] SDF format, chain MA [auth 1F] SDF format, chain IA [auth 1E] MOL2 format, chain EA [auth 1B] MOL2 format, chain HA [auth 1B] MOL2 format, chain RA [auth 1K] MOL2 format, chain UA [auth 1L] MOL2 format, chain VA [auth 1M] MOL2 format, chain Y [auth 1A] MOL2 format, chain MA [auth 1F] MOL2 format, chain IA [auth 1E] mmCIF format, chain EA [auth 1B] mmCIF format, chain HA [auth 1B] mmCIF format, chain RA [auth 1K] mmCIF format, chain UA [auth 1L] mmCIF format, chain VA [auth 1M] mmCIF format, chain Y [auth 1A] mmCIF format, chain MA [auth 1F] mmCIF format, chain IA [auth 1E]	EA [auth 1B] HA [auth 1B] IA [auth 1E] MA [auth 1F] RA [auth 1K] EA [auth 1B], HA [auth 1B], IA [auth 1E], MA [auth 1F], RA [auth 1K], UA [auth 1L], VA [auth 1M], Y [auth 1A]	CARDIOLIPIN C₈₁ H₁₅₆ O₁₇ P₂ XVTUQDWPJJBEHJ-KZCWQMDCSA-L		Interactions Focus chain EA [auth 1B] Focus chain HA [auth 1B] Focus chain IA [auth 1E] Focus chain MA [auth 1F] Focus chain RA [auth 1K] Focus chain UA [auth 1L] Focus chain VA [auth 1M] Focus chain Y [auth 1A] Interactions & Density Focus chain EA [auth 1B] Focus chain HA [auth 1B] Focus chain IA [auth 1E] Focus chain MA [auth 1F] Focus chain RA [auth 1K] Focus chain UA [auth 1L] Focus chain VA [auth 1M] Focus chain Y [auth 1A]
PC7 Query on PC7 Download:Ideal Coordinates CCD File SDF format, chain PA [auth 1G] SDF format, chain QA [auth 1H] MOL2 format, chain PA [auth 1G] MOL2 format, chain QA [auth 1H] mmCIF format, chain PA [auth 1G] mmCIF format, chain QA [auth 1H]	PA [auth 1G], QA [auth 1H]	(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		Interactions Focus chain PA [auth 1G] Focus chain QA [auth 1H] Interactions & Density Focus chain PA [auth 1G] Focus chain QA [auth 1H]
PTY Query on PTY Download:Ideal Coordinates CCD File SDF format, chain OA [auth 1F] SDF format, chain KA [auth 1E] MOL2 format, chain OA [auth 1F] MOL2 format, chain KA [auth 1E] mmCIF format, chain OA [auth 1F] mmCIF format, chain KA [auth 1E]	KA [auth 1E], OA [auth 1F]	PHOSPHATIDYLETHANOLAMINE C₄₀ H₈₀ N O₈ P NJGIRBISCGPRPF-KXQOOQHDSA-N		Interactions Focus chain KA [auth 1E] Focus chain OA [auth 1F] Interactions & Density Focus chain KA [auth 1E] Focus chain OA [auth 1F]
3PH Query on 3PH Download:Ideal Coordinates CCD File SDF format, chain SA [auth 1K] SDF format, chain TA [auth 1K] SDF format, chain YA [auth 1R] SDF format, chain Z [auth 1A] SDF format, chain JA [auth 1E] SDF format, chain GA [auth 1B] SDF format, chain FA [auth 1B] MOL2 format, chain SA [auth 1K] MOL2 format, chain TA [auth 1K] MOL2 format, chain YA [auth 1R] MOL2 format, chain Z [auth 1A] MOL2 format, chain JA [auth 1E] MOL2 format, chain GA [auth 1B] MOL2 format, chain FA [auth 1B] mmCIF format, chain SA [auth 1K] mmCIF format, chain TA [auth 1K] mmCIF format, chain YA [auth 1R] mmCIF format, chain Z [auth 1A] mmCIF format, chain JA [auth 1E] mmCIF format, chain GA [auth 1B] mmCIF format, chain FA [auth 1B]	FA [auth 1B] GA [auth 1B] JA [auth 1E] SA [auth 1K] TA [auth 1K] FA [auth 1B], GA [auth 1B], JA [auth 1E], SA [auth 1K], TA [auth 1K], YA [auth 1R], Z [auth 1A]	1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE C₃₉ H₇₇ O₈ P YFWHNAWEOZTIPI-DIPNUNPCSA-N		Interactions Focus chain FA [auth 1B] Focus chain GA [auth 1B] Focus chain JA [auth 1E] Focus chain SA [auth 1K] Focus chain TA [auth 1K] Focus chain YA [auth 1R] Focus chain Z [auth 1A] Interactions & Density Focus chain FA [auth 1B] Focus chain GA [auth 1B] Focus chain JA [auth 1E] Focus chain SA [auth 1K] Focus chain TA [auth 1K] Focus chain YA [auth 1R] Focus chain Z [auth 1A]
HEC Query on HEC Download:Ideal Coordinates CCD File SDF format, chain DA [auth 1B] SDF format, chain LA [auth 1E] SDF format, chain W [auth 1A] SDF format, chain X [auth 1A] SDF format, chain NA [auth 1F] SDF format, chain CA [auth 1B] MOL2 format, chain DA [auth 1B] MOL2 format, chain LA [auth 1E] MOL2 format, chain W [auth 1A] MOL2 format, chain X [auth 1A] MOL2 format, chain NA [auth 1F] MOL2 format, chain CA [auth 1B] mmCIF format, chain DA [auth 1B] mmCIF format, chain LA [auth 1E] mmCIF format, chain W [auth 1A] mmCIF format, chain X [auth 1A] mmCIF format, chain NA [auth 1F] mmCIF format, chain CA [auth 1B]	CA [auth 1B] DA [auth 1B] LA [auth 1E] NA [auth 1F] W [auth 1A] CA [auth 1B], DA [auth 1B], LA [auth 1E], NA [auth 1F], W [auth 1A], X [auth 1A]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain CA [auth 1B] Focus chain DA [auth 1B] Focus chain LA [auth 1E] Focus chain NA [auth 1F] Focus chain W [auth 1A] Focus chain X [auth 1A] Interactions & Density Focus chain CA [auth 1B] Focus chain DA [auth 1B] Focus chain LA [auth 1E] Focus chain NA [auth 1F] Focus chain W [auth 1A] Focus chain X [auth 1A]
UQ5 Query on UQ5 Download:Ideal Coordinates CCD File SDF format, chain AA [auth 1B] SDF format, chain BA [auth 1B] SDF format, chain U [auth 1A] SDF format, chain V [auth 1A] MOL2 format, chain AA [auth 1B] MOL2 format, chain BA [auth 1B] MOL2 format, chain U [auth 1A] MOL2 format, chain V [auth 1A] mmCIF format, chain AA [auth 1B] mmCIF format, chain BA [auth 1B] mmCIF format, chain U [auth 1A] mmCIF format, chain V [auth 1A]	AA [auth 1B], BA [auth 1B], U [auth 1A], V [auth 1A]	2,3-DIMETHOXY-5-METHYL-6-(3,11,15,19-TETRAMETHYL-EICOSA-2,6,10,14,18-PENTAENYL)-[1,4]BENZOQUINONE C₃₄ H₅₀ O₄ NYFAQDMDAFCWPU-UVCHAVPFSA-N		Interactions Focus chain AA [auth 1B] Focus chain BA [auth 1B] Focus chain U [auth 1A] Focus chain V [auth 1A] Interactions & Density Focus chain AA [auth 1B] Focus chain BA [auth 1B] Focus chain U [auth 1A] Focus chain V [auth 1A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain WA [auth 1M] SDF format, chain XA [auth 1N] MOL2 format, chain WA [auth 1M] MOL2 format, chain XA [auth 1N] mmCIF format, chain WA [auth 1M] mmCIF format, chain XA [auth 1N]	WA [auth 1M], XA [auth 1N]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain WA [auth 1M] Focus chain XA [auth 1N] Interactions & Density Focus chain WA [auth 1M] Focus chain XA [auth 1N]