7TLJ | pdb_00007tlj

Rhodobacter sphaeroides Mitochondrial respiratory chain complex

PDB DOI: https://doi.org/10.2210/pdb7TLJ/pdb
EM Map EMD-25989: EMDB EMDataResource

Classification: OXIDOREDUCTASE
Organism(s): Cereibacter sphaeroides
Expression System: Escherichia coli
Mutation(s): No
Membrane Protein: Yes OPM PDBTM MemProtMD

Deposited: 2022-01-18 Released: 2023-02-08
Deposition Author(s): Xia, D., Zhou, F., Esser, L., Huang, R.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.91 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

Conformation Switch of Rieske ISP subunit is revealed by the Crystal Structure of Bacterial Cytochrome bc1 in Complex with Azoxystrobin

Xia, D., Esser, L., Zhou, F.

To be published.

Macromolecule Content

Total Structure Weight: 234.17 kDa
Atom Count: 14,242
Modeled Residue Count: 1,774
Deposited Residue Count: 2,056
Unique protein chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b	A, E	445	Cereibacter sphaeroides	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q02761 (Cereibacter sphaeroides) Explore Q02761 Go to UniProtKB: Q02761
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q02761
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c1	B, F	272	Cereibacter sphaeroides	Mutation(s): 0 Gene Names: petC, fbcC Membrane Entity: Yes
UniProt
Find proteins for Q02760 (Cereibacter sphaeroides) Explore Q02760 Go to UniProtKB: Q02760
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q02760
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquinol-cytochrome c reductase iron-sulfur subunit	C, G	187	Cereibacter sphaeroides	Mutation(s): 0 EC: 7.1.1.8 Membrane Entity: Yes
UniProt
Find proteins for Q02762 (Cereibacter sphaeroides) Explore Q02762 Go to UniProtKB: Q02762
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q02762
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
14 kDa peptide of ubiquinol-cytochrome c2 oxidoreductase complex	D, H	124	Cereibacter sphaeroides	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P16536 (Cereibacter sphaeroides) Explore P16536 Go to UniProtKB: P16536
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P16536
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LOP Query on LOP Download:Ideal Coordinates CCD File SDF format, chain R [auth E] SDF format, chain L [auth A] MOL2 format, chain R [auth E] MOL2 format, chain L [auth A] mmCIF format, chain R [auth E] mmCIF format, chain L [auth A]	L [auth A], R [auth E]	(1R)-2-{[(R)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(DODECANOYLOXY)METHYL]ETHYL (9Z)-OCTADEC-9-ENOATE C₃₅ H₆₈ N O₈ P FUUNMZKPCMPCHT-ILGKRYBBSA-N		Interactions Focus chain L [auth A] Focus chain R [auth E] Interactions & Density Focus chain L [auth A] Focus chain R [auth E]
HEC Query on HEC Download:Ideal Coordinates CCD File SDF format, chain S [auth F] SDF format, chain M [auth B] MOL2 format, chain S [auth F] MOL2 format, chain M [auth B] mmCIF format, chain S [auth F] mmCIF format, chain M [auth B]	M [auth B], S [auth F]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain M [auth B] Focus chain S [auth F] Interactions & Density Focus chain M [auth B] Focus chain S [auth F]
HEM Query on HEM Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain P [auth E] SDF format, chain O [auth E] SDF format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain P [auth E] MOL2 format, chain O [auth E] MOL2 format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain P [auth E] mmCIF format, chain O [auth E] mmCIF format, chain J [auth A]	I [auth A], J [auth A], O [auth E], P [auth E]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain O [auth E] Focus chain P [auth E] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain O [auth E] Focus chain P [auth E]
PQU (Subject of Investigation/LOI) Query on PQU Download:Ideal Coordinates CCD File SDF format, chain Q [auth E] SDF format, chain K [auth A] MOL2 format, chain Q [auth E] MOL2 format, chain K [auth A] mmCIF format, chain Q [auth E] mmCIF format, chain K [auth A]	K [auth A], Q [auth E]	(5S)-3-anilino-5-methyl-5-(6-phenoxypyridin-3-yl)-1,3-oxazolidine-2,4-dione C₂₁ H₁₇ N₃ O₄ QOFLFGUNPBNKDO-NRFANRHFSA-N		Interactions Focus chain K [auth A] Focus chain Q [auth E] Interactions & Density Focus chain K [auth A] Focus chain Q [auth E]
FES Query on FES Download:Ideal Coordinates CCD File SDF format, chain T [auth G] SDF format, chain N [auth C] MOL2 format, chain T [auth G] MOL2 format, chain N [auth C] mmCIF format, chain T [auth G] mmCIF format, chain N [auth C]	N [auth C], T [auth G]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain N [auth C] Focus chain T [auth G] Interactions & Density Focus chain N [auth C] Focus chain T [auth G]