9OCY | pdb_00009ocy

Cryo-EM structure of the CIII2 with YlbA from Bacillus subtilis

PDB DOI: https://doi.org/10.2210/pdb9OCY/pdb
EM Map EMD-70335: EMDB EMDataResource

Classification: ELECTRON TRANSPORT
Organism(s): Bacillus subtilis
Expression System: Bacillus subtilis
Mutation(s): No

Deposited: 2025-04-25 Released: 2026-11-04
Deposition Author(s): Gu, M., Zheng, W., Zong, Y., Zhang, K., Zhu, J.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Cryo-EM structure of the CIII2 with YlbA from Bacillus subtilis

Gu, M., Zheng, W., Zong, Y., Zhang, K., Zhu, J.

To be published.

Macromolecule Content

Total Structure Weight: 236.49 kDa
Atom Count: 16,370
Modeled Residue Count: 1,975
Deposited Residue Count: 2,000
Unique protein chains: 9

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Menaquinol:cytochrome c reductase iron-sulfur subunit	A, J [auth a]	167	Bacillus subtilis	Mutation(s): 0 Gene Names: qcrA, bfcA, BSU22560
UniProt
Find proteins for P46911 (Bacillus subtilis (strain 168)) Explore P46911 Go to UniProtKB: P46911
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P46911
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Menaquinol:cytochrome c reductase cytochrome b subunit	B, K [auth b]	224	Bacillus subtilis	Mutation(s): 0 Gene Names: qcrB, bfcB, BSU22550
UniProt
Find proteins for P46912 (Bacillus subtilis (strain 168)) Explore P46912 Go to UniProtKB: P46912
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P46912
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Menaquinol:cytochrome c reductase cytochrome c subunit	C, L [auth c]	255	Bacillus subtilis	Mutation(s): 0 Gene Names: qcrC, bfcC, BSU22540
UniProt
Find proteins for P46913 (Bacillus subtilis (strain 168)) Explore P46913 Go to UniProtKB: P46913
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P46913
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
YqgW	D, M [auth d]	57	Bacillus subtilis	Mutation(s): 0 Gene Names: yqgW, BSU24800
UniProt
Find proteins for P54500 (Bacillus subtilis (strain 168)) Explore P54500 Go to UniProtKB: P54500
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P54500
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Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
YqgY	E, N [auth e]	81	Bacillus subtilis	Mutation(s): 0 Gene Names: yqgY, BSU24780
UniProt
Find proteins for P54502 (Bacillus subtilis (strain 168)) Explore P54502 Go to UniProtKB: P54502
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P54502
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
QcrF	F, O [auth f]	23	Bacillus subtilis	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
QcrG	G, P [auth g]	29	Bacillus subtilis	Mutation(s): 0
Entity Groups
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
YqzM	H, Q [auth h]	44	Bacillus subtilis	Mutation(s): 0 Gene Names: yqzM, BSU25569
UniProt
Find proteins for C0H453 (Bacillus subtilis (strain 168)) Explore C0H453 Go to UniProtKB: C0H453
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C0H453
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Reference Sequence

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| 3D Structure

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
YlbA	I, R [auth i]	120	Bacillus subtilis	Mutation(s): 0 Gene Names: ylbA, BSU14940
UniProt
Find proteins for O34743 (Bacillus subtilis (strain 168)) Explore O34743 Go to UniProtKB: O34743
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O34743
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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 GA [auth b] MOL2 format, chain GA [auth b] mmCIF format, chain GA [auth b]	GA [auth b]	CARDIOLIPIN C₈₁ H₁₅₆ O₁₇ P₂ XVTUQDWPJJBEHJ-KZCWQMDCSA-L		Interactions Focus chain GA [auth b] Interactions & Density Focus chain GA [auth b]
PC1 Query on PC1 Download:Ideal Coordinates CCD File SDF format, chain AA [auth E] MOL2 format, chain AA [auth E] mmCIF format, chain AA [auth E]	AA [auth E]	1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE C₄₄ H₈₈ N O₈ P NRJAVPSFFCBXDT-HUESYALOSA-N		Interactions Focus chain AA [auth E] Interactions & Density Focus chain AA [auth E]
PEE Query on PEE Download:Ideal Coordinates CCD File SDF format, chain Z [auth C] SDF format, chain LA [auth h] SDF format, chain KA [auth e] SDF format, chain JA [auth d] MOL2 format, chain Z [auth C] MOL2 format, chain LA [auth h] MOL2 format, chain KA [auth e] MOL2 format, chain JA [auth d] mmCIF format, chain Z [auth C] mmCIF format, chain LA [auth h] mmCIF format, chain KA [auth e] mmCIF format, chain JA [auth d]	JA [auth d], KA [auth e], LA [auth h], Z [auth C]	1,2-dioleoyl-sn-glycero-3-phosphoethanolamine C₄₁ H₇₈ N O₈ P MWRBNPKJOOWZPW-NYVOMTAGSA-N		Interactions Focus chain JA [auth d] Focus chain KA [auth e] Focus chain LA [auth h] Focus chain Z [auth C] Interactions & Density Focus chain JA [auth d] Focus chain KA [auth e] Focus chain LA [auth h] Focus chain Z [auth C]
MQ7 Query on MQ7 Download:Ideal Coordinates CCD File SDF format, chain X [auth B] SDF format, chain W [auth B] SDF format, chain HA [auth c] SDF format, chain CA [auth b] MOL2 format, chain X [auth B] MOL2 format, chain W [auth B] MOL2 format, chain HA [auth c] MOL2 format, chain CA [auth b] mmCIF format, chain X [auth B] mmCIF format, chain W [auth B] mmCIF format, chain HA [auth c] mmCIF format, chain CA [auth b]	CA [auth b], HA [auth c], W [auth B], X [auth B]	MENAQUINONE-7 C₄₆ H₆₄ O₂ RAKQPZMEYJZGPI-LJWNYQGCSA-N		Interactions Focus chain CA [auth b] Focus chain HA [auth c] Focus chain W [auth B] Focus chain X [auth B] Interactions & Density Focus chain CA [auth b] Focus chain HA [auth c] Focus chain W [auth B] Focus chain X [auth B]
HEC Query on HEC Download:Ideal Coordinates CCD File SDF format, chain Y [auth C] SDF format, chain T [auth B] SDF format, chain IA [auth c] SDF format, chain DA [auth b] MOL2 format, chain Y [auth C] MOL2 format, chain T [auth B] MOL2 format, chain IA [auth c] MOL2 format, chain DA [auth b] mmCIF format, chain Y [auth C] mmCIF format, chain T [auth B] mmCIF format, chain IA [auth c] mmCIF format, chain DA [auth b]	DA [auth b], IA [auth c], T [auth B], Y [auth C]	HEME C C₃₄ H₃₆ Fe N₄ O₄ YZTICFPLOXKSQO-RGGAHWMASA-L		Interactions Focus chain DA [auth b] Focus chain IA [auth c] Focus chain T [auth B] Focus chain Y [auth C] Interactions & Density Focus chain DA [auth b] Focus chain IA [auth c] Focus chain T [auth B] Focus chain Y [auth C]
HEM Query on HEM Download:Ideal Coordinates CCD File SDF format, chain V [auth B] SDF format, chain U [auth B] SDF format, chain FA [auth b] SDF format, chain EA [auth b] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain FA [auth b] MOL2 format, chain EA [auth b] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain FA [auth b] mmCIF format, chain EA [auth b]	EA [auth b], FA [auth b], U [auth B], V [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain EA [auth b] Focus chain FA [auth b] Focus chain U [auth B] Focus chain V [auth B] Interactions & Density Focus chain EA [auth b] Focus chain FA [auth b] Focus chain U [auth B] Focus chain V [auth B]
FES Query on FES Download:Ideal Coordinates CCD File SDF format, chain S [auth A] SDF format, chain BA [auth a] MOL2 format, chain S [auth A] MOL2 format, chain BA [auth a] mmCIF format, chain S [auth A] mmCIF format, chain BA [auth a]	BA [auth a], S [auth A]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain BA [auth a] Focus chain S [auth A] Interactions & Density Focus chain BA [auth a] Focus chain S [auth A]