9TDM | pdb_00009tdm

Cryo-EM structure of AccA3/AccD4/AccD5/AccE5 in complex with Propionyl-CoA

PDB DOI: https://doi.org/10.2210/pdb9TDM/pdb
EM Map EMD-55802: EMDB EMDataResource

Classification: TRANSFERASE
Organism(s): Mycolicibacterium smegmatis MC2 155
Mutation(s): No

Deposited: 2025-11-24 Released: 2026-06-10
Deposition Author(s): Mullapudi, E., Thai, H.M., de Carvalho, L.P.S., Wilmanns, M.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.40 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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

Literature

Cryo-EM structure of AccA3/AccD4/AccD5/AccE5 in complex with Propionyl-CoA

Mullapudi, E., Thai, H.M., de Carvalho, L.P.S., Wilmanns, M.

To be published.

Macromolecule Content

Total Structure Weight: 878.31 kDa
Atom Count: 57,982
Modeled Residue Count: 7,618
Deposited Residue Count: 8,174
Unique protein chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Biotin-dependent acyl-coenzyme A carboxylase alpha3 subunit	A [auth A3a] B [auth A3b] C [auth A3c] D [auth A3d] E [auth A3e] A [auth A3a], B [auth A3b], C [auth A3c], D [auth A3d], E [auth A3e], F [auth A3f], G [auth A3g], H [auth A3h]	598	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0 EC: 6.3.4.14
UniProt
Find proteins for A0QTE1 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QTE1 Go to UniProtKB: A0QTE1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0QTE1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Propionyl-CoA carboxylase beta chain	I [auth D4a], J [auth D4b]	517	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0 EC: 6.4.1.3
UniProt
Find proteins for A0R616 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0R616 Go to UniProtKB: A0R616
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0R616
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Propionyl-CoA carboxylase beta chain	K [auth D5a], L [auth D5b], M [auth D5c], N [auth D5d]	542	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0 EC: 6.4.1.3
UniProt
Find proteins for A0QTE7 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QTE7 Go to UniProtKB: A0QTE7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0QTE7
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetyl-/propionyl-coenzyme A carboxylase AccE5	O [auth E5a], P [auth E5b]	94	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0
UniProt
Find proteins for A0QTE6 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QTE6 Go to UniProtKB: A0QTE6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0QTE6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1VU (Subject of Investigation/LOI) Query on 1VU Download:Ideal Coordinates CCD File SDF format, chain AA [auth D5d] SDF format, chain Y [auth D5b] SDF format, chain Z [auth D5c] SDF format, chain X [auth D5a] MOL2 format, chain AA [auth D5d] MOL2 format, chain Y [auth D5b] MOL2 format, chain Z [auth D5c] MOL2 format, chain X [auth D5a] mmCIF format, chain AA [auth D5d] mmCIF format, chain Y [auth D5b] mmCIF format, chain Z [auth D5c] mmCIF format, chain X [auth D5a]	AA [auth D5d], X [auth D5a], Y [auth D5b], Z [auth D5c]	propionyl Coenzyme A C₂₄ H₄₀ N₇ O₁₇ P₃ S QAQREVBBADEHPA-IEXPHMLFSA-N		Interactions Focus chain AA [auth D5d] Focus chain X [auth D5a] Focus chain Y [auth D5b] Focus chain Z [auth D5c] Interactions & Density Focus chain AA [auth D5d] Focus chain X [auth D5a] Focus chain Y [auth D5b] Focus chain Z [auth D5c]
ATP (Subject of Investigation/LOI) Query on ATP Download:Ideal Coordinates CCD File SDF format, chain T [auth A3e] SDF format, chain Q [auth A3a] MOL2 format, chain T [auth A3e] MOL2 format, chain Q [auth A3a] mmCIF format, chain T [auth A3e] mmCIF format, chain Q [auth A3a]	Q [auth A3a], T [auth A3e]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain Q [auth A3a] Focus chain T [auth A3e] Interactions & Density Focus chain Q [auth A3a] Focus chain T [auth A3e]
BTI (Subject of Investigation/LOI) Query on BTI Download:Ideal Coordinates CCD File SDF format, chain R [auth A3a] SDF format, chain S [auth A3d] SDF format, chain W [auth A3h] SDF format, chain V [auth A3f] SDF format, chain U [auth A3e] MOL2 format, chain R [auth A3a] MOL2 format, chain S [auth A3d] MOL2 format, chain W [auth A3h] MOL2 format, chain V [auth A3f] MOL2 format, chain U [auth A3e] mmCIF format, chain R [auth A3a] mmCIF format, chain S [auth A3d] mmCIF format, chain W [auth A3h] mmCIF format, chain V [auth A3f] mmCIF format, chain U [auth A3e]	R [auth A3a], S [auth A3d], U [auth A3e], V [auth A3f], W [auth A3h]	5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL C₁₀ H₁₆ N₂ O₂ S ARDNWGMSCXSPBF-CIUDSAMLSA-N		Interactions Focus chain R [auth A3a] Focus chain S [auth A3d] Focus chain U [auth A3e] Focus chain V [auth A3f] Focus chain W [auth A3h] Interactions & Density Focus chain R [auth A3a] Focus chain S [auth A3d] Focus chain U [auth A3e] Focus chain V [auth A3f] Focus chain W [auth A3h]