9MVZ | pdb_00009mvz

Deposited: 2025-01-16 Released: 2025-07-30
Deposition Author(s): Zhang, Z., Maharjan, R., Gregor, W.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

(2025) Sci Adv 11: eadx1129-eadx1129

PubMed Abstract:
We coexpressed the mycobacterial membrane protein large 5 (MmpL5) transporter and MmpS5 adaptor proteins in Mycobacterium smegmatis and defined their structures from detergent-solubilized crude membranes. We observed that MmpL5 presents as a monomer in complex with the cytosolic meromycolate extension acyl carrier protein M (AcpM), where these AcpM-MmpL5 complexes generate regular two-dimensional arrays. We also provide structural information to show that M. smegmatis MmpL5 assembles as a trimer that interacts with MmpS5 and AcpM to form the tripartite complex AcpM-MmpL5-MmpS5 that spans both the inner and outer membranes of the mycobacterium. In addition, we found that MmpL5 and AcpM are able to form the trimeric AcpM-MmpL5 complex. The structural data reveal that the full-length MmpL5 trimer is capable of spanning the entire mycobacterial cell envelope to transport substrates. However, this assembly requires the presence of MmpS5 to stabilize secondary structural features of the MmpL5 periplasmic subdomains.

Organizational Affiliation

Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.

Macromolecule Content

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MmpL5 protein	A [auth D], D [auth E], E [auth F]	967	Mycolicibacterium smegmatis	Mutation(s): 0 Gene Names: MSMEG_1382
UniProt
Find proteins for A0A1Y0CC73 (Mycobacterium dioxanotrophicus) Explore A0A1Y0CC73 Go to UniProtKB: A0A1Y0CC73
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1Y0CC73
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Meromycolate extension acyl carrier protein	B [auth G], F [auth H], G [auth I]	99	Mycolicibacterium smegmatis	Mutation(s): 0 Gene Names: acpM, MSMEG_4326, MSMEI_4226
UniProt
Find proteins for A0A1Y0C2R4 (Mycobacterium dioxanotrophicus) Explore A0A1Y0C2R4 Go to UniProtKB: A0A1Y0C2R4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1Y0C2R4
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
MmpS5 protein	C, H [auth A], I [auth B]	138	Mycolicibacterium smegmatis	Mutation(s): 0 Gene Names: MSMEG_1381
UniProt
Find proteins for A0A1Y0CC77 (Mycobacterium dioxanotrophicus) Explore A0A1Y0CC77 Go to UniProtKB: A0A1Y0CC77
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1Y0CC77
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PNS Query on PNS Download Ideal Coordinates CCD File SDF format, chain L [auth I] SDF format, chain K [auth H] SDF format, chain J [auth G] MOL2 format, chain L [auth I] MOL2 format, chain K [auth H] MOL2 format, chain J [auth G] mmCIF format, chain L [auth I] mmCIF format, chain K [auth H] mmCIF format, chain J [auth G]	J [auth G], K [auth H], L [auth I]	4'-PHOSPHOPANTETHEINE C₁₁ H₂₃ N₂ O₇ P S JDMUPRLRUUMCTL-VIFPVBQESA-N		Interactions Focus chain J [auth G] Focus chain K [auth H] Focus chain L [auth I] Interactions & Density Focus chain J [auth G] Focus chain K [auth H] Focus chain L [auth I]