8JF2

Cryo-EM structure of tetrameric DltB/DltC complex

PDB DOI: https://doi.org/10.2210/pdb8JF2/pdb
EM Map EMD-36207: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Streptococcus thermophilus LMG 18311
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No
Membrane Protein: Yes PDBTMMemProtMD

Deposited: 2023-05-17 Released: 2024-05-22
Deposition Author(s): Zhang, P., Liu, Z.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.50 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.

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 8JEM

Literature

Structural insights into the transporting and catalyzing mechanism of DltB in LTA D-alanylation.

Zhang, P., Liu, Z.

(2024) Nat Commun 15: 3404-3404

PubMed: 38649359 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41467-024-47783-7
Primary Citation of Related Structures:
8JEM, 8JES, 8JF2

PubMed Abstract:
DltB, a model member of the Membrane-Bound O-AcylTransferase (MBOAT) superfamily, plays a crucial role in D-alanylation of the lipoteichoic acid (LTA), a significant component of the cell wall of gram-positive bacteria. This process stabilizes the cell wall structure, influences bacterial virulence, and modulates the host immune response. Despite its significance, the role of DltB is not well understood. Through biochemical analysis and cryo-EM imaging, we discover that Streptococcus thermophilus DltB forms a homo-tetramer on the cell membrane. We further visualize DltB in an apo form, in complex with DltC, and in complex with its inhibitor amsacrine (m-AMSA). Each tetramer features a central hole. The C-tunnel of each protomer faces the intratetramer interface and provides access to the periphery membrane. Each protomer binds a DltC without changing the tetrameric organization. A phosphatidylglycerol (PG) molecule in the substrate-binding site may serve as an LTA carrier. The inhibitor m-AMSA bound to the L-tunnel of each protomer blocks the active site. The tetrameric organization of DltB provides a scaffold for catalyzing D-alanyl transfer and regulating the channel opening and closing. Our findings unveil DltB's dual function in the D-alanylation pathway, and provide insight for targeting DltB as a anti-virulence antibiotic.

Organizational Affiliation

Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China. pingfeng.zhang@whu.edu.cn.

Macromolecule Content

Total Structure Weight: 261.54 kDa
Atom Count: 17,676
Modelled Residue Count: 1,990
Deposited Residue Count: 2,076
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Teichoic acid D-alanyltransferase	A, B, C, D	440	Streptococcus thermophilus LMG 18311	Mutation(s): 0 Gene Names: dltB, stu0762 EC: 2.3.1 Membrane Entity: Yes
UniProt
Find proteins for Q5M4V4 (Streptococcus thermophilus (strain ATCC BAA-250 / LMG 18311)) Explore Q5M4V4 Go to UniProtKB: Q5M4V4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5M4V4
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
D-alanyl carrier protein	E [auth F], F [auth G], G [auth H], H [auth I]	79	Streptococcus thermophilus LMG 18311	Mutation(s): 0 Gene Names: dltC, stu0763
UniProt
Find proteins for Q5M4V3 (Streptococcus thermophilus (strain ATCC BAA-250 / LMG 18311)) Explore Q5M4V3 Go to UniProtKB: Q5M4V3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5M4V3
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGT (Subject of Investigation/LOI) Query on PGT Download Ideal Coordinates CCD File SDF format, chain GA [auth C] SDF format, chain HA [auth D] SDF format, chain I [auth A] SDF format, chain O [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain HA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain O [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth C] mmCIF format, chain GA [auth C] mmCIF format, chain HA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain O [auth B] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth C]	GA [auth C] HA [auth D] I [auth A] O [auth B] X [auth B] GA [auth C], HA [auth D], I [auth A], O [auth B], X [auth B], Y [auth C]	(1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE C₄₀ H₇₉ O₁₀ P KBPVYRBBONZJHF-AMAPPZPBSA-N		Interactions Focus chain GA [auth C] Focus chain HA [auth D] Focus chain I [auth A] Focus chain O [auth B] Focus chain X [auth B] Focus chain Y [auth C] Interactions & Density Focus chain GA [auth C] Focus chain HA [auth D] Focus chain I [auth A] Focus chain O [auth B] Focus chain X [auth B] Focus chain Y [auth C]
DGA (Subject of Investigation/LOI) Query on DGA Download Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain Z [auth C] MOL2 format, chain N [auth B] MOL2 format, chain Z [auth C] mmCIF format, chain N [auth B] mmCIF format, chain Z [auth C]	N [auth B], Z [auth C]	DIACYL GLYCEROL C₃₉ H₇₆ O₅ UHUSDOQQWJGJQS-QNGWXLTQSA-N		Interactions Focus chain N [auth B] Focus chain Z [auth C] Interactions & Density Focus chain N [auth B] Focus chain Z [auth C]
LMT Query on LMT Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth C] SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain EA [auth C] SDF format, chain IA [auth D] SDF format, chain JA [auth D] SDF format, chain K [auth A] SDF format, chain KA [auth D] SDF format, chain LA [auth D] SDF format, chain M [auth A] SDF format, chain MA [auth D] SDF format, chain NA [auth D] SDF format, chain OA [auth D] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain FA [auth C] SDF format, chain J [auth A] SDF format, chain L [auth A] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain IA [auth D] MOL2 format, chain JA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain LA [auth D] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth D] MOL2 format, chain NA [auth D] MOL2 format, chain OA [auth D] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain FA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain L [auth A] mmCIF format, chain AA [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain IA [auth D] mmCIF format, chain JA [auth D] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth D] mmCIF format, chain LA [auth D] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth D] mmCIF format, chain NA [auth D] mmCIF format, chain OA [auth D] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain FA [auth C] mmCIF format, chain J [auth A] mmCIF format, chain L [auth A]	AA [auth C] BA [auth C] CA [auth C] DA [auth C] EA [auth C] AA [auth C], BA [auth C], CA [auth C], DA [auth C], EA [auth C], FA [auth C], IA [auth D], J [auth A], JA [auth D], K [auth A], KA [auth D], L [auth A], LA [auth D], M [auth A], MA [auth D], NA [auth D], OA [auth D], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B]	DODECYL-BETA-D-MALTOSIDE C₂₄ H₄₆ O₁₁ NLEBIOOXCVAHBD-QKMCSOCLSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain IA [auth D] Focus chain J [auth A] Focus chain JA [auth D] Focus chain K [auth A] Focus chain KA [auth D] Focus chain L [auth A] Focus chain LA [auth D] Focus chain M [auth A] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain IA [auth D] Focus chain J [auth A] Focus chain JA [auth D] Focus chain K [auth A] Focus chain KA [auth D] Focus chain L [auth A] Focus chain LA [auth D] Focus chain M [auth A] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B]