8C4E | pdb_00008c4e

F-actin decorated by SipA426-685

PDB DOI: https://doi.org/10.2210/pdb8C4E/pdb
EM Map EMD-16425: EMDB EMDataResource

Classification: CELL INVASION
Organism(s): Gallus gallus, Salmonella
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-01-03 Released: 2024-01-17
Deposition Author(s): Yuan, B., Wald, J., Marlovits, T.C.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.60 Å
Aggregation State: FILAMENT
Reconstruction Method: HELICAL

wwPDB Validation 3D Report Full Report

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

Literature

Structural basis for subversion of host cell actin cytoskeleton during Salmonella infection.

Yuan, B., Scholz, J., Wald, J., Thuenauer, R., Hennell James, R., Ellenberg, I., Windhorst, S., Faix, J., Marlovits, T.C.

(2023) Sci Adv 9: eadj5777-eadj5777

PubMed: 38064550 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/sciadv.adj5777
Primary Citation Related Structures:
8C4C, 8C4E

PubMed Abstract:
Secreted bacterial type III secretion system (T3SS) proteins are essential for successful infection by many human pathogens. Both T3SS translocator SipC and effector SipA are critical for Salmonella infection by subversion of the host cell cytoskeleton, but the precise molecular interplay between them remains unknown. Here, using cryo-electron microscopy, we show that SipA binds along the F-actin grooves with a unique binding pattern. SipA stabilizes F-actin through charged interface residues and appears to prevent inorganic phosphate release through closure of the "back door" of adenosine 5'-triphosphate pocket. We also show that SipC enhances the binding of SipA to F-actin, thus demonstrating that a sequential presence of T3SS proteins in host cells is associated with a sequence of infection events-starting with actin nucleation, filament growth, and stabilization. Together, our data explain the coordinated interplay of a precisely tuned and highly effective mechanism during Salmonella infection and provide a blueprint for interfering with Salmonella effectors acting on actin.

Organizational Affiliation

University Medical Center Hamburg-Eppendorf (UKE), Institute of Structural and Systems Biology, Hamburg, Germany.

Macromolecule Content

Total Structure Weight: 454.91 kDa
Atom Count: 28,796
Modeled Residue Count: 3,648
Deposited Residue Count: 4,060
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin, alpha skeletal muscle	A, B, C, D, E A, B, C, D, E, F, G, H	377	Gallus gallus	Mutation(s): 0 EC: 3.6.4
UniProt
Find proteins for P68139 (Gallus gallus) Explore P68139 Go to UniProtKB: P68139
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P68139
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cell invasion protein SipA	I [auth K], J [auth L], K [auth M], L [auth N]	261	Salmonella	Mutation(s): 0 Gene Names: sipA, sspA
UniProt
Find proteins for P0CL52 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P0CL52 Go to UniProtKB: P0CL52
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0CL52
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP (Subject of Investigation/LOI) Query on ADP Download:Ideal Coordinates CCD File SDF format, chain Z [auth E] SDF format, chain W [auth D] SDF format, chain S [auth C] SDF format, chain Q [auth B] SDF format, chain M [auth A] SDF format, chain JA [auth H] SDF format, chain FA [auth G] SDF format, chain CA [auth F] MOL2 format, chain Z [auth E] MOL2 format, chain W [auth D] MOL2 format, chain S [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain M [auth A] MOL2 format, chain JA [auth H] MOL2 format, chain FA [auth G] MOL2 format, chain CA [auth F] mmCIF format, chain Z [auth E] mmCIF format, chain W [auth D] mmCIF format, chain S [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain M [auth A] mmCIF format, chain JA [auth H] mmCIF format, chain FA [auth G] mmCIF format, chain CA [auth F]	CA [auth F] FA [auth G] JA [auth H] M [auth A] Q [auth B] CA [auth F], FA [auth G], JA [auth H], M [auth A], Q [auth B], S [auth C], W [auth D], Z [auth E]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain CA [auth F] Focus chain FA [auth G] Focus chain JA [auth H] Focus chain M [auth A] Focus chain Q [auth B] Focus chain S [auth C] Focus chain W [auth D] Focus chain Z [auth E] Interactions & Density Focus chain CA [auth F] Focus chain FA [auth G] Focus chain JA [auth H] Focus chain M [auth A] Focus chain Q [auth B] Focus chain S [auth C] Focus chain W [auth D] Focus chain Z [auth E]
PO4 (Subject of Investigation/LOI) Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain X [auth D] SDF format, chain U [auth C] SDF format, chain P [auth B] SDF format, chain N [auth A] SDF format, chain IA [auth H] SDF format, chain EA [auth G] SDF format, chain DA [auth F] SDF format, chain AA [auth E] MOL2 format, chain X [auth D] MOL2 format, chain U [auth C] MOL2 format, chain P [auth B] MOL2 format, chain N [auth A] MOL2 format, chain IA [auth H] MOL2 format, chain EA [auth G] MOL2 format, chain DA [auth F] MOL2 format, chain AA [auth E] mmCIF format, chain X [auth D] mmCIF format, chain U [auth C] mmCIF format, chain P [auth B] mmCIF format, chain N [auth A] mmCIF format, chain IA [auth H] mmCIF format, chain EA [auth G] mmCIF format, chain DA [auth F] mmCIF format, chain AA [auth E]	AA [auth E] DA [auth F] EA [auth G] IA [auth H] N [auth A] AA [auth E], DA [auth F], EA [auth G], IA [auth H], N [auth A], P [auth B], U [auth C], X [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain AA [auth E] Focus chain DA [auth F] Focus chain EA [auth G] Focus chain IA [auth H] Focus chain N [auth A] Focus chain P [auth B] Focus chain U [auth C] Focus chain X [auth D] Interactions & Density Focus chain AA [auth E] Focus chain DA [auth F] Focus chain EA [auth G] Focus chain IA [auth H] Focus chain N [auth A] Focus chain P [auth B] Focus chain U [auth C] Focus chain X [auth D]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain Y [auth E] SDF format, chain V [auth D] SDF format, chain T [auth C] SDF format, chain R [auth B] SDF format, chain O [auth A] SDF format, chain HA [auth H] SDF format, chain GA [auth G] SDF format, chain BA [auth F] MOL2 format, chain Y [auth E] MOL2 format, chain V [auth D] MOL2 format, chain T [auth C] MOL2 format, chain R [auth B] MOL2 format, chain O [auth A] MOL2 format, chain HA [auth H] MOL2 format, chain GA [auth G] MOL2 format, chain BA [auth F] mmCIF format, chain Y [auth E] mmCIF format, chain V [auth D] mmCIF format, chain T [auth C] mmCIF format, chain R [auth B] mmCIF format, chain O [auth A] mmCIF format, chain HA [auth H] mmCIF format, chain GA [auth G] mmCIF format, chain BA [auth F]	BA [auth F] GA [auth G] HA [auth H] O [auth A] R [auth B] BA [auth F], GA [auth G], HA [auth H], O [auth A], R [auth B], T [auth C], V [auth D], Y [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BA [auth F] Focus chain GA [auth G] Focus chain HA [auth H] Focus chain O [auth A] Focus chain R [auth B] Focus chain T [auth C] Focus chain V [auth D] Focus chain Y [auth E] Interactions & Density Focus chain BA [auth F] Focus chain GA [auth G] Focus chain HA [auth H] Focus chain O [auth A] Focus chain R [auth B] Focus chain T [auth C] Focus chain V [auth D] Focus chain Y [auth E]