8UEE

Atomic structure of Salmonella SipA/F-actin complex by cryo-EM

PDB DOI: https://doi.org/10.2210/pdb8UEE/pdb
EM Map EMD-42161: EMDB EMDataResource

Classification: CELL INVASION
Organism(s): Oryctolagus cuniculus, Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-10-01 Released: 2023-12-27
Deposition Author(s): Niedzialkowska, E., Runyan, L., Kudryashova, E., Kudryashov, D.S., Egelman, E.H.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.20 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

Atomic structure of Salmonella SipA/F-actin complex by cryo-EM

Niedzialkowska, E., Runyan, L., Kudryashova, E., Kudryashov, D.S., Egelman, E.H.

To be published.

Macromolecule Content

Total Structure Weight: 410.61 kDa
Atom Count: 25,924
Modelled Residue Count: 3,285
Deposited Residue Count: 3,669
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin, alpha skeletal muscle	A [auth F] B [auth H] C [auth I] D [auth J] E [auth K] A [auth F], B [auth H], C [auth I], D [auth J], E [auth K], F [auth L], G [auth M]	375	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for P68135 (Oryctolagus cuniculus) Explore P68135 Go to UniProtKB: P68135
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P68135
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cell invasion protein SipA	H [auth B], I [auth C], J [auth D], K [auth A]	261	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	Mutation(s): 0 Gene Names: sipA, sspA, STM2882
UniProt
Find proteins for P0CL52 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P0CL52 Go to UniProtKB: P0CL52
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% 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 AA [auth L] SDF format, chain DA [auth M] SDF format, chain L [auth F] SDF format, chain O [auth H] SDF format, chain U [auth J] SDF format, chain X [auth K] SDF format, chain R [auth I] MOL2 format, chain AA [auth L] MOL2 format, chain DA [auth M] MOL2 format, chain L [auth F] MOL2 format, chain O [auth H] MOL2 format, chain U [auth J] MOL2 format, chain X [auth K] MOL2 format, chain R [auth I]	AA [auth L] DA [auth M] L [auth F] O [auth H] R [auth I] AA [auth L], DA [auth M], L [auth F], O [auth H], R [auth I], U [auth J], X [auth K]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain AA [auth L] Focus chain DA [auth M] Focus chain L [auth F] Focus chain O [auth H] Focus chain R [auth I] Focus chain U [auth J] Focus chain X [auth K] Interactions & Density Focus chain AA [auth L] Focus chain DA [auth M] Focus chain L [auth F] Focus chain O [auth H] Focus chain R [auth I] Focus chain U [auth J] Focus chain X [auth K]
PO4 (Subject of Investigation/LOI) Query on PO4 Download Ideal Coordinates CCD File SDF format, chain FA [auth M] SDF format, chain N [auth F] SDF format, chain Q [auth H] SDF format, chain T [auth I] SDF format, chain W [auth J] SDF format, chain Z [auth K] SDF format, chain CA [auth L] MOL2 format, chain FA [auth M] MOL2 format, chain N [auth F] MOL2 format, chain Q [auth H] MOL2 format, chain T [auth I] MOL2 format, chain W [auth J] MOL2 format, chain Z [auth K] MOL2 format, chain CA [auth L]	CA [auth L] FA [auth M] N [auth F] Q [auth H] T [auth I] CA [auth L], FA [auth M], N [auth F], Q [auth H], T [auth I], W [auth J], Z [auth K]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain CA [auth L] Focus chain FA [auth M] Focus chain N [auth F] Focus chain Q [auth H] Focus chain T [auth I] Focus chain W [auth J] Focus chain Z [auth K] Interactions & Density Focus chain CA [auth L] Focus chain FA [auth M] Focus chain N [auth F] Focus chain Q [auth H] Focus chain T [auth I] Focus chain W [auth J] Focus chain Z [auth K]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain BA [auth L] SDF format, chain EA [auth M] SDF format, chain M [auth F] SDF format, chain P [auth H] SDF format, chain S [auth I] SDF format, chain Y [auth K] SDF format, chain V [auth J] MOL2 format, chain BA [auth L] MOL2 format, chain EA [auth M] MOL2 format, chain M [auth F] MOL2 format, chain P [auth H] MOL2 format, chain S [auth I] MOL2 format, chain Y [auth K] MOL2 format, chain V [auth J]	BA [auth L] EA [auth M] M [auth F] P [auth H] S [auth I] BA [auth L], EA [auth M], M [auth F], P [auth H], S [auth I], V [auth J], Y [auth K]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BA [auth L] Focus chain EA [auth M] Focus chain M [auth F] Focus chain P [auth H] Focus chain S [auth I] Focus chain V [auth J] Focus chain Y [auth K] Interactions & Density Focus chain BA [auth L] Focus chain EA [auth M] Focus chain M [auth F] Focus chain P [auth H] Focus chain S [auth I] Focus chain V [auth J] Focus chain Y [auth K]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
HIC Query on HIC	A [auth F] B [auth H] C [auth I] D [auth J] E [auth K] A [auth F], B [auth H], C [auth I], D [auth J], E [auth K], F [auth L], G [auth M]	L-PEPTIDE LINKING	C₇ H₁₁ N₃ O₂		HIS

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.20 Å
Aggregation State: FILAMENT
Reconstruction Method: HELICAL

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.3
MODEL REFINEMENT	Coot	0.9.8.1
RECONSTRUCTION	cryoSPARC	4.0.2

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-12-27

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM122510
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM114666