8VFM: Cell invasion protein SipA

Name: PDB 8VFM: Salmonella effector protein SipA decorated actin filament
Published: 2024-12-25
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: cell invasion

Salmonella effector protein SipA decorated actin filament. Determined by electron microscopy at 3.6 Å resolution. Released 25 Dec 2024.

Method: Electron microscopy
Resolution: 3.6 Å
Organisms: Salmonella, Gallus gallus
Chains: 12
Atoms: 28,316
Mol. weight: 636.65 kDa
Ligands: ADP, MG
Released: 25 Dec 2024

Explore 8VFM in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8VFM contains 232 α-helices and 176 β-strands across 12 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chains A, B, C and I: 12 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	520	1	2
α-helix	530-531	2
α-helix	532-535	4
α-helix	542-553	12
α-helix	555	1
β-strand	556	1	2
α-helix	557	1
α-helix	562-572	11
α-helix	580-590	11
α-helix	593-595	3
α-helix	597-611	15
α-helix	616-623	8
α-helix	625-629	5
α-helix	641-650	10

Chains J, L, M, N, R, S, U and W: 23 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	6-7	2
β-strand	8-11	4	5
β-strand	16-21	6	5
β-strand	29-32	4	5
β-strand	35-38	4	6
β-strand	53-54	2	6
α-helix	56-60	5
α-helix	62-64	3
β-strand	65-68	4	6
β-strand	71-72	2	7
β-strand	75-76	2	7
α-helix	79-87	9
α-helix	88-94	7
β-strand	105-107	3	5
α-helix	114-127	14
β-strand	131-132	2	8
β-strand	134-136	3	5
α-helix	137-145	9
β-strand	151-155	5	9
β-strand	160-162	3	9
β-strand	165	1	10
β-strand	170	1	10
α-helix	172-174	3
β-strand	176-178	3	9
α-helix	182-193	12
α-helix	194-196	3
α-helix	203-216	14
α-helix	223-231	9
β-strand	238-241	4	11
β-strand	247-250	4	11
α-helix	253-256	4
α-helix	257-261	5
α-helix	264-266	3
α-helix	276-284	9
α-helix	290-294	5
β-strand	297-300	4	9
α-helix	302-305	4
α-helix	309-320	12
β-strand	330	1	9
α-helix	335-337	3
α-helix	338-346	9
β-strand	357-358	2	8
α-helix	359-362	4
α-helix	367-372	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cell invasion protein SipA	A, B, C, I	protein	685	Salmonella	P0CL52 (AlphaFold model)
Actin, alpha skeletal muscle	J, L, M, N, R, S, U, W	protein	377	Gallus gallus	P68139 (AlphaFold model)

Sequence of entity 1 (A, B, C, I), FASTA

>8VFM_1 Cell invasion protein SipA (chains A, B, C, I)
MVTSVRTQPPVIMPGMQTEIKTQATNLAANLSAVRESATATLSGEIKGPQLEDFPALIKQ
ASLDALFKCGKDAEALKEVFTNSNNVAGKKAIMEFAGLFRSALNATSDSPEAKTLLMKVG
AEYTAQIIKDGLKEKSAFGPWLPETKKAEAKLENLEKQLLDIIKNNTGGELSKLSTNLVM
QEVMPYIASCIEHNFGCTLDPLTRSNLTHLVDKAAAKAVEALDMCHQKLTQEQGTSVGRE
ARHLEMQTLIPLLLRNVFAQIPADKLPDPKIPEPAAGPVPDGGKKAEPTGINININIDSS
NHSVDNSKHINNSRSHVDNSQRHIDNSNHDNSRKTIDNSRTFIDNSQRNGESHHSTNSSN
VSHSHSRVDSTTHQTETAHSASTGAIDHGIAGKIDVTAHATAEAVTNASSESKDGKVVTS
EKGTTGETTSFDEVDGVTSKSIIGKPVQATVHGVDDNKQQSQTAEIVNVKPLASQLAGVE
NVKTDTLQSDTTVITGNKAGTTDNDNSQTDKTGPFSGLKFKQNSFLSTVPSVTNMHSMHF
DARETFLGVIRKALEPDTSTPFPVRRAFDGLRAEILPNDTIKSAALKAQCSDIDKHPELK
AKMETLKEVITHHPQKEKLAEIALQFAREAGLTRLKGETDYVLSNVLDGLIGDGSWRAGP
AYESYLNKPGVDRVITTVDGLHMQR

Sequence of entity 2 (J, L, M, N, R, S, U, W), FASTA

>8VFM_2 Actin, alpha skeletal muscle (chains J, L, M, N, R, S, U, W)
MCDEDETTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEA
QSKRGILTLKYPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREK
MTQIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRL
DLAGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEK
SYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNV
MSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWIT
KQEYDEAGPSIVHRKCF

Ligands and cofactors

ID	Name	Formula	Copies
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	8
MG	Magnesium ion	Mg	8

Primary citation

Cryo-EM structure of the bacterial effector protein SipA bound to F-actin reveals a unique mechanism for filament stabilization. Guo, E., Chou, S.Z., Lara-Tejero, M. et al. bioRxiv (2024). DOI 10.1101/2023.12.21.572903 · PubMed

Other PDB entries of the same protein (UniProt P0CL52 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1Q5Z 1.8 Å, Crystal Structure of the C-terminal Actin Binding Domain of Salmonella Invasion Protein…
2FM9 2.0 Å, Structure of Salmonella SipA residues 48-264
2FM8 2.2 Å, Crystal Structure of the Salmonella Secretion Chaperone InvB in Complex with SipA
8C4E 2.6 Å, F-actin decorated by SipA426-685
8C4C 2.7 Å, F-actin decorated by SipA497-669
8UEE 3.2 Å, Atomic structure of Salmonella SipA/F-actin complex by cryo-EM

Browse structure collections

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