7DN9: Salmonella effector

Crystal structure of Salmonella effector in complex with NAD and host co-factor ARF1. Determined by X-ray diffraction at 3.29 Å resolution. Released 15 Dec 2021.

Method
X-ray diffraction
Resolution
3.29 Å
Organisms
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720), Homo sapiens
Chains
8
Atoms
15,092
Mol. weight
222.05 kDa
Ligands
GDP, MG, NAD
Released
15 Dec 2021

Explore 7DN9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7DN9 contains 100 α-helices and 80 β-strands across 8 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, C, E and G: 16 helices, 12 β-strands

ElementResiduesLengthSheet
α-helix74-9926
α-helix101-11515
α-helix122-13413
β-strand137-14261
α-helix149-1546
β-strand157-15822
α-helix174-18512
α-helix188-1914
α-helix197-1993
β-strand20513
β-strand21113
α-helix218-2203
α-helix2221
β-strand223-22861
α-helix238-2403
β-strand243-24751
α-helix249-2546
β-strand255-25841
α-helix271-2733
β-strand275-27621
α-helix280-2867
α-helix296-3049
α-helix310-3123
β-strand325-32841
β-strand332-33322
β-strand338-34361
α-helix352-36615
β-strand371-37331
Chain B: 9 helices, 8 β-strands
ElementResiduesLengthSheet
β-strand18-2474
α-helix30-3910
β-strand51-5884
β-strand61-6884
α-helix76-783
α-helix79-824
β-strand87-9374
α-helix97-993
α-helix100-11112
α-helix114-1163
β-strand120-12674
α-helix136-1438
α-helix145-1473
β-strand153-15754
β-strand15915
β-strand16415
α-helix166-17611
Chains D, F and H: 9 helices, 8 β-strands
ElementResiduesLengthSheet
β-strand18-2479
α-helix30-3910
β-strand51-5889
β-strand61-6889
α-helix76-783
α-helix79-824
β-strand87-9379
α-helix97-993
α-helix100-11112
α-helix114-1163
β-strand120-12679
α-helix136-1438
α-helix145-1473
β-strand153-15759
β-strand159110
β-strand164110
α-helix166-17510

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Putative cytoplasmic proteinA, C, E, Gprotein312Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)Q8ZPY9 (AlphaFold model)
ADP-ribosylation factor 1B, D, F, Hprotein165Homo sapiensP84077 (AlphaFold model)
Sequence of entity 1 (A, C, E, G), FASTA
>7DN9_1 Putative cytoplasmic protein (chains A, C, E, G)
LSFDEVFCGLSNEERKKVYGRLFGKQVLAHIHSRCQRDADIIREKALRRISRECGAEIDC
ALLLNKMVDILQNARLTINFNAAKIDFVSLLKNKEYLNSYALGCRPGDLPAYNVGRDSVE
TKAFELEKLADSPYAPYGQTGGFSVAYTPNSRTFSTTSRPIYAALDFLNGENGGASAYGK
SFFELNDNVKTNCTFSPFDIYGHRFGLDTSKLSTFWHMENLIASCQNDFFGYNCFKSLVK
MAKDEKFLAHSNYGKGYEGNYIDAHIHGDVCLFRDIKHVYLSLQENSYSKSQLYDYAKQI
NQALNRDCIILY
Sequence of entity 2 (B, D, F, H), FASTA
>7DN9_2 ADP-ribosylation factor 1 (chains B, D, F, H)
EMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGLDKIRP
LWRHYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDELRDAVLLVFANKQDLPNAMNA
AEITDKLGLHSLRHRNWYIQATCATSGDGLYEGLDWLSNQLRNQK

Ligands and cofactors

IDNameFormulaCopies
GDPGuanosine-5'-diphosphateC10 H15 N5 O11 P24
MGMagnesium ionMg4
NADNicotinamide-adenine-dinucleotideC21 H27 N7 O14 P24

Primary citation

ARF GTPases activate Salmonella effector SopF to ADP-ribosylate host V-ATPase and inhibit endomembrane damage-induced autophagy. Xu, Y., Cheng, S., Zeng, H. et al. Nat Struct Mol Biol (2022) 29:67-77. DOI 10.1038/s41594-021-00710-6 · PubMed

Other PDB entries of the same protein (UniProt Q8ZPY9 (AlphaFold model), which also has an AlphaFold model), best resolution first:

Browse structure collections

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