7DN8: Salmonella effector SopF

Crystal structure of Salmonella effector SopF in complex with ARF1. Determined by X-ray diffraction at 2.61 Å resolution. Released 15 Dec 2021.

Method
X-ray diffraction
Resolution
2.61 Å
Organisms
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720), Homo sapiens
Chains
8
Atoms
15,225
Mol. weight
217.84 kDa
Ligands
MG, GDP
Released
15 Dec 2021

Explore 7DN8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7DN8 contains 100 α-helices and 76 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 and C: 17 helices, 12 β-strands

ElementResiduesLengthSheet
α-helix74-9926
α-helix101-11515
α-helix122-13514
β-strand137-14265
α-helix149-1546
β-strand157-15826
α-helix174-18613
α-helix188-1914
α-helix197-1993
β-strand20517
β-strand21117
α-helix218-2203
α-helix2221
β-strand223-22865
α-helix238-2403
β-strand243-24755
α-helix249-2546
β-strand255-25845
α-helix271-2733
β-strand275-27625
α-helix280-2867
α-helix296-3049
α-helix310-3123
α-helix320-3223
β-strand325-32845
β-strand332-33326
β-strand338-34365
α-helix352-36615
β-strand371-37335
Chains B, D and H: 8 helices, 6 β-strands
ElementResiduesLengthSheet
β-strand17-2378
α-helix30-3910
β-strand51-5888
β-strand61-6888
α-helix75-828
β-strand87-9378
α-helix97-993
α-helix100-11112
α-helix114-1163
β-strand120-12678
α-helix136-1438
α-helix145-1473
β-strand153-15758
α-helix166-17611
Chain E: 17 helices, 14 β-strands
ElementResiduesLengthSheet
α-helix74-9926
α-helix101-11515
α-helix122-13514
β-strand137-14269
β-strand144110
α-helix149-1546
β-strand157-158211
α-helix174-18613
α-helix188-1914
α-helix197-1993
β-strand205112
β-strand211112
α-helix218-2203
α-helix2221
β-strand223-22869
α-helix238-2403
β-strand243-24759
α-helix249-2546
β-strand255-25849
α-helix271-2733
β-strand275-27629
α-helix280-2867
α-helix296-3049
α-helix310-3123
α-helix320-3223
β-strand325-32849
β-strand332-333211
β-strand338-34369
β-strand348110
α-helix352-36615
β-strand371-37339
Chain F: 8 helices, 6 β-strands
ElementResiduesLengthSheet
β-strand17-23713
α-helix30-3910
β-strand51-58813
β-strand61-68813
α-helix75-828
β-strand87-93713
α-helix97-993
α-helix100-11112
α-helix114-1163
β-strand120-126713
α-helix136-1438
α-helix145-1473
β-strand153-157513
α-helix166-17510
Chain G: 17 helices, 14 β-strands
ElementResiduesLengthSheet
α-helix74-9926
α-helix101-11515
α-helix123-13513
β-strand137-142614
β-strand144115
α-helix149-1546
β-strand157-158216
α-helix174-18613
α-helix188-1914
α-helix197-1993
β-strand205117
β-strand211117
α-helix218-2203
α-helix2221
β-strand223-228614
α-helix238-2403
β-strand243-247514
α-helix249-2546
β-strand255-258414
α-helix271-2733
β-strand275-276214
α-helix280-2867
α-helix296-3049
α-helix310-3123
α-helix320-3223
β-strand325-328414
β-strand332-333216
β-strand338-343614
β-strand348115
α-helix352-36615
β-strand371-373314

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Putative cytoplasmic proteinA, C, E, Gprotein305Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)Q8ZPY9 (AlphaFold model)
ADP-ribosylation factor 1B, D, F, Hprotein169Homo sapiensP84077 (AlphaFold model)
Sequence of entity 1 (A, C, E, G), FASTA
>7DN8_1 Putative cytoplasmic protein (chains A, C, E, G)
GRPSNEERKKVYGRLFGKQVLAHIHSRCQRDADIIREKALRRISRECGAEIDCALLLNKM
VDILQNARLTINFNAAKIDFVSLLKNKEYLNSYALGCRPGDLPAYNVGRDSVETKAFELE
KLADSPYAPYGQTGGFSVAYTPNSRTFSTTSRPIYAALDFLNGENGGASAYGKSFFELND
NVKTNCTFSPFDIYGHRFGLDTSKLSTFWHMENLIASCQNDFFGYNCFKSLVKMAKDEKF
LAHSNYGKGYEGNYIEAHIHGDVCLFRDIKHVYLSLQENSYSKSQLYDYAKQINQALNRD
CIILY
Sequence of entity 2 (B, D, F, H), FASTA
>7DN8_2 ADP-ribosylation factor 1 (chains B, D, F, H)
SGRPEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGLD
KIRPLWRHYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDELRDAVLLVFANKQDLPN
AMNAAEITDKLGLHSLRHRNWYIQATCATSGDGLYEGLDWLSNQLRNQK

Ligands and cofactors

IDNameFormulaCopies
MGMagnesium ionMg4
GDPGuanosine-5'-diphosphateC10 H15 N5 O11 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:

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