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- PDB-7dn8: Crystal structure of Salmonella effector SopF in complex with ARF1 -

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Basic information

Entry
Database: PDB / ID: 7dn8
TitleCrystal structure of Salmonella effector SopF in complex with ARF1
Components
  • ADP-ribosylation factor 1
  • Putative cytoplasmic protein
KeywordsTRANSFERASE / ADP-ribosyltransferase
Function / homology
Function and homology information


mitotic cleavage furrow ingression / trans-Golgi Network Vesicle Budding / Glycosphingolipid transport / regulation of receptor internalization / Intra-Golgi traffic / regulation of Arp2/3 complex-mediated actin nucleation / Synthesis of PIPs at the Golgi membrane / Nef Mediated CD4 Down-regulation / dendritic spine organization / long-term synaptic depression ...mitotic cleavage furrow ingression / trans-Golgi Network Vesicle Budding / Glycosphingolipid transport / regulation of receptor internalization / Intra-Golgi traffic / regulation of Arp2/3 complex-mediated actin nucleation / Synthesis of PIPs at the Golgi membrane / Nef Mediated CD4 Down-regulation / dendritic spine organization / long-term synaptic depression / COPI-dependent Golgi-to-ER retrograde traffic / Lysosome Vesicle Biogenesis / Golgi Associated Vesicle Biogenesis / cell leading edge / Synthesis of PIPs at the plasma membrane / intracellular copper ion homeostasis / COPI-mediated anterograde transport / vesicle-mediated transport / MHC class II antigen presentation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / sarcomere / small monomeric GTPase / intracellular protein transport / cellular response to virus / neuron projection / postsynaptic density / protein domain specific binding / Golgi membrane / focal adhesion / nucleotide binding / GTPase activity / GTP binding / magnesium ion binding / protein-containing complex / RNA binding / extracellular exosome / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Protein of unknown function DUF3626 / Protein of unknown function (DUF3626) / ADP-ribosylation factor 1-5 / Small GTPase superfamily, ARF type / Small GTPase Arf domain profile. / Sar1p-like members of the Ras-family of small GTPases / Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family / ARF-like small GTPases; ARF, ADP-ribosylation factor / Rab subfamily of small GTPases ...Protein of unknown function DUF3626 / Protein of unknown function (DUF3626) / ADP-ribosylation factor 1-5 / Small GTPase superfamily, ARF type / Small GTPase Arf domain profile. / Sar1p-like members of the Ras-family of small GTPases / Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family / ARF-like small GTPases; ARF, ADP-ribosylation factor / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / ADP-ribosylation factor 1 / Cytoplasmic protein
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6084 Å
AuthorsDing, J. / Shao, F.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2022
Title: ARF GTPases activate Salmonella effector SopF to ADP-ribosylate host V-ATPase and inhibit endomembrane damage-induced autophagy.
Authors: Xu, Y. / Cheng, S. / Zeng, H. / Zhou, P. / Ma, Y. / Li, L. / Liu, X. / Shao, F. / Ding, J.
History
DepositionDec 9, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Putative cytoplasmic protein
D: ADP-ribosylation factor 1
A: Putative cytoplasmic protein
B: ADP-ribosylation factor 1
E: Putative cytoplasmic protein
F: ADP-ribosylation factor 1
G: Putative cytoplasmic protein
H: ADP-ribosylation factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,84316
Polymers215,9738
Non-polymers1,8708
Water8,305461
1
C: Putative cytoplasmic protein
D: ADP-ribosylation factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4614
Polymers53,9932
Non-polymers4682
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-28 kcal/mol
Surface area20330 Å2
MethodPISA
2
A: Putative cytoplasmic protein
B: ADP-ribosylation factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4614
Polymers53,9932
Non-polymers4682
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-29 kcal/mol
Surface area20330 Å2
MethodPISA
3
E: Putative cytoplasmic protein
F: ADP-ribosylation factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4614
Polymers53,9932
Non-polymers4682
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-29 kcal/mol
Surface area20390 Å2
MethodPISA
4
G: Putative cytoplasmic protein
H: ADP-ribosylation factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4614
Polymers53,9932
Non-polymers4682
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-29 kcal/mol
Surface area20340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.737, 104.902, 105.603
Angle α, β, γ (deg.)90.00, 104.88, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Putative cytoplasmic protein


Mass: 34658.098 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Gene: STM1239 / Plasmid: pGEX6p-2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8ZPY9
#2: Protein
ADP-ribosylation factor 1


Mass: 19335.039 Da / Num. of mol.: 4 / Mutation: Q71L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARF1 / Plasmid: pSUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P84077
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 461 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 10.5% PEG 3350, 120mM alpha-ketoglutarate, 100mM Tris-HCl pH 8.0

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97861 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97861 Å / Relative weight: 1
ReflectionResolution: 2.608→46.66 Å / Num. obs: 67310 / % possible obs: 99.6 % / Redundancy: 3.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.076 / Rrim(I) all: 0.091 / Net I/σ(I): 11.67
Reflection shellResolution: 2.608→2.68 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 2.27 / Num. unique obs: 4866 / CC1/2: 0.783 / Rrim(I) all: 0.565 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6084→46.651 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2399 1993 2.96 %
Rwork0.2011 --
obs0.2022 67285 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6084→46.651 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14648 0 116 461 15225
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00215144
X-RAY DIFFRACTIONf_angle_d0.48620468
X-RAY DIFFRACTIONf_dihedral_angle_d10.2389004
X-RAY DIFFRACTIONf_chiral_restr0.0412208
X-RAY DIFFRACTIONf_plane_restr0.0032628
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.61-2.67360.36421450.28694615X-RAY DIFFRACTION100
2.6736-2.74590.32631420.26354645X-RAY DIFFRACTION100
2.7459-2.82670.29411430.24474675X-RAY DIFFRACTION100
2.8267-2.91790.2641410.23314637X-RAY DIFFRACTION100
2.9179-3.02220.30831440.22684644X-RAY DIFFRACTION100
3.0222-3.14320.29091430.22244623X-RAY DIFFRACTION100
3.1432-3.28620.25061420.21924684X-RAY DIFFRACTION100
3.2862-3.45940.29081430.21614658X-RAY DIFFRACTION100
3.4594-3.6760.27641400.20574634X-RAY DIFFRACTION100
3.676-3.95970.24981410.18874658X-RAY DIFFRACTION100
3.9597-4.35790.20611480.17284702X-RAY DIFFRACTION100
4.3579-4.98790.18011420.16754676X-RAY DIFFRACTION100
4.9879-6.28180.21261410.19194680X-RAY DIFFRACTION100
6.2818-46.650.1851380.18854761X-RAY DIFFRACTION99

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