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- PDB-7dn9: Crystal structure of Salmonella effector in complex with NAD and ... -

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Basic information

Entry
Database: PDB / ID: 7dn9
TitleCrystal structure of Salmonella effector in complex with NAD and host co-factor ARF1
Components
  • ADP-ribosylation factor 1ARF1
  • Putative cytoplasmic proteinCytoplasm
KeywordsTRANSFERASE / ADP-ribosyltransferase
Function / homology
Function and homology information


Glycosphingolipid transport / mitotic cleavage furrow ingression / trans-Golgi Network Vesicle Budding / regulation of receptor internalization / regulation of Arp2/3 complex-mediated actin nucleation / Intra-Golgi traffic / Synthesis of PIPs at the Golgi membrane / Nef Mediated CD4 Down-regulation / dendritic spine organization / long-term synaptic depression ...Glycosphingolipid transport / mitotic cleavage furrow ingression / trans-Golgi Network Vesicle Budding / regulation of receptor internalization / regulation of Arp2/3 complex-mediated actin nucleation / Intra-Golgi traffic / 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 / postsynaptic density / neuron projection / protein domain specific binding / Golgi membrane / focal adhesion / GTPase activity / GTP binding / magnesium ion binding / protein-containing complex / RNA binding / extracellular exosome / plasma membrane / cytosol
Similarity search - Function
Protein of unknown function DUF3626 / Protein of unknown function (DUF3626) / ADP-ribosylation factor 1-5 / small GTPase Arf family 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 / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / ADP-ribosylation factor 1 / Putative cytoplasmic protein
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.29 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

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Assembly

Deposited unit
A: Putative cytoplasmic protein
B: ADP-ribosylation factor 1
C: Putative cytoplasmic protein
D: 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)222,04620
Polymers217,5228
Non-polymers4,52412
Water0
1
A: Putative cytoplasmic protein
B: ADP-ribosylation factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5125
Polymers54,3812
Non-polymers1,1313
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4700 Å2
ΔGint-40 kcal/mol
Surface area20390 Å2
MethodPISA
2
C: Putative cytoplasmic protein
D: ADP-ribosylation factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5125
Polymers54,3812
Non-polymers1,1313
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-40 kcal/mol
Surface area20450 Å2
MethodPISA
3
E: Putative cytoplasmic protein
F: ADP-ribosylation factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5125
Polymers54,3812
Non-polymers1,1313
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4700 Å2
ΔGint-40 kcal/mol
Surface area20360 Å2
MethodPISA
4
G: Putative cytoplasmic protein
H: ADP-ribosylation factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5125
Polymers54,3812
Non-polymers1,1313
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4700 Å2
ΔGint-39 kcal/mol
Surface area20400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.711, 105.576, 105.839
Angle α, β, γ (deg.)90.00, 104.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Putative cytoplasmic protein / Cytoplasm


Mass: 35443.977 Da / Num. of mol.: 4 / Mutation: E325D
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 / ARF1


Mass: 18936.600 Da / Num. of mol.: 4 / Mutation: Q71L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARF1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P84077
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


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


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
Has ligand of interestY

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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: 52.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 13% PEG 3350, 300mM sodium citrate, 100mM Bis-Tris pH 6.5

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.287→46.92 Å / Num. obs: 33860 / % possible obs: 97.1 % / Redundancy: 2.86 % / CC1/2: 0.975 / Rmerge(I) obs: 0.156 / Rrim(I) all: 0.193 / Net I/σ(I): 5.79
Reflection shellResolution: 3.29→3.37 Å / Redundancy: 2.63 % / Rmerge(I) obs: 0.501 / Mean I/σ(I) obs: 2.03 / Num. unique obs: 2301 / CC1/2: 0.733 / Rrim(I) all: 0.625 / % possible all: 92.6

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.29→46.91 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2768 2002 5.91 %
Rwork0.2364 --
obs0.2388 33850 99.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.29→46.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14800 0 292 0 15092
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00215412
X-RAY DIFFRACTIONf_angle_d0.42720856
X-RAY DIFFRACTIONf_dihedral_angle_d13.9895716
X-RAY DIFFRACTIONf_chiral_restr0.042264
X-RAY DIFFRACTIONf_plane_restr0.0022656
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.29-3.370.34891380.31852158X-RAY DIFFRACTION95
3.37-3.460.31461430.29272290X-RAY DIFFRACTION100
3.46-3.560.3431420.28432252X-RAY DIFFRACTION100
3.56-3.680.31621410.26882268X-RAY DIFFRACTION100
3.68-3.810.28281460.24892288X-RAY DIFFRACTION100
3.81-3.960.2831460.23072242X-RAY DIFFRACTION99
3.96-4.140.24481410.22182281X-RAY DIFFRACTION99
4.14-4.360.22621380.2162268X-RAY DIFFRACTION99
4.36-4.630.27351440.20922286X-RAY DIFFRACTION100
4.63-4.990.23131440.20582281X-RAY DIFFRACTION100
4.99-5.490.28461450.2142287X-RAY DIFFRACTION100
5.49-6.280.30031370.23282275X-RAY DIFFRACTION100
6.28-7.910.28041490.23912321X-RAY DIFFRACTION100
7.91-46.910.25621480.23472351X-RAY DIFFRACTION100

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