[English] 日本語
Yorodumi
- PDB-7dn9: Crystal structure of Salmonella effector in complex with NAD and ... -

+
Open data


ID or keywords:

Loading...

-
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 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 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 ...Protein of unknown function DUF3626 / Protein of unknown function (DUF3626) / ADP-ribosylation factor 1-5 / Small GTPase superfamily, ARF type / 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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water00
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

-
Components

#1: Protein
Putative cytoplasmic protein


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


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


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


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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more