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- PDB-8sdw: Crystal structure of the non-myristoylated mutant [L8K]Arf1 in co... -

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Basic information

Entry
Database: PDB / ID: 8sdw
TitleCrystal structure of the non-myristoylated mutant [L8K]Arf1 in complex with a GDP analogue
ComponentsADP-ribosylation factor 1ARF1
KeywordsPROTEIN TRANSPORT / GTPase / G protein / GDP
Function / homology
Function and homology information


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 ...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
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-3'-MONOPHOSPHATE-5'-DIPHOSPHATE / ADP-ribosylation factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsRosenberg Jr., E.M. / Randazzo, P.A. / Esser, L. / Xia, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)BC007365 United States
CitationJournal: Plos One / Year: 2024
Title: Point mutations in Arf1 reveal cooperative effects of the N-terminal extension and myristate for GTPase-activating protein catalytic activity.
Authors: Rosenberg Jr., E.M. / Jian, X. / Soubias, O. / Jackson, R.A. / Gladu, E. / Andersen, E. / Esser, L. / Sodt, A.J. / Xia, D. / Byrd, R.A. / Randazzo, P.A.
History
DepositionApr 7, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ADP-ribosylation factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2853
Polymers20,7381
Non-polymers5472
Water5,332296
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.654, 55.015, 78.472
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ADP-ribosylation factor 1 / ARF1


Mass: 20737.764 Da / Num. of mol.: 1 / Mutation: L8K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARF1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21(DE3) / References: UniProt: P84077, small monomeric GTPase
#2: Chemical ChemComp-G3D / GUANOSINE-3'-MONOPHOSPHATE-5'-DIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 296 / Source method: isolated from a natural source / Formula: H2O
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: 2.17 Å3/Da / Density % sol: 43.26 % / Description: Needle-like crystals
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 0.2 M Sodium nitrate, 20% w/v Polyethylene glycol 3,350, pH 6.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 18613 / % possible obs: 98.7 % / Redundancy: 6.2 % / CC1/2: 0.996 / CC star: 0.999 / Rpim(I) all: 0.025 / Χ2: 0.981 / Net I/σ(I): 27.1
Reflection shell
Resolution (Å)Num. unique obsCC1/2Diffraction-ID
1.75-1.788190.9761
1.78-1.819180.9831
1.81-1.859120.9861
1.85-1.899240.9881
1.89-1.939110.9921
1.93-1.979360.9921
1.97-2.029180.991
2.02-2.079230.9931
2.07-2.149260.9941
2.14-2.29150.9951
2.2-2.289240.9951
2.28-2.389230.9961
2.38-2.489540.9971
2.48-2.619390.9971
2.61-2.789360.9961
2.78-2.999380.9961
2.99-3.299350.9971
3.29-3.779480.9971
3.77-4.759790.9971
4.75-5010350.9971

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Processing

Software
NameVersionClassification
PHENIX1.20rc3-4406refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→39.24 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.21 --
Rwork0.19 --
obs-18573 98.96 %
Refinement stepCycle: LAST / Resolution: 1.75→39.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1322 0 33 296 1651
LS refinement shellResolution: 1.75→1.81 Å /
RfactorNum. reflection
Rfree0.2323 1852
Rwork0.2151 -

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