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- PDB-3n5c: Crystal Structure of Arf6DELTA13 complexed with GDP -

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Basic information

Entry
Database: PDB / ID: 3n5c
TitleCrystal Structure of Arf6DELTA13 complexed with GDP
ComponentsADP-ribosylation factor 6ARF6
KeywordsPROTEIN TRANSPORT / Small G protein / Small GTP-binding protein / Arf / ADP-ribosylation factor 6 / Traffic / ENDOCYTOSIS / UNFOLDED PROTEIN
Function / homology
Function and homology information


erythrocyte apoptotic process / maintenance of postsynaptic density structure / regulation of dendritic spine development / establishment of epithelial cell polarity / negative regulation of receptor-mediated endocytosis / protein localization to endosome / negative regulation of dendrite development / ruffle assembly / negative regulation of protein localization to cell surface / regulation of Rac protein signal transduction ...erythrocyte apoptotic process / maintenance of postsynaptic density structure / regulation of dendritic spine development / establishment of epithelial cell polarity / negative regulation of receptor-mediated endocytosis / protein localization to endosome / negative regulation of dendrite development / ruffle assembly / negative regulation of protein localization to cell surface / regulation of Rac protein signal transduction / positive regulation of keratinocyte migration / positive regulation of focal adhesion disassembly / regulation of filopodium assembly / endocytic recycling / thioesterase binding / MET receptor recycling / filopodium membrane / protein localization to cell surface / Flemming body / TBC/RABGAPs / cortical actin cytoskeleton organization / positive regulation of actin filament polymerization / hepatocyte apoptotic process / cleavage furrow / regulation of presynapse assembly / synaptic vesicle endocytosis / endocytic vesicle / signaling adaptor activity / vesicle-mediated transport / ruffle / cellular response to nerve growth factor stimulus / small monomeric GTPase / G protein activity / liver development / protein localization to plasma membrane / positive regulation of protein secretion / positive regulation of protein localization to plasma membrane / intracellular protein transport / positive regulation of neuron projection development / recycling endosome membrane / GDP binding / presynapse / Clathrin-mediated endocytosis / nervous system development / cell cortex / early endosome membrane / postsynapse / cell differentiation / cell adhesion / endosome / cell cycle / cell division / focal adhesion / GTPase activity / glutamatergic synapse / GTP binding / Golgi apparatus / extracellular exosome / membrane / plasma membrane / cytosol
Similarity search - Function
ADP-ribosylation factor 6 / 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 nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase ...ADP-ribosylation factor 6 / 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 nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / ADP-ribosylation factor 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsAizel, K. / Biou, V. / Cherfils, J.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: SAXS and X-ray crystallography suggest an unfolding model for the GDP/GTP conformational switch of the small GTPase Arf6.
Authors: Biou, V. / Aizel, K. / Roblin, P. / Thureau, A. / Jacquet, E. / Hansson, S. / Guibert, B. / Guittet, E. / van Heijenoort, C. / Zeghouf, M. / Perez, J. / Cherfils, J.
History
DepositionMay 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ADP-ribosylation factor 6
B: ADP-ribosylation factor 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3427
Polymers37,3492
Non-polymers9935
Water3,099172
1
A: ADP-ribosylation factor 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1894
Polymers18,6741
Non-polymers5143
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ADP-ribosylation factor 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1533
Polymers18,6741
Non-polymers4792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.470, 49.720, 143.070
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 6 / ARF6


Mass: 18674.404 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 14-175
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARF6 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P62330
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H2O

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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: 1.83 Å3/Da / Density % sol: 32.85 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2 M NaCl and 20% PEG 3350, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 21, 2009
RadiationMonochromator: Silicon 1,1,1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.82→41 Å / Num. all: 25617 / Num. obs: 25431 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 27.08 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 14.5
Reflection shellResolution: 1.82→1.93 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.587 / Mean I/σ(I) obs: 2.7 / Num. unique all: 2675 / Rsym value: 0.587 / % possible all: 97.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
BUSTER2.8.0refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1E0S

1e0s


Resolution: 1.82→40.83 Å / Cor.coef. Fo:Fc: 0.9608 / Cor.coef. Fo:Fc free: 0.9534 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber 1999
RfactorNum. reflection% reflectionSelection details
Rfree0.1954 1272 5 %RANDOM
Rwork0.1705 ---
all0.1718 25617 --
obs0.1718 25431 97.7 %-
Displacement parametersBiso mean: 31.38 Å2
Baniso -1Baniso -2Baniso -3
1--0.2398 Å20 Å20 Å2
2--0.3958 Å20 Å2
3----0.156 Å2
Refine analyzeLuzzati coordinate error obs: 0.182 Å
Refinement stepCycle: LAST / Resolution: 1.82→40.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2500 0 59 172 2731
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.0126092
X-RAY DIFFRACTIONt_angle_deg1.0835392
X-RAY DIFFRACTIONt_dihedral_angle_d9412
X-RAY DIFFRACTIONt_trig_c_planes662
X-RAY DIFFRACTIONt_gen_planes3655
X-RAY DIFFRACTIONt_it260920
X-RAY DIFFRACTIONt_nbd15
X-RAY DIFFRACTIONt_omega_torsion3.72
X-RAY DIFFRACTIONt_other_torsion15.79
X-RAY DIFFRACTIONt_chiral_improper_torsion3305
X-RAY DIFFRACTIONt_ideal_dist_contact31344
LS refinement shellResolution: 1.82→1.89 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2491 141 5.01 %
Rwork0.2013 2675 -
all0.2037 2816 -
obs-2675 97 %

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