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- PDB-2j5x: STRUCTURE OF THE SMALL G PROTEIN ARF6 IN COMPLEX WITH GTPGAMMAS -

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Basic information

Entry
Database: PDB / ID: 2j5x
TitleSTRUCTURE OF THE SMALL G PROTEIN ARF6 IN COMPLEX WITH GTPGAMMAS
ComponentsADP-RIBOSYLATION FACTOR 6
KeywordsPROTEIN TRANSPORT / MEMBRANE TRAFFIC / RAS / ARF / ARF6 / G PROTEIN / MYRISTATE / TRANSPORT / ER-GOLGI TRANSPORT / NUCLEOTIDE-BINDING / LIPOPROTEIN / GTP-BINDING / GOLGI APPARATUS
Function / homology
Function and homology information


erythrocyte apoptotic process / protein localization to cleavage furrow / maintenance of postsynaptic density structure / positive regulation of mitotic cytokinetic process / regulation of dendritic spine development / establishment of epithelial cell polarity / protein localization to endosome / negative regulation of protein localization to cell surface / negative regulation of dendrite development / negative regulation of receptor-mediated endocytosis ...erythrocyte apoptotic process / protein localization to cleavage furrow / maintenance of postsynaptic density structure / positive regulation of mitotic cytokinetic process / regulation of dendritic spine development / establishment of epithelial cell polarity / protein localization to endosome / negative regulation of protein localization to cell surface / negative regulation of dendrite development / negative regulation of receptor-mediated endocytosis / regulation of Rac protein signal transduction / ruffle assembly / positive regulation of keratinocyte migration / positive regulation of focal adhesion disassembly / regulation of filopodium assembly / MET receptor recycling / thioesterase binding / endocytic recycling / filopodium membrane / Flemming body / protein localization to cell surface / 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 / small monomeric GTPase / cellular response to nerve growth factor stimulus / 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 / midbody / 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
5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE / ADP-ribosylation factor 6
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsPasqualato, S. / Menetrey, J. / Franco, M. / Cherfils, J.
CitationJournal: Embo Rep. / Year: 2001
Title: The Structural Gdp-GTP Cycle of Human Arf6.
Authors: Pasqualato, S. / Menetrey, J. / Franco, M. / Cherfils, J.
History
DepositionSep 20, 2006Deposition site: PDBE / Processing site: PDBE
SupersessionSep 21, 2006ID: 1HFV
Revision 1.0Sep 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

Downloads & links

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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)41,3476
Polymers40,2202
Non-polymers1,1274
Water57632
1
A: ADP-RIBOSYLATION FACTOR 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6743
Polymers20,1101
Non-polymers5642
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: ADP-RIBOSYLATION FACTOR 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6743
Polymers20,1101
Non-polymers5642
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)72.895, 72.895, 131.489
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.999932, -0.011239, 0.003138), (0.010826, -0.793178, 0.608894), (-0.004354, 0.608886, 0.793246)
Vector: 174.44279, -1.514, 0.7045)

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Components

#1: Protein ADP-RIBOSYLATION FACTOR 6 / ARF6


Mass: 20110.166 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P62330
#2: Chemical ChemComp-GSP / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE


Mass: 539.246 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3S
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.28 Å3/Da / Density % sol: 45.69 %
Crystal growpH: 4.6 / Details: pH 4.60

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.934
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 26, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 8616 / % possible obs: 93.1 % / Observed criterion σ(I): 2 / Redundancy: 6 % / Biso Wilson estimate: 94.5 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 25.2
Reflection shellResolution: 2.8→2.98 Å / % possible all: 83.6

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ARF1DELTA17-GDPNHP, FROM GOLDBERG J.

Resolution: 2.8→29.97 Å / Rfactor Rfree error: 0.009 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0.5
Details: THE FIRST TEN RESIDUES IN CHAIN A AND B WERE NOT VISIBLE IN THE DENSITY MAPS.
RfactorNum. reflection% reflectionSelection details
Rfree0.276 923 10.7 %RANDOM
Rwork0.234 ---
obs0.234 8616 93.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.1885 Å2 / ksol: 0.33714 e/Å3
Displacement parametersBiso mean: 50.6 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.56 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.8→29.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2635 0 66 32 2733
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.471.5
X-RAY DIFFRACTIONc_mcangle_it2.582
X-RAY DIFFRACTIONc_scbond_it1.722
X-RAY DIFFRACTIONc_scangle_it2.82.5
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.399 120 9.6 %
Rwork0.349 1128 -
obs--83.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4GSP.PARGSP.TOP

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