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- PDB-3lvr: The crystal structure of ASAP3 in complex with Arf6 in transition... -

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Basic information

Entry
Database: PDB / ID: 3lvr
TitleThe crystal structure of ASAP3 in complex with Arf6 in transition state soaked with Calcium
ComponentsArf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 3, ADP-ribosylation factor 6
KeywordsPROTEIN TRANSPORT / Arf6 / ASAP3 / UPLC1 / GDP / Calcium / ArfGAP / Arf / Linkers / Alternative splicing / ANK repeat / Coiled coil / Cytoplasm / Metal-binding / Phosphoprotein / Polymorphism / Zinc / Zinc-finger / Cell membrane / Endosome / ER-Golgi transport / Golgi apparatus / GTP-binding / Lipoprotein / Myristate / Nucleotide-binding / Transport
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 / regulation of stress fiber assembly / 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 / GTPase activator activity / 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 / positive regulation of GTPase activity / recycling endosome membrane / GDP binding / cell migration / presynapse / Clathrin-mediated endocytosis / nervous system development / cell cortex / early endosome membrane / postsynapse / cell differentiation / cell adhesion / endosome / cell cycle / cell division / focal adhesion / intracellular membrane-bounded organelle / GTPase activity / glutamatergic synapse / GTP binding / Golgi apparatus / extracellular exosome / nucleoplasm / membrane / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #950 / Arf GTPase activating protein, ASAP3 / : / ASAP, PH domain / Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein / Arf GTPase activating protein / ADP-ribosylation factor 6 / BAR domain of APPL family / Arf GTPase activating protein / ArfGAP domain superfamily ...Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #950 / Arf GTPase activating protein, ASAP3 / : / ASAP, PH domain / Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein / Arf GTPase activating protein / ADP-ribosylation factor 6 / BAR domain of APPL family / Arf GTPase activating protein / ArfGAP domain superfamily / Putative GTPase activating protein for Arf / ARF GTPase-activating proteins domain profile. / Putative GTP-ase activating proteins for the small GTPase, ARF / BAR domain / ARFGAP/RecO-like zinc finger / small GTPase Arf family profile. / Annexin V; domain 1 / 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 / AH/BAR domain superfamily / Ankyrin repeat-containing domain / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Rab subfamily of small GTPases / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Small GTP-binding protein domain / PH-like domain superfamily / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ALUMINUM FLUORIDE / GUANOSINE-5'-DIPHOSPHATE / ADP-ribosylation factor 6 / Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.38 Å
AuthorsIsmail, S.A. / Vetter, I.R. / Sot, B. / Wittinghofer, A.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2010
Title: The structure of an Arf-ArfGAP complex reveals a Ca2+ regulatory mechanism
Authors: Ismail, S.A. / Vetter, I.R. / Sot, B. / Wittinghofer, A.
History
DepositionFeb 22, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 9, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Nov 1, 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_ref_seq_dif.details / _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
E: Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 3, ADP-ribosylation factor 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4836
Polymers54,8261
Non-polymers6575
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)146.450, 146.450, 49.620
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

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Components

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Protein , 1 types, 1 molecules E

#1: Protein Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 3, ADP-ribosylation factor 6 / ASAP3 / Development and differentiation-enhancing factor-like 1 / Protein up-regulated in liver ...ASAP3 / Development and differentiation-enhancing factor-like 1 / Protein up-regulated in liver cancer 1 / Arf6 / UPLC1


Mass: 54825.930 Da / Num. of mol.: 1
Fragment: GAP and Ankyrin domain, residues 416-697, residues 11-175
Source method: isolated from a genetically manipulated source
Details: Missing the N-terminus amphipathic helix for Arf6
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) synthetic construct (others)
Gene: ASAP3, ARF6 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TDY4, PDB-3LVQ, UniProt: P62330

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Non-polymers , 6 types, 11 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#5: Chemical ChemComp-AF3 / ALUMINUM FLUORIDE / Aluminium fluoride


Mass: 83.977 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AlF3
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsNLSSDSSLSSPSALNSLSSPSALNSTASNSPGIEGLS IS A FLEXIBLE LINKER REGION. THIS ENTRY USES NON-SEQUENTIAL NUMBERING.

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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: 2.8 Å3/Da / Density % sol: 56.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 13% PEG 8000, 150mM Magnesium Acetate, 100mM MOPS(pH 7.5); Crystals were then soaked in 30mM CaCl2 , VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.3838 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 4, 2009
RadiationMonochromator: SAGITALLY - HORIZONTALLY FOCUSED SI(111) MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3838 Å / Relative weight: 1
ReflectionResolution: 3.38→29.46 Å / Num. all: 8310 / Num. obs: 8310 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.85 % / Rmerge(I) obs: 0.101 / Rsym value: 0.08 / Net I/σ(I): 19
Reflection shellResolution: 3.38→3.5 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.575 / Mean I/σ(I) obs: 3.5 / Num. unique all: 1657 / Rsym value: 0.676 / % possible all: 99.5

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Processing

Software
NameVersionClassification
ProDCdata collection
MOLREPphasing
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3LVQ

3lvq


Resolution: 3.38→29.46 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.901 / SU B: 56.231 / SU ML: 0.451 / Cross valid method: THROUGHOUT / ESU R Free: 0.61 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28129 437 5 %RANDOM
Rwork0.20746 ---
obs0.21095 8294 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 125.397 Å2
Baniso -1Baniso -2Baniso -3
1--6.75 Å2-3.38 Å20 Å2
2---6.75 Å20 Å2
3---10.13 Å2
Refinement stepCycle: LAST / Resolution: 3.38→29.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3257 0 35 6 3298
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0223348
X-RAY DIFFRACTIONr_angle_refined_deg1.0581.9774540
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4735415
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.46524.211152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.90115575
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.861525
X-RAY DIFFRACTIONr_chiral_restr0.0760.2513
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022509
X-RAY DIFFRACTIONr_nbd_refined0.2010.21544
X-RAY DIFFRACTIONr_nbtor_refined0.2990.22257
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2114
X-RAY DIFFRACTIONr_metal_ion_refined0.1130.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1950.227
X-RAY DIFFRACTIONr_mcbond_it0.2231.52129
X-RAY DIFFRACTIONr_mcangle_it0.40523329
X-RAY DIFFRACTIONr_scbond_it0.44631375
X-RAY DIFFRACTIONr_scangle_it0.8134.51211
LS refinement shellResolution: 3.381→3.467 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 32 -
Rwork0.249 601 -
obs-601 100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.33681.1971-0.00319.7407-0.89694.9919-0.10940.0863-0.79440.06450.1212-0.47160.7445-0.4123-0.0118-0.51140.1040.1519-0.3132-0.1904-0.496637.70931.5561-3.219
211.39750.28850.31947.87830.02375.7939-0.2783-0.30390.89540.33460.00960.8382-0.1207-0.27490.2687-0.710.08650.1309-0.6942-0.1082-0.477420.594955.77455.3018
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1E423 - 679
2X-RAY DIFFRACTION2A11 - 174

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