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

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Basic information

Entry
Database: PDB / ID: 3lvq
TitleThe crystal structure of ASAP3 in complex with Arf6 in transition state
ComponentsArf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 3, ADP-ribosylation factor 6
KeywordsPROTEIN TRANSPORT / Arf / GAP / GDP / ASAP3 / UPLC1 / Arf6 / ArfGAP / 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 / protein localization to cleavage furrow / positive regulation of mitotic cytokinetic process / negative regulation of dendrite development / establishment of epithelial cell polarity / regulation of dendritic spine development / regulation of Rac protein signal transduction / protein localization to endosome / negative regulation of protein localization to cell surface ...erythrocyte apoptotic process / maintenance of postsynaptic density structure / protein localization to cleavage furrow / positive regulation of mitotic cytokinetic process / negative regulation of dendrite development / establishment of epithelial cell polarity / regulation of dendritic spine development / regulation of Rac protein signal transduction / protein localization to endosome / negative regulation of protein localization to cell surface / negative regulation of receptor-mediated endocytosis / ruffle assembly / positive regulation of keratinocyte migration / regulation of filopodium assembly / positive regulation of focal adhesion disassembly / MET receptor recycling / endocytic recycling / thioesterase binding / regulation of stress fiber assembly / Flemming body / filopodium membrane / TBC/RABGAPs / protein localization to cell surface / cortical actin cytoskeleton organization / hepatocyte apoptotic process / positive regulation of actin filament polymerization / cleavage furrow / positive regulation of GTPase activity / endocytic vesicle / synaptic vesicle endocytosis / regulation of presynapse assembly / vesicle-mediated transport / ruffle / signaling adaptor activity / GTPase activator activity / small monomeric GTPase / positive regulation of protein secretion / protein localization to plasma membrane / positive regulation of protein localization to plasma membrane / intracellular protein transport / liver development / positive regulation of neuron projection development / cellular response to nerve growth factor stimulus / recycling endosome membrane / GDP binding / cell migration / nervous system development / presynapse / Clathrin-mediated endocytosis / G protein activity / midbody / early endosome membrane / cell cortex / cell differentiation / postsynapse / cell adhesion / endosome / cell division / focal adhesion / intracellular membrane-bounded organelle / GTPase activity / GTP binding / glutamatergic synapse / Golgi apparatus / extracellular exosome / zinc ion binding / nucleoplasm / membrane / plasma membrane / cytoplasm / 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 / ARFGAP/RecO-like zinc finger / BAR domain / Small GTPase superfamily, ARF type / Annexin V; domain 1 / Small GTPase Arf domain profile. / Sar1p-like members of the Ras-family of small GTPases / Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family / AH/BAR domain superfamily / ARF-like small GTPases; ARF, ADP-ribosylation factor / Ankyrin repeat-containing domain / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Rab subfamily of small GTPases / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 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 1.4Dec 5, 2018Group: Advisory / Data collection / Structure summary
Category: pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_residues
Item: _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_unobs_or_zero_occ_residues.auth_seq_id
Revision 1.5Nov 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.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
Revision 1.6Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)55,4676
Polymers54,8261
Non-polymers6415
Water905
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)146.290, 146.290, 49.520
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, UniProt: P62330

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Non-polymers , 5 types, 10 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.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GDP / GUANOSINE-5'-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


Mass: 83.977 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AlF3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsNLSSDSSLSSPSALNSLSSPSALNSTASNSPGIEGLS IS A FLEXIBLE LINKER REGION.

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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: 2.79 Å3/Da / Density % sol: 55.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 13% PEG 8000, 150mM Magnesium Acetate, 100mM MOPS(pH 7.5), VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 16, 2009
RadiationMonochromator: SAGITALLY - HORIZONTALLY FOCUSED SI(111) MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.38→29.42 Å / Num. obs: 8700 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 9.25 % / Rmerge(I) obs: 0.066 / Rsym value: 0.079 / Net I/σ(I): 22.52 / Num. measured all: 80498
Reflection shellResolution: 3.38→3.5 Å / Redundancy: 9.45 % / Rmerge(I) obs: 0.339 / Mean I/σ(I) obs: 4.94 / Num. unique all: 847 / Rsym value: 0.55 / % possible all: 99.8

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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 ENTRIES 2B0o and 2J5X

2b0o

2j5x


Resolution: 3.38→29.42 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.904 / SU B: 58.227 / SU ML: 0.482 / Cross valid method: THROUGHOUT / ESU R Free: 0.558 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2568 435 5 %RANDOM
Rwork0.21881 ---
all0.2207 ---
obs0.2207 8263 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: 136.436 Å2
Baniso -1Baniso -2Baniso -3
1--5.06 Å2-2.53 Å20 Å2
2---5.06 Å20 Å2
3---7.59 Å2
Refinement stepCycle: LAST / Resolution: 3.38→29.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3262 0 35 5 3302
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223354
X-RAY DIFFRACTIONr_angle_refined_deg1.1461.9774550
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.635417
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.68124.211152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.64115575
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4721525
X-RAY DIFFRACTIONr_chiral_restr0.0820.2514
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022517
X-RAY DIFFRACTIONr_nbd_refined0.210.21552
X-RAY DIFFRACTIONr_nbtor_refined0.30.22254
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.2117
X-RAY DIFFRACTIONr_metal_ion_refined0.0590.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2170.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1150.21
LS refinement shellResolution: 3.38→3.467 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 30 -
Rwork0.272 585 -
obs-585 100 %

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