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- PDB-5c6r: Crystal structure of PH domain of ASAP1 -

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Basic information

Entry
Database: PDB / ID: 5c6r
TitleCrystal structure of PH domain of ASAP1
ComponentsArf-GAP
KeywordsSIGNALING PROTEIN / PH domain / ASPA1
Function / homology
Function and homology information


VxPx cargo-targeting to cilium / positive regulation of membrane tubulation / negative regulation of dendritic spine development / protein localization to cilium / podosome / regulation of postsynapse organization / phosphatidylserine binding / phosphatidylinositol-3,4,5-trisphosphate binding / cilium assembly / phosphatidylinositol-4,5-bisphosphate binding ...VxPx cargo-targeting to cilium / positive regulation of membrane tubulation / negative regulation of dendritic spine development / protein localization to cilium / podosome / regulation of postsynapse organization / phosphatidylserine binding / phosphatidylinositol-3,4,5-trisphosphate binding / cilium assembly / phosphatidylinositol-4,5-bisphosphate binding / GTPase activator activity / trans-Golgi network membrane / dendritic spine / Golgi membrane / glutamatergic synapse / metal ion binding / cytosol
Similarity search - Function
ASAP1, BAR domain / ASAP1, SH3 domain / ASAP, PH domain / Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein / 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 ...ASAP1, BAR domain / ASAP1, SH3 domain / ASAP, PH domain / Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein / 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 / AH/BAR domain superfamily / Variant SH3 domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / 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 / Ankyrin repeat-containing domain superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / PHOSPHATE ION / Arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsXia, D. / Tang, W.K.
CitationJournal: Structure / Year: 2015
Title: Molecular Basis for Cooperative Binding of Anionic Phospholipids to the PH Domain of the Arf GAP ASAP1.
Authors: Jian, X. / Tang, W.K. / Zhai, P. / Roy, N.S. / Luo, R. / Gruschus, J.M. / Yohe, M.E. / Chen, P.W. / Li, Y. / Byrd, R.A. / Xia, D. / Randazzo, P.A.
History
DepositionJun 23, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2015Group: Database references
Revision 1.2Sep 27, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_ncs_dom_lim
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Arf-GAP
B: Arf-GAP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1477
Polymers34,5062
Non-polymers6405
Water61334
1
A: Arf-GAP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7995
Polymers17,2531
Non-polymers5454
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Arf-GAP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3482
Polymers17,2531
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.120, 48.120, 111.333
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 0 / Auth seq-ID: 333 - 439 / Label seq-ID: 32 - 138

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Arf-GAP / 130 kDa phosphatidylinositol 4 / 5-bisphosphate-dependent ARF1 GTPase-activating protein / ADP- ...130 kDa phosphatidylinositol 4 / 5-bisphosphate-dependent ARF1 GTPase-activating protein / ADP-ribosylation factor-directed GTPase-activating protein 1 / ARF GTPase-activating protein 1 / Development and differentiation-enhancing factor 1 / Differentiation-enhancing factor 1 / PIP2-dependent ARF1 GAP


Mass: 17253.229 Da / Num. of mol.: 2 / Fragment: PH domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Asap1, Ddef1, Kiaa1249, Shag1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9QWY8
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.87 Å3/Da / Density % sol: 34.14 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: 100 mM Na2HPO4, 100 mM Tris, pH 8.0 and 48% PEG400 (v/v)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 22383 / % possible obs: 95.4 % / Redundancy: 4.6 % / Net I/σ(I): 15.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DA0

2da0


Resolution: 1.8→48.12 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.922 / SU B: 8.571 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.141 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25986 1165 5.2 %RANDOM
Rwork0.20801 ---
obs0.21068 21190 95.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.008 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20 Å20 Å2
2--0.56 Å20 Å2
3----1.12 Å2
Refinement stepCycle: 1 / Resolution: 1.8→48.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1757 0 40 34 1831
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0191831
X-RAY DIFFRACTIONr_bond_other_d0.0080.021791
X-RAY DIFFRACTIONr_angle_refined_deg1.9991.9552445
X-RAY DIFFRACTIONr_angle_other_deg1.63634127
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8225218
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.23924.43288
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.10315351
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6081512
X-RAY DIFFRACTIONr_chiral_restr0.1130.2258
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022027
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02431
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5822.96872
X-RAY DIFFRACTIONr_mcbond_other2.5832.958871
X-RAY DIFFRACTIONr_mcangle_it4.3314.4131087
X-RAY DIFFRACTIONr_mcangle_other4.3294.4151088
X-RAY DIFFRACTIONr_scbond_it3.2653.568959
X-RAY DIFFRACTIONr_scbond_other3.2593.568959
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.3365.1381358
X-RAY DIFFRACTIONr_long_range_B_refined8.60923.4941939
X-RAY DIFFRACTIONr_long_range_B_other8.60723.4931939
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 11684 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.15 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 76 -
Rwork0.346 1167 -
obs--71.48 %
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)
14.68230.48710.05812.5363-0.22141.99840.0142-0.4980.34420.19040.0141-0.0126-0.1360.0522-0.02830.0523-0.0139-0.01860.1674-0.04950.0417-4.266321.22260.3176
23.90480.3128-1.74332.65590.06363.0182-0.02630.18640.0084-0.20290.02130.05710.02550.03870.00510.04070.009-0.00730.11360.01610.0044-29.773411.8214-3.0211
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A333 - 444
2X-RAY DIFFRACTION2B333 - 444

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