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- PDB-7yis: Crystal structure of N-terminal PH domain of ARAP3 protein in com... -

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Basic information

Entry
Database: PDB / ID: 7yis
TitleCrystal structure of N-terminal PH domain of ARAP3 protein in complex with inositol 1,3,4,5-tetrakisphosphate
ComponentsArf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 3
KeywordsCYTOSOLIC PROTEIN / ARAP3 / PH domain / complex / inositol 1 / 3 / 4 / 5-tetrakisphosphate
Function / homology
Function and homology information


phosphatidylinositol-3,4-bisphosphate binding / phosphatidylinositol-3,4,5-trisphosphate binding / CDC42 GTPase cycle / RHOA GTPase cycle / RAC3 GTPase cycle / vesicle-mediated transport / ruffle / RAC1 GTPase cycle / cytoskeleton organization / regulation of actin cytoskeleton organization ...phosphatidylinositol-3,4-bisphosphate binding / phosphatidylinositol-3,4,5-trisphosphate binding / CDC42 GTPase cycle / RHOA GTPase cycle / RAC3 GTPase cycle / vesicle-mediated transport / ruffle / RAC1 GTPase cycle / cytoskeleton organization / regulation of actin cytoskeleton organization / lamellipodium / cytoskeleton / signal transduction / zinc ion binding / plasma membrane / cytoplasm
Similarity search - Function
ARAP, RhoGAP domain / : / 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 / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain profile. ...ARAP, RhoGAP domain / : / 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 / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain profile. / Ras-associating (RA) domain / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Rho GTPase activation protein / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / PH domain / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Chem-4PT / Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsZhang, Y.J. / Liu, Y.R. / Wu, B.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Int J Mol Sci / Year: 2023
Title: Structural Insights Uncover the Specific Phosphoinositide Recognition by the PH1 Domain of Arap3.
Authors: Zhang, Y. / Ge, L. / Xu, L. / Liu, Y. / Wang, J. / Liu, C. / Zhao, H. / Xing, L. / Wang, J. / Wu, B.
History
DepositionJul 18, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 3, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7732
Polymers13,0571
Non-polymers7161
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.154, 74.154, 109.850
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 3 / Centaurin-delta-3 / Cnt-d3


Mass: 13056.944 Da / Num. of mol.: 1 / Fragment: PH1 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARAP3, CENTD3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8WWN8
#2: Chemical ChemComp-4PT / (2R)-3-{[(S)-{[(2S,3R,5S,6S)-2,6-DIHYDROXY-3,4,5-TRIS(PHOSPHONOOXY)CYCLOHEXYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-2-(1-HYDROXY BUTOXY)PROPYL BUTYRATE / DIC4-PHOSPHATIDYLINOSITOL(3,4,5)TRISPHOSPHATE


Mass: 716.350 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H36O22P4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 3.34 Å3/Da / Density % sol: 63.16 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Ammonium sulfate, 0.1 M Sodium acetate trihydrate (pH 4.6), 30% v/v Polyethylene glycol 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9798 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 3.297→50 Å / Num. obs: 3029 / % possible obs: 100 % / Redundancy: 9.6 % / Biso Wilson estimate: 63.73 Å2 / Rmerge(I) obs: 0.196 / Net I/σ(I): 16
Reflection shellResolution: 3.297→3.36 Å / Rmerge(I) obs: 0.487 / Num. unique obs: 146

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Processing

Software
NameVersionClassification
PHENIX1.19.2-4158refinement
SCALAdata scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FAO

1fao


Resolution: 3.3→32.11 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 17.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.276 251 9.53 %
Rwork0.2244 2382 -
obs0.2292 2633 87.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 127.48 Å2 / Biso mean: 57.3664 Å2 / Biso min: 30.16 Å2
Refinement stepCycle: final / Resolution: 3.3→32.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms795 0 43 0 838
Biso mean--61.53 --
Num. residues----98
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.3-4.150.31081180.25111167128589
4.15-32.110.25581330.20821215134887
Refinement TLS params.Method: refined / Origin x: 30.7448 Å / Origin y: -11.955 Å / Origin z: 3.5196 Å
111213212223313233
T0.2314 Å20.0438 Å20.0124 Å2-0.2553 Å2-0.022 Å2--0.4372 Å2
L4.6433 °21.1065 °20.7992 °2-6.6578 °21.0641 °2--6.6257 °2
S-0.2046 Å °0.2714 Å °0.2071 Å °0.1961 Å °0.5715 Å °-0.1924 Å °-0.05 Å °0.0109 Å °-0.3452 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 286 through 383)

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