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- PDB-3lju: Crystal structure of full length centaurin alpha-1 bound with the... -

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Basic information

Entry
Database: PDB / ID: 3lju
TitleCrystal structure of full length centaurin alpha-1 bound with the head group of PIP3
ComponentsArf-GAP with dual PH domain-containing protein 1
KeywordsHYDROLASE ACTIVATOR / Structural Genomics Consortium / GAP / GTPase activation / SGC / Metal-binding / Nucleus / Phosphoprotein / Zinc-finger
Function / homology
Function and homology information


inositol 1,3,4,5 tetrakisphosphate binding / phosphatidylinositol bisphosphate binding / regulation of GTPase activity / phosphatidylinositol-3,4,5-trisphosphate binding / Nuclear signaling by ERBB4 / GTPase activator activity / cell surface receptor signaling pathway / intracellular membrane-bounded organelle / metal ion binding / nucleus ...inositol 1,3,4,5 tetrakisphosphate binding / phosphatidylinositol bisphosphate binding / regulation of GTPase activity / phosphatidylinositol-3,4,5-trisphosphate binding / Nuclear signaling by ERBB4 / GTPase activator activity / cell surface receptor signaling pathway / intracellular membrane-bounded organelle / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
ADAP, PH domain 1 / ADAP, PH domain 2 / Arf GTPase activating protein / 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 / Annexin V; domain 1 ...ADAP, PH domain 1 / ADAP, PH domain 2 / Arf GTPase activating protein / 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 / Annexin V; domain 1 / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / Roll / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Chem-IP9 / Arf-GAP with dual PH domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.702 Å
AuthorsShen, L. / Tong, Y. / Tempel, W. / MacKenzie, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Phosphorylation-independent dual-site binding of the FHA domain of KIF13 mediates phosphoinositide transport via centaurin alpha1.
Authors: Tong, Y. / Tempel, W. / Wang, H. / Yamada, K. / Shen, L. / Senisterra, G.A. / MacKenzie, F. / Chishti, A.H. / Park, H.W.
History
DepositionJan 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_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
X: Arf-GAP with dual PH domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7184
Polymers45,0001
Non-polymers1,7193
Water5,296294
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.727, 66.414, 127.219
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Arf-GAP with dual PH domain-containing protein 1 / Centaurin-alpha-1 / Cnt-a1 / Putative MAPK-activating protein PM25


Mass: 44999.777 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADAP1, CENTA1 / Plasmid: pET28-mhl (GI:134105571) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: O75689
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-IP9 / (2R)-3-{[(R)-{[(1S,2S,3R,4S,5S,6S)-2,6-dihydroxy-3,4,5-tris(phosphonooxy)cyclohexyl]oxy}(hydroxy)phosphoryl]oxy}propane -1,2-diyl dioctanoate / L-a-Phosphatidyl-D-myo-inositol 3,4,5-triphosphate, dioctanoyl / [(2R)-3-[[(2S,3S,5R,6S)-2,6-dihydroxy-3,4,5-triphosphonooxy-cyclohexyl]oxy-hydroxy-phosphoryl]oxy-2-octanoyloxy-propyl] octanoate


Mass: 826.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H50O22P4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 294 / 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: 2.5 Å3/Da / Density % sol: 50.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 20% PEG3350, 0.2M ammonium chloride. Protein buffer: 0.02M HEPES pH 7.3, 0.3M sodium chloride, 0.001M TCEP, 5% glyccerol, 2.0mg/mL L-alpha-Phosphatidyl-D-myo-inositol 3,4,5-triphosphate, ...Details: 20% PEG3350, 0.2M ammonium chloride. Protein buffer: 0.02M HEPES pH 7.3, 0.3M sodium chloride, 0.001M TCEP, 5% glyccerol, 2.0mg/mL L-alpha-Phosphatidyl-D-myo-inositol 3,4,5-triphosphate, dioctanoyl, from SIGMA, catalog no. P9953, vapor diffusion, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 11, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 48266 / % possible obs: 98.8 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.108 / Χ2: 1.938 / Net I/σ(I): 9.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.7-1.732.80.47623380.55297.3
1.73-1.763.30.45223500.59898.2
1.76-1.794.10.39323990.63499.1
1.79-1.834.40.35723890.67399.3
1.83-1.874.40.31923920.68899.6
1.87-1.914.40.28723950.91699.3
1.91-1.964.40.2423950.93199.4
1.96-2.024.40.20424081.0799.5
2.02-2.074.40.18324111.33299.5
2.07-2.144.50.15624131.40499.5
2.14-2.224.50.14424121.57799.5
2.22-2.314.50.14124081.80699.6
2.31-2.414.50.12324211.80999.5
2.41-2.544.60.11524502.18999.7
2.54-2.74.60.10624192.33499.6
2.7-2.914.50.09624502.94399.4
2.91-3.24.40.09124433.81199.3
3.2-3.664.30.07724594.63898.4
3.66-4.614.20.06324554.29697.8
4.61-504.40.05524593.2592.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.5.0102refinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3FEH

3feh


Resolution: 1.702→20 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.918 / WRfactor Rfree: 0.219 / WRfactor Rwork: 0.182 / SU B: 2.029 / SU ML: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.109 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: REFINED INDIVIDUALLY. The programs coot and PRODRG and MOLPROBITY servers were also used during refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.231 2437 5.056 %RANDOM
Rwork0.191 ---
obs0.193 48202 98.714 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 13.169 Å2
Baniso -1Baniso -2Baniso -3
1--0.767 Å20 Å20 Å2
2--0.176 Å20 Å2
3---0.591 Å2
Refinement stepCycle: LAST / Resolution: 1.702→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3036 0 53 294 3383
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223215
X-RAY DIFFRACTIONr_bond_other_d0.0010.022284
X-RAY DIFFRACTIONr_angle_refined_deg1.4741.9574366
X-RAY DIFFRACTIONr_angle_other_deg0.8623.0015453
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0675381
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.74822.289166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.40115521
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.1481533
X-RAY DIFFRACTIONr_chiral_restr0.1060.2445
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213566
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02743
X-RAY DIFFRACTIONr_mcbond_it2.41421875
X-RAY DIFFRACTIONr_mcbond_other0.8162753
X-RAY DIFFRACTIONr_mcangle_it3.53733009
X-RAY DIFFRACTIONr_scbond_it3.05821340
X-RAY DIFFRACTIONr_scangle_it4.58531352
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.702-1.7460.3211770.2533185352695.349
1.746-1.7930.2811810.213254347398.906
1.793-1.8450.2331580.1823168334599.432
1.845-1.9010.241500.1933092326199.417
1.901-1.9630.2151650.1962972315799.366
1.963-2.0310.2581440.1862908307099.414
2.031-2.1070.2491580.1922799296799.663
2.107-2.1920.2071660.1872677285799.51
2.192-2.2880.241330.1872614276199.493
2.288-2.3980.1891360.1832480262899.543
2.398-2.5260.2341360.1852367251399.602
2.526-2.6770.231100.1912281240099.625
2.677-2.8580.2291210.1932119225099.556
2.858-3.0810.251970.211990210099.381
3.081-3.3680.252950.2091839195099.179
3.368-3.7520.228850.1921665178598.039
3.752-4.3070.184770.1631488159797.996
4.307-5.2150.187730.1581275137198.322
5.215-7.1360.29480.1971027110197.639
7.136-200.259270.2356571882.451

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