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- PDB-1ksg: Complex of Arl2 and PDE delta, Crystal Form 1 -

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Basic information

Entry
Database: PDB / ID: 1ksg
TitleComplex of Arl2 and PDE delta, Crystal Form 1
Components
  • RETINAL ROD RHODOPSIN-SENSITIVE CGMP 3',5'-CYCLIC PHOSPHODIESTERASE DELTA-SUBUNIT
  • arf-like protein 2
KeywordsSIGNALING PROTEIN/HYDROLASE / small GTPase / small GTP-binding protein / Arf family / effector molecule / immunoglobuline-like fold / GDI / SIGNALING PROTEIN-HYDROLASE COMPLEX
Function / homology
Function and homology information


Transport of nucleosides and free purine and pyrimidine bases across the plasma membrane / ARL13B-mediated ciliary trafficking of INPP5E / RAS processing / GTPase inhibitor activity / negative regulation of GTPase activity / bicellular tight junction assembly / maintenance of protein location in nucleus / centrosome cycle / positive regulation of cell-substrate adhesion / regulation of glycolytic process ...Transport of nucleosides and free purine and pyrimidine bases across the plasma membrane / ARL13B-mediated ciliary trafficking of INPP5E / RAS processing / GTPase inhibitor activity / negative regulation of GTPase activity / bicellular tight junction assembly / maintenance of protein location in nucleus / centrosome cycle / positive regulation of cell-substrate adhesion / regulation of glycolytic process / regulation of aerobic respiration / regulation of microtubule polymerization / lateral plasma membrane / positive regulation of microtubule polymerization / visual perception / cytoplasmic vesicle membrane / mitochondrial intermembrane space / small GTPase binding / RAS processing / GDP binding / cytoplasmic vesicle / cytoskeleton / cilium / ciliary basal body / intracellular membrane-bounded organelle / GTPase activity / centrosome / GTP binding / nucleolus / mitochondrion / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
ADP-ribosylation factor-like protein 2 / ADP-ribosylation factor-like protein 2/3 / GMP phosphodiesterase, delta subunit / Retinal rod rhodopsin-sensitive cGMP 3', 5'-cyclic phosphodiesterase, delta subunit / GMP phosphodiesterase, delta subunit / GMP phosphodiesterase, delta subunit superfamily / GMP-PDE, delta subunit / Small GTPase Arf domain profile. / Coagulation Factor XIII; Chain A, domain 1 / Sar1p-like members of the Ras-family of small GTPases ...ADP-ribosylation factor-like protein 2 / ADP-ribosylation factor-like protein 2/3 / GMP phosphodiesterase, delta subunit / Retinal rod rhodopsin-sensitive cGMP 3', 5'-cyclic phosphodiesterase, delta subunit / GMP phosphodiesterase, delta subunit / GMP phosphodiesterase, delta subunit superfamily / GMP-PDE, delta subunit / Small GTPase Arf domain profile. / Coagulation Factor XIII; Chain A, 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 / Distorted Sandwich / Rab subfamily of small GTPases / Small GTP-binding protein domain / Immunoglobulin E-set / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta / ADP-ribosylation factor-like protein 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / combination of Molecular Replacement, SAD phasing / Resolution: 2.3 Å
AuthorsHanzal-Bayer, M. / Renault, L. / Roversi, P. / Wittinghofer, A. / Hillig, R.C.
Citation
Journal: EMBO J. / Year: 2002
Title: The complex of Arl2-GTP and PDE delta: from structure to function.
Authors: Hanzal-Bayer, M. / Renault, L. / Roversi, P. / Wittinghofer, A. / Hillig, R.C.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Coexpression, copurification, crystallization and preliminary X-ray analysis of a complex of Arl2-GTP and PDE delta
Authors: Renault, L. / Hanzal-Bayer, M. / Hillig, R.C.
#2: Journal: Structure / Year: 2000
Title: Structural and biochemical properties show Arl3-GDP as a distinct GTP-binding protein
Authors: Hillig, R.C. / Hanzal-Bayer, M. / Linari, M. / Becker, J. / Wittinghofer, A. / Renault, L.
#3: Journal: FEBS Lett. / Year: 1999
Title: The delta subunit of rod specific cyclic GMP phosphodiesterase, PDE delta, interacts with the Arf-like protein Arl3 in a GTP specific manner
Authors: Linari, M. / Hanzal-Bayer, M. / Becker, J.
History
DepositionJan 13, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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_conn.ptnr2_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
Revision 1.4Aug 16, 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

Downloads & links

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Assembly

Deposited unit
A: arf-like protein 2
B: RETINAL ROD RHODOPSIN-SENSITIVE CGMP 3',5'-CYCLIC PHOSPHODIESTERASE DELTA-SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1674
Polymers38,6192
Non-polymers5472
Water1,02757
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.100, 45.700, 74.700
Angle α, β, γ (deg.)90.00, 94.00, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe deposited coordinates represent the biological assembly (consisting of one Arl2 molecule (bound to GDP/PO4) and one PDE delta molecule)

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Components

#1: Protein arf-like protein 2


Mass: 21034.053 Da / Num. of mol.: 1 / Mutation: S33L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: ARL2 / Plasmid: pGEX KG / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: Q9D0J4
#2: Protein RETINAL ROD RHODOPSIN-SENSITIVE CGMP 3',5'-CYCLIC PHOSPHODIESTERASE DELTA-SUBUNIT / GMP-PDE DELTA / P17 PROTEIN


Mass: 17585.121 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDE6D or PDED / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): B834
References: UniProt: O43924, 3',5'-cyclic-nucleotide phosphodiesterase
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.1 Å3/Da / Density % sol: 40.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 5000 MME, HEPES, MgCl2, beta mercaptoethanol, GTP, glycerol as cryo protectant, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Details: Renault, L., (2001) Acta Crystallogr., Sect.D, 57, 1167.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
19-12 %PEG5000 MME1reservoir
20.1 MHEPES1reservoirpH7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.782 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 21, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.782 Å / Relative weight: 1
ReflectionResolution: 2.3→19.7 Å / Num. all: 14251 / Num. obs: 14251 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 27.9 Å2 / Rsym value: 0.065 / Net I/σ(I): 14.8
Reflection shellResolution: 2.3→2.35 Å / Redundancy: 3 % / Mean I/σ(I) obs: 5.8 / Rsym value: 0.235 / % possible all: 99.7
Reflection
*PLUS
Rmerge(I) obs: 0.065
Reflection shell
*PLUS
Highest resolution: 2.3 Å / % possible obs: 99.7 % / Rmerge(I) obs: 0.235

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Processing

Software
NameVersionClassification
AMoREphasing
ARP/wARPmodel building
SHARP(SAD PHASING)phasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: combination of Molecular Replacement, SAD phasing
Starting model: ARL3-GDP, pdb entry 1fzq

1fzq


Resolution: 2.3→19.73 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 901500.34 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.301 1406 9.9 %RANDOM
Rwork0.255 ---
all0.26 14238 --
obs0.26 14238 97.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.5746 Å2 / ksol: 0.369833 e/Å3
Displacement parametersBiso mean: 45.1 Å2
Baniso -1Baniso -2Baniso -3
1-7.91 Å20 Å25.12 Å2
2---3.48 Å20 Å2
3----4.42 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.46 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.3→19.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2507 0 33 57 2597
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.12
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.39 250 10.5 %
Rwork0.314 2137 -
obs--99.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAM
X-RAY DIFFRACTION3GTP.PARAM
X-RAY DIFFRACTION4WATER_REP.PARAM
Refinement
*PLUS
Lowest resolution: 19.7 Å / % reflection Rfree: 10 % / Rfactor all: 0.26 / Rfactor obs: 0.255 / Rfactor Rfree: 0.301 / Rfactor Rwork: 0.255
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.12
LS refinement shell
*PLUS
Highest resolution: 2.3 Å / Rfactor Rfree: 0.39 / Rfactor Rwork: 0.314 / Rfactor obs: 0.314

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