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- PDB-1ksj: Complex of Arl2 and PDE delta, Crystal Form 2 (SeMet) -

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Basic information

Entry
Database: PDB / ID: 1ksj
TitleComplex of Arl2 and PDE delta, Crystal Form 2 (SeMet)
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 / acetylcholine transport / ARL13B-mediated ciliary trafficking of INPP5E / RAS processing / GTPase inhibitor activity / bicellular tight junction assembly / maintenance of protein location in nucleus / response to stimulus / positive regulation of cell-substrate adhesion / centrosome cycle ...Transport of nucleosides and free purine and pyrimidine bases across the plasma membrane / acetylcholine transport / ARL13B-mediated ciliary trafficking of INPP5E / RAS processing / GTPase inhibitor activity / bicellular tight junction assembly / maintenance of protein location in nucleus / response to stimulus / positive regulation of cell-substrate adhesion / centrosome cycle / negative regulation of GTPase activity / 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 / cilium / small GTPase binding / RAS processing / GDP binding / microtubule cytoskeleton / protein folding / cytoplasmic vesicle / cytoskeleton / focal adhesion / GTPase activity / centrosome / GTP binding / nucleolus / Golgi apparatus / mitochondrion / nucleoplasm / nucleus / cytosol / cytoplasm
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 family 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 family 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 / Rab subfamily of small GTPases / Distorted Sandwich / Small GTP-binding protein domain / Immunoglobulin E-set / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / PHOSPHATE ION / 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: 2.6 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 11, 2017Group: Refinement description / Category: software
Revision 1.4Oct 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_alt_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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.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 1.5Apr 3, 2024Group: 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)40,3577
Polymers39,1932
Non-polymers1,1645
Water1,892105
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.815, 65.726, 103.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121
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

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Protein , 2 types, 2 molecules AB

#1: Protein arf-like protein 2


Mass: 21297.752 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 / E.C.3.1.4.17 / GMP-PDE DELTA / P17 PROTEIN


Mass: 17895.719 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

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Non-polymers , 6 types, 110 molecules

#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#6: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#7: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


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


Mass: 18.015 Da / Num. of mol.: 105 / 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: 1.9 Å3/Da / Density % sol: 36 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 5000 MME, HEPES, MgCl2, beta mercaptoethanol, GTP, PEG 400 as cryo protectant, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.964 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 9, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.964 Å / Relative weight: 1
ReflectionResolution: 2.6→19.8 Å / Num. all: 9926 / Num. obs: 9926 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.7 % / Biso Wilson estimate: 56 Å2 / Rsym value: 0.081 / Net I/σ(I): 25.1
Reflection shellResolution: 2.6→2.65 Å / Redundancy: 9.6 % / Mean I/σ(I) obs: 7 / Num. unique all: 558 / Rsym value: 0.391 / % possible all: 100

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
ARP/wARPmodel building
SHARP(SAD PHASING)phasing
BUSTERrefinement
BETAVERSIONrefinement
RefinementMethod to determine structure: combination of Molecular Replacement, SAD phasing
Starting model: human Arf1-GppNHp, N-terminally truncated by 17 residues (J. Goldberg, Cell. 95:237-248, 1998)

Resolution: 2.6→19.8 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.264 953 9.6 %RANDOM
Rwork0.209 ---
all0.214 9910 --
obs0.214 9910 --
Displacement parametersBiso mean: 43.6 Å2
Refine analyze
ObsFree
Luzzati coordinate error0.227 Å-
Luzzati sigma a-0.021 Å0.00057 Å
Refinement stepCycle: LAST / Resolution: 2.6→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2482 0 70 105 2657
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_angle_deg0.9
X-RAY DIFFRACTIONo_bond_d0.007
LS refinement shellResolution: 2.6→2.76 Å
RfactorNum. reflection
Rfree0.358 141
Rwork0.232 1564
obs-1714

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