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- PDB-4gok: The Crystal structure of Arl2GppNHp in complex with UNC119a -

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Basic information

Entry
Database: PDB / ID: 4gok
TitleThe Crystal structure of Arl2GppNHp in complex with UNC119a
Components
  • ADP-ribosylation factor-like protein 2
  • Protein unc-119 homolog A
KeywordsSIGNALING PROTEIN / Small G proteins / Arl / Arf / GDI-like solubilizing factors / Cilia
Function / homology
Function and homology information


Transport of nucleosides and free purine and pyrimidine bases across the plasma membrane / negative regulation of caveolin-mediated endocytosis / negative regulation of clathrin-dependent endocytosis / RAS processing / 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 / negative regulation of caveolin-mediated endocytosis / negative regulation of clathrin-dependent endocytosis / RAS processing / 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 / lipoprotein transport / positive regulation of protein tyrosine kinase activity / spindle midzone / regulation of microtubule polymerization / mitotic cytokinesis / lateral plasma membrane / phototransduction / intercellular bridge / positive regulation of microtubule polymerization / visual perception / mitochondrial intermembrane space / endocytosis / spindle pole / GDP binding / nervous system development / chemical synaptic transmission / ciliary basal body / GTPase activity / synapse / lipid binding / 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 / 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 / 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
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Protein unc-119 homolog A / ADP-ribosylation factor-like protein 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsIsmail, S. / Xiang-Chen, Y. / Miertzschke, M. / Vetter, I. / Koerner, C. / Wittinghofer, A.
CitationJournal: Embo J. / Year: 2012
Title: Structural basis for Arl3-specific release of myristoylated ciliary cargo from UNC119.
Authors: Ismail, S.A. / Chen, Y.X. / Miertzschke, M. / Vetter, I.R. / Koerner, C. / Wittinghofer, A.
History
DepositionAug 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2012Group: Database references
Revision 1.2Sep 13, 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 / database_2 / pdbx_initial_refinement_model / 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_asym_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.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: ADP-ribosylation factor-like protein 2
G: Protein unc-119 homolog A
A: ADP-ribosylation factor-like protein 2
C: Protein unc-119 homolog A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,2318
Polymers92,1384
Non-polymers1,0934
Water25214
1
B: ADP-ribosylation factor-like protein 2
G: Protein unc-119 homolog A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6164
Polymers46,0692
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-23 kcal/mol
Surface area15340 Å2
MethodPISA
2
A: ADP-ribosylation factor-like protein 2
C: Protein unc-119 homolog A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6164
Polymers46,0692
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-23 kcal/mol
Surface area15350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.450, 61.080, 143.620
Angle α, β, γ (deg.)90.00, 101.33, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein ADP-ribosylation factor-like protein 2


Mass: 19072.695 Da / Num. of mol.: 2 / Mutation: Q70L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Arl2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9D0J4
#2: Protein Protein unc-119 homolog A / Retinal protein 4 / hRG4


Mass: 26996.385 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UNC119, RG4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13432
#3: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.37 Å3/Da / Density % sol: 48.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2% PEG400 and 2M Ammonium Sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 28, 2008
RadiationMonochromator: SAGITALLY - HORIZONTALLY FOCUSED SI(111) MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→29.85 Å / Num. all: 26616 / Num. obs: 26616 / % possible obs: 99.2 % / Redundancy: 3.98 % / Rmerge(I) obs: 0.219 / Net I/σ(I): 9.39
Reflection shellResolution: 2.6→2.65 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 3 / Num. unique all: 1462 / % possible all: 99.3

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Processing

Software
NameVersionClassification
XDSdata scaling
MOLREPphasing
REFMAC5.6.0093refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KSH, 3GQQ

1ksh

3gqq


Resolution: 2.6→29.85 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.904 / SU B: 10.871 / SU ML: 0.235 / Cross valid method: THROUGHOUT / ESU R: 0.713 / ESU R Free: 0.358 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.29697 1331 5 %RANDOM
Rwork0.24525 ---
obs0.24772 25284 99.25 %-
all-25284 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.741 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å20 Å20.09 Å2
2---0.4 Å20 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 2.6→29.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5154 0 66 14 5234
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0225334
X-RAY DIFFRACTIONr_angle_refined_deg1.7141.9697215
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.045627
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.85723.308263
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.45815913
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9091544
X-RAY DIFFRACTIONr_chiral_restr0.1090.2783
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214016
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 88 -
Rwork0.324 1751 -
obs--99.03 %

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