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- PDB-4goj: The Crystal Structure of full length Arl3GppNHp in complex with U... -

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Basic information

Entry
Database: PDB / ID: 4goj
TitleThe Crystal Structure of full length Arl3GppNHp in complex with UNC119a
Components
  • ADP-ribosylation factor-like protein 3
  • Protein unc-119 homolog A
KeywordsSIGNALING PROTEIN / Small G protein Arl / GDI-like solubilizing factors / Cilia
Function / homology
Function and homology information


Trafficking of myristoylated proteins to the cilium / negative regulation of caveolin-mediated endocytosis / photoreceptor cell development / negative regulation of clathrin-dependent endocytosis / protein localization to ciliary membrane / intraciliary transport / post-Golgi vesicle-mediated transport / ciliary transition zone / photoreceptor connecting cilium / Golgi to plasma membrane transport ...Trafficking of myristoylated proteins to the cilium / negative regulation of caveolin-mediated endocytosis / photoreceptor cell development / negative regulation of clathrin-dependent endocytosis / protein localization to ciliary membrane / intraciliary transport / post-Golgi vesicle-mediated transport / ciliary transition zone / photoreceptor connecting cilium / Golgi to plasma membrane transport / lipoprotein transport / smoothened signaling pathway / small GTPase-mediated signal transduction / positive regulation of protein tyrosine kinase activity / spindle midzone / mitotic cytokinesis / axoneme / cilium assembly / phototransduction / intercellular bridge / cytoplasmic microtubule / visual perception / spindle microtubule / kidney development / endocytosis / spindle pole / GDP binding / nervous system development / protein transport / midbody / microtubule binding / chemical synaptic transmission / cilium / ciliary basal body / Golgi membrane / GTPase activity / synapse / centrosome / lipid binding / GTP binding / magnesium ion binding / Golgi apparatus / nucleoplasm / nucleus / cytosol
Similarity search - Function
: / 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-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 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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_sheet / 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_sheet.number_strands / _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
A: ADP-ribosylation factor-like protein 3
B: ADP-ribosylation factor-like protein 3
C: Protein unc-119 homolog A
D: Protein unc-119 homolog A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,0258
Polymers96,9324
Non-polymers1,0934
Water3,135174
1
A: ADP-ribosylation factor-like protein 3
C: Protein unc-119 homolog A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0124
Polymers48,4662
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2780 Å2
ΔGint-18 kcal/mol
Surface area15700 Å2
MethodPISA
2
B: ADP-ribosylation factor-like protein 3
D: Protein unc-119 homolog A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0124
Polymers48,4662
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint-18 kcal/mol
Surface area15560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.750, 103.300, 119.890
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 ADP-ribosylation factor-like protein 3


Mass: 21469.496 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Arl3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WUL7
#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.: 174 / 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: 2.23 Å3/Da / Density % sol: 44.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 3.4 M Sodium Formate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 29, 2012
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: 2.1→29.97 Å / Num. all: 51107 / Num. obs: 51107 / % possible obs: 99.6 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 13.06
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 5.53 % / Rmerge(I) obs: 0.395 / Num. unique all: 6574 / Rsym value: 0.383 / % possible all: 99.7

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Processing

Software
NameVersionClassification
XDSdata scaling
MOLREPphasing
REFMAC5.6.0093refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BH6, 3GQQ

3bh6

3gqq


Resolution: 2.1→29.97 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.921 / SU B: 5.065 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.215 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24832 2556 5 %RANDOM
Rwork0.21357 ---
obs0.21533 48550 99.62 %-
all-48550 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.952 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20 Å20 Å2
2---0.53 Å20 Å2
3---0.14 Å2
Refinement stepCycle: LAST / Resolution: 2.1→29.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5453 0 66 174 5693
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0225661
X-RAY DIFFRACTIONr_angle_refined_deg1.1471.9717668
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.085673
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.38723.915281
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.51715991
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0661541
X-RAY DIFFRACTIONr_chiral_restr0.0820.2843
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214273
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 168 -
Rwork0.259 3294 -
obs--99.68 %

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