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- PDB-5l7k: The crystal structure of myristoylated NPHP3 peptide in complex w... -

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Basic information

Entry
Database: PDB / ID: 5l7k
TitleThe crystal structure of myristoylated NPHP3 peptide in complex with UNC119a
Components
  • GLY-THR-ALA-SER-SER-LEU
  • Protein unc-119 homolog A
KeywordsLIPID BINDING PROTEIN / Protein Transport / myristoylation / Beta-sandwish
Function / homology
Function and homology information


determination of intestine left/right asymmetry / determination of stomach left/right asymmetry / regulation of planar cell polarity pathway involved in neural tube closure / maintenance of animal organ identity / determination of pancreatic left/right asymmetry / ureter development / Trafficking of myristoylated proteins to the cilium / negative regulation of caveolin-mediated endocytosis / convergent extension involved in gastrulation / negative regulation of clathrin-dependent endocytosis ...determination of intestine left/right asymmetry / determination of stomach left/right asymmetry / regulation of planar cell polarity pathway involved in neural tube closure / maintenance of animal organ identity / determination of pancreatic left/right asymmetry / ureter development / Trafficking of myristoylated proteins to the cilium / negative regulation of caveolin-mediated endocytosis / convergent extension involved in gastrulation / negative regulation of clathrin-dependent endocytosis / regulation of Wnt signaling pathway, planar cell polarity pathway / epithelial cilium movement involved in determination of left/right asymmetry / kidney morphogenesis / determination of liver left/right asymmetry / atrial septum development / photoreceptor cell maintenance / determination of left/right symmetry / lipoprotein transport / intercellular bridge / heart looping / phototransduction / mitotic cytokinesis / cilium assembly / positive regulation of protein tyrosine kinase activity / spindle midzone / visual perception / kidney development / lung development / negative regulation of canonical Wnt signaling pathway / cilium / Wnt signaling pathway / spindle pole / endocytosis / nervous system development / chemical synaptic transmission / centrosome / lipid binding / synapse / extracellular region / cytosol
Similarity search - Function
GMP phosphodiesterase, delta subunit / GMP phosphodiesterase, delta subunit / GMP phosphodiesterase, delta subunit superfamily / GMP-PDE, delta subunit / Tetratricopeptide repeat / : / Coagulation Factor XIII; Chain A, domain 1 / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats ...GMP phosphodiesterase, delta subunit / GMP phosphodiesterase, delta subunit / GMP phosphodiesterase, delta subunit superfamily / GMP-PDE, delta subunit / Tetratricopeptide repeat / : / Coagulation Factor XIII; Chain A, domain 1 / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Distorted Sandwich / Tetratricopeptide-like helical domain superfamily / Immunoglobulin E-set / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
MYRISTIC ACID / Protein unc-119 homolog A / Nephrocystin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsFansa, E.K. / Jaiswal, M. / Wittinghofer, A.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Novel Biochemical and Structural Insights into the Interaction of Myristoylated Cargo with Unc119 Protein and Their Release by Arl2/3.
Authors: Jaiswal, M. / Fansa, E.K. / Kosling, S.K. / Mejuch, T. / Waldmann, H. / Wittinghofer, A.
History
DepositionJun 3, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein unc-119 homolog A
B: GLY-THR-ALA-SER-SER-LEU
G: Protein unc-119 homolog A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3134
Polymers43,0853
Non-polymers2281
Water84747
1
A: Protein unc-119 homolog A
B: GLY-THR-ALA-SER-SER-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0383
Polymers21,8102
Non-polymers2281
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-1 kcal/mol
Surface area8380 Å2
MethodPISA
2
G: Protein unc-119 homolog A


Theoretical massNumber of molelcules
Total (without water)21,2751
Polymers21,2751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.270, 88.270, 105.940
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41

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Components

#1: Protein Protein unc-119 homolog A / Retinal protein 4 / hRG4


Mass: 21275.129 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
#2: Protein/peptide GLY-THR-ALA-SER-SER-LEU


Mass: 534.562 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q7Z494*PLUS
#3: Chemical ChemComp-MYR / MYRISTIC ACID / Myristic acid


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2 / Source: (synth.) Homo sapiens (human)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.64 Å3/Da / Density % sol: 53.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 1.75 M (NH4)2SO4, 0.1 M CAPS (pH 10.0) and 0.2 M Li2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97862 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97862 Å / Relative weight: 1
ReflectionResolution: 2.1→28.35 Å / Num. obs: 22466 / % possible obs: 99.9 % / Redundancy: 11.3 % / Rmerge(I) obs: 0.123 / Net I/σ(I): 13.47
Reflection shellResolution: 2.1→2.2 Å / Rmerge(I) obs: 0.746

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.7.0032refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RBQ

3rbq


Resolution: 2.1→28.35 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.921 / SU B: 5.989 / SU ML: 0.159 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.229 / ESU R Free: 0.209
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2782 1183 5 %RANDOM
Rwork0.2157 ---
obs0.2188 22466 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 160.69 Å2 / Biso mean: 63.751 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å2-0 Å2-0 Å2
2---0.43 Å2-0 Å2
3---0.86 Å2
Refinement stepCycle: final / Resolution: 2.1→28.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2734 0 0 47 2781
Biso mean---50.27 -
Num. residues----328
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192812
X-RAY DIFFRACTIONr_bond_other_d0.0020.022607
X-RAY DIFFRACTIONr_angle_refined_deg1.4411.9533786
X-RAY DIFFRACTIONr_angle_other_deg0.843.0036001
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4395322
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.94423.026152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.95915474
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8951523
X-RAY DIFFRACTIONr_chiral_restr0.0890.2392
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213140
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02715
X-RAY DIFFRACTIONr_mcbond_it4.0376.191303
X-RAY DIFFRACTIONr_mcbond_other4.0316.1871302
X-RAY DIFFRACTIONr_mcangle_it6.0459.2621620
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 87 -
Rwork0.295 1660 -
all-1747 -
obs--100 %

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