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- PDB-4j6s: 14-3-3gamma complexed with the N-terminal sequence of tyrosine hy... -

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Basic information

Entry
Database: PDB / ID: 4j6s
Title14-3-3gamma complexed with the N-terminal sequence of tyrosine hydroxylase (residues 1-43)
Components
  • 14-3-3 protein gamma
  • N-terminal motif of tyrosine hydroxylase
KeywordsHYDROLASE / 14-3-3 proteins / peptide binding / Dopamine synthesis / signal transduction / regulatory proteins / tyrosine hydroxylase / phosphorylation
Function / homology
Function and homology information


tyrosine 3-monooxygenase / tyrosine 3-monooxygenase activity / phytoalexin metabolic process / dopamine biosynthetic process from tyrosine / phthalate metabolic process / glycoside metabolic process / terpene metabolic process / isoquinoline alkaloid metabolic process / norepinephrine biosynthetic process / embryonic camera-type eye morphogenesis ...tyrosine 3-monooxygenase / tyrosine 3-monooxygenase activity / phytoalexin metabolic process / dopamine biosynthetic process from tyrosine / phthalate metabolic process / glycoside metabolic process / terpene metabolic process / isoquinoline alkaloid metabolic process / norepinephrine biosynthetic process / embryonic camera-type eye morphogenesis / hyaloid vascular plexus regression / epinephrine biosynthetic process / circadian sleep/wake cycle / Catecholamine biosynthesis / aminergic neurotransmitter loading into synaptic vesicle / dopamine binding / response to pyrethroid / eye photoreceptor cell development / response to isolation stress / melanosome membrane / sphingolipid metabolic process / response to ether / synaptic transmission, dopaminergic / tetrahydrobiopterin binding / response to herbicide / mating behavior / dopamine biosynthetic process / regulation of neuron differentiation / amino acid binding / regulation of heart contraction / eating behavior / pigmentation / response to corticosterone / response to zinc ion / protein kinase C inhibitor activity / cellular response to alkaloid / social behavior / Regulation of localization of FOXO transcription factors / response to immobilization stress / phosphoserine residue binding / smooth endoplasmic reticulum / Activation of BAD and translocation to mitochondria / response to light stimulus / regulation of signal transduction / anatomical structure morphogenesis / cellular response to manganese ion / protein targeting / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / cellular response to glucose starvation / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / response to electrical stimulus / heart morphogenesis / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / negative regulation of TORC1 signaling / Recruitment of NuMA to mitotic centrosomes / response to salt stress / Anchoring of the basal body to the plasma membrane / protein sequestering activity / response to amphetamine / visual perception / AURKA Activation by TPX2 / response to nutrient levels / ferric iron binding / fatty acid metabolic process / learning / response to activity / locomotory behavior / Translocation of SLC2A4 (GLUT4) to the plasma membrane / cellular response to glucose stimulus / TP53 Regulates Metabolic Genes / protein kinase C binding / animal organ morphogenesis / insulin-like growth factor receptor binding / negative regulation of protein kinase activity / regulation of synaptic plasticity / ferrous iron binding / terminal bouton / cytoplasmic side of plasma membrane / receptor tyrosine kinase binding / cerebral cortex development / memory / cellular response to growth factor stimulus / response to peptide hormone / oxygen binding / cellular response to nicotine / cellular response to insulin stimulus / Regulation of PLK1 Activity at G2/M Transition / cellular response to xenobiotic stimulus / synaptic vesicle / presynapse / response to estradiol / heart development / cytoplasmic vesicle / perikaryon / response to ethanol / response to lipopolysaccharide
Similarity search - Function
Tyrosine 3-monooxygenase / Tyrosine hydroxylase, conserved site / Tyrosine 3-monooxygenase, catalytic domain / : / Tyrosine hydroxylase N terminal / Tyrosine 3-monooxygenase-like, ACT domain / Tyrosine 3-monooxygenase-like / Aromatic amino acid hydroxylase, iron/copper binding site / Biopterin-dependent aromatic amino acid hydroxylases signature. / Aromatic amino acid hydroxylase ...Tyrosine 3-monooxygenase / Tyrosine hydroxylase, conserved site / Tyrosine 3-monooxygenase, catalytic domain / : / Tyrosine hydroxylase N terminal / Tyrosine 3-monooxygenase-like, ACT domain / Tyrosine 3-monooxygenase-like / Aromatic amino acid hydroxylase, iron/copper binding site / Biopterin-dependent aromatic amino acid hydroxylases signature. / Aromatic amino acid hydroxylase / Aromatic amino acid hydroxylase, C-terminal / Aromatic amino acid monoxygenase, C-terminal domain superfamily / Aromatic amino acid hydroxylase superfamily / Biopterin-dependent aromatic amino acid hydroxylase / Biopterin-dependent aromatic amino acid hydroxylase family profile. / ACT-like domain / 14-3-3 domain / Delta-Endotoxin; domain 1 / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily / 14-3-3 protein / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Tyrosine 3-monooxygenase / 14-3-3 protein gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.08 Å
AuthorsMileni, M. / Martinez, A. / Stevens, R.C.
CitationJournal: J.Mol.Biol. / Year: 2014
Title: The N-terminal sequence of tyrosine hydroxylase is a conformationally versatile motif that binds 14-3-3 proteins and membranes.
Authors: Skjevik, A.A. / Mileni, M. / Baumann, A. / Halskau, O. / Teigen, K. / Stevens, R.C. / Martinez, A.
History
DepositionFeb 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2014Group: Database references
Revision 1.2Apr 21, 2021Group: Database references / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / struct_conn / struct_ref_seq_dif
Item: _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Sep 20, 2023Group: 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

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Assembly

Deposited unit
A: 14-3-3 protein gamma
B: 14-3-3 protein gamma
C: 14-3-3 protein gamma
D: 14-3-3 protein gamma
E: N-terminal motif of tyrosine hydroxylase
F: N-terminal motif of tyrosine hydroxylase
G: N-terminal motif of tyrosine hydroxylase
H: N-terminal motif of tyrosine hydroxylase


Theoretical massNumber of molelcules
Total (without water)136,1008
Polymers136,1008
Non-polymers00
Water00
1
A: 14-3-3 protein gamma
B: 14-3-3 protein gamma
E: N-terminal motif of tyrosine hydroxylase
F: N-terminal motif of tyrosine hydroxylase


Theoretical massNumber of molelcules
Total (without water)68,0504
Polymers68,0504
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 14-3-3 protein gamma
D: 14-3-3 protein gamma
G: N-terminal motif of tyrosine hydroxylase
H: N-terminal motif of tyrosine hydroxylase


Theoretical massNumber of molelcules
Total (without water)68,0504
Polymers68,0504
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.190, 115.120, 136.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.969915, -0.173886, 0.170376), (-0.169959, -0.984738, -0.037484), (0.174294, 0.0074, -0.984666)2.45011, -5.52172, -28.90455
3given(-0.991492, -0.038446, -0.124363), (-0.113003, -0.219996, 0.968933), (-0.064611, 0.974743, 0.21378)-47.99815, 5.6204, -8.37577
4given(-0.966844, 0.142667, -0.2118), (0.238886, 0.21214, -0.947592), (-0.090259, -0.966769, -0.239187)-46.93277, -3.89462, -28.48492

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Components

#1: Protein
14-3-3 protein gamma / Protein kinase C inhibitor protein 1 / KCIP-1 / 14-3-3 protein gamma / N-terminally processed


Mass: 29165.545 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YWHAG / Production host: Escherichia coli (E. coli) / References: UniProt: P61981
#2: Protein/peptide
N-terminal motif of tyrosine hydroxylase / Tyrosine 3-hydroxylase / TH


Mass: 4859.459 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P07101*PLUS, tyrosine 3-monooxygenase
Sequence detailsTHE CRYSTALLIZED SEQUENCE CORRESPONDING TO TYROSINE 3-MONOOXYGENASE REPRESENTS THE SPLICING-ISOFORM ...THE CRYSTALLIZED SEQUENCE CORRESPONDING TO TYROSINE 3-MONOOXYGENASE REPRESENTS THE SPLICING-ISOFORM TH1. THIS FORM IS THE MOST ABUNDANT IN BRAIN AND IS THE ONE USED FOR THE CURRENT WORK. THE CLOSEST DATABASE REFERENCE ACCESSION CODE IS THE UNPROT ENTRY P07101-3

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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: 2.44 Å3/Da / Density % sol: 49.53 %
Crystal growTemperature: 283 K / Method: vapor diffusion / pH: 7.1
Details: 30% PEG 2000 MME, 0.1M Potassium Thiocyanate, pH 7.1, VAPOR DIFFUSION, temperature 283.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0331 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 15, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0331 Å / Relative weight: 1
ReflectionResolution: 3.08→30 Å / Num. all: 22015 / Num. obs: 111792 / % possible obs: 87.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.1 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 11.6
Reflection shellResolution: 3.08→3.16 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.492 / Mean I/σ(I) obs: 3.29 / Num. unique all: 1656 / % possible all: 90

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Processing

Software
NameVersionClassification
XDSpackagedata scaling
PHASERphasing
REFMAC5.7.0029refinement
XDSpackagedata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A4O

1a4o


Resolution: 3.08→29.9 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.899 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.514 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25377 1100 5 %RANDOM
Rwork0.21004 ---
obs0.21223 20915 86.95 %-
all-22015 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 68.709 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å2-0 Å2
2---0.51 Å20 Å2
3---0.44 Å2
Refinement stepCycle: LAST / Resolution: 3.08→29.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7970 0 0 0 7970
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0198078
X-RAY DIFFRACTIONr_bond_other_d00.027674
X-RAY DIFFRACTIONr_angle_refined_deg1.1921.97110901
X-RAY DIFFRACTIONr_angle_other_deg3.587317671
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0925982
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.46524.915413
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.284151513
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8521559
X-RAY DIFFRACTIONr_chiral_restr0.0620.21220
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029121
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021778
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.08→3.16 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 83 -
Rwork0.281 1565 -
obs--89.86 %

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