[English] 日本語
Yorodumi
- PDB-4j6s: 14-3-3gamma complexed with the N-terminal sequence of tyrosine hy... -

+
Open data


ID or keywords:

Loading...

-
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 / isoquinoline alkaloid metabolic process / terpene 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 / isoquinoline alkaloid metabolic process / terpene metabolic process / norepinephrine biosynthetic process / embryonic camera-type eye morphogenesis / circadian sleep/wake cycle / epinephrine biosynthetic process / Catecholamine biosynthesis / hyaloid vascular plexus regression / response to pyrethroid / aminergic neurotransmitter loading into synaptic vesicle / dopamine binding / positive regulation of cell-cell adhesion / response to isolation stress / eye photoreceptor cell development / phosphorylation-dependent protein binding / sphingolipid metabolic process / response to ether / melanosome membrane / positive regulation of T cell mediated immune response to tumor cell / synaptic transmission, dopaminergic / tetrahydrobiopterin binding / response to herbicide / mating behavior / regulation of neuron differentiation / dopamine biosynthetic process / response to corticosterone / pigmentation / response to zinc ion / eating behavior / cellular response to alkaloid / amino acid binding / protein kinase C inhibitor activity / regulation of heart contraction / social behavior / response to immobilization stress / Regulation of localization of FOXO transcription factors / response to light stimulus / anatomical structure morphogenesis / Activation of BAD and translocation to mitochondria / cellular response to manganese ion / regulation of signal transduction / smooth endoplasmic reticulum / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / protein targeting / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / response to electrical stimulus / heart morphogenesis / cellular response to glucose starvation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / negative regulation of TORC1 signaling / insulin-like growth factor receptor binding / response to salt stress / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / visual perception / Transcriptional and post-translational regulation of MITF-M expression and activity / Recruitment of mitotic centrosome proteins and complexes / response to amphetamine / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / ferric iron binding / protein sequestering activity / AURKA Activation by TPX2 / protein kinase C binding / learning / animal organ morphogenesis / negative regulation of protein kinase activity / response to activity / fatty acid metabolic process / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / locomotory behavior / response to nutrient levels / cellular response to glucose stimulus / ferrous iron binding / terminal bouton / cellular response to growth factor stimulus / cerebral cortex development / regulation of synaptic plasticity / receptor tyrosine kinase binding / oxygen binding / memory / response to peptide hormone / positive regulation of T cell activation / cellular response to nicotine / cytoplasmic side of plasma membrane / cellular response to insulin stimulus / Regulation of PLK1 Activity at G2/M Transition / intracellular protein localization / synaptic vesicle / cellular response to xenobiotic stimulus / response to estradiol / presynapse
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
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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
Has protein modificationY
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more