[English] 日本語
Yorodumi
- EMDB-11309: Partial structure of tyrosine hydroxylase in complex with dopamin... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-11309
TitlePartial structure of tyrosine hydroxylase in complex with dopamine showing the catalytic domain and an alpha-helix from the regulatory domain involved in dopamine binding.
Map data
Sample
  • Complex: Tyrosine Hydroxylase
    • Protein or peptide: Tyrosine 3-monooxygenase
    • Protein or peptide: SER-LEU-ILE-GLU-ASP-ALA-ARG-LYS-GLU-ARG-GLU-ALA-ALA-VAL-ALA-ALA-ALA-ALA
  • Ligand: L-DOPAMINE
  • Ligand: FE (III) ION
KeywordsTetramer / Dopamine / Catecholamine / Brain / Parkinson / OXIDOREDUCTASE
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 / response to isolation stress / eye photoreceptor cell development / sphingolipid metabolic process / response to ether / melanosome membrane / synaptic transmission, dopaminergic / tetrahydrobiopterin binding / response to herbicide / mating behavior / dopamine biosynthetic process / response to corticosterone / pigmentation / response to zinc ion / eating behavior / cellular response to alkaloid / amino acid binding / regulation of heart contraction / social behavior / response to immobilization stress / response to light stimulus / anatomical structure morphogenesis / cellular response to manganese ion / smooth endoplasmic reticulum / response to electrical stimulus / heart morphogenesis / response to salt stress / visual perception / response to amphetamine / ferric iron binding / learning / animal organ morphogenesis / response to activity / fatty acid metabolic process / 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 / oxygen binding / memory / response to peptide hormone / cellular response to nicotine / cytoplasmic side of plasma membrane / synaptic vesicle / cellular response to xenobiotic stimulus / response to estradiol / heart development / cytoplasmic vesicle / perikaryon / response to lipopolysaccharide / response to ethanol / response to hypoxia / neuron projection / protein domain specific binding / axon / dendrite / perinuclear region of cytoplasm / enzyme binding / mitochondrion / identical protein binding / nucleus / cytosol / cytoplasm
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
Similarity search - Domain/homology
Tyrosine 3-monooxygenase
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsBueno-Carrasco MT / Cuellar J
Funding support Spain, 2 items
OrganizationGrant numberCountry
Research Council of NorwayFRIMEDBIO 261826 Spain
Spanish Ministry of Science, Innovation, and UniversitiesPID2019-105872GB-I00 Spain
CitationJournal: Nat Commun / Year: 2022
Title: Structural mechanism for tyrosine hydroxylase inhibition by dopamine and reactivation by Ser40 phosphorylation.
Authors: María Teresa Bueno-Carrasco / Jorge Cuéllar / Marte I Flydal / César Santiago / Trond-André Kråkenes / Rune Kleppe / José R López-Blanco / Miguel Marcilla / Knut Teigen / Sara Alvira ...Authors: María Teresa Bueno-Carrasco / Jorge Cuéllar / Marte I Flydal / César Santiago / Trond-André Kråkenes / Rune Kleppe / José R López-Blanco / Miguel Marcilla / Knut Teigen / Sara Alvira / Pablo Chacón / Aurora Martinez / José M Valpuesta /
Abstract: Tyrosine hydroxylase (TH) catalyzes the rate-limiting step in the biosynthesis of dopamine (DA) and other catecholamines, and its dysfunction leads to DA deficiency and parkinsonisms. Inhibition by ...Tyrosine hydroxylase (TH) catalyzes the rate-limiting step in the biosynthesis of dopamine (DA) and other catecholamines, and its dysfunction leads to DA deficiency and parkinsonisms. Inhibition by catecholamines and reactivation by S40 phosphorylation are key regulatory mechanisms of TH activity and conformational stability. We used Cryo-EM to determine the structures of full-length human TH without and with DA, and the structure of S40 phosphorylated TH, complemented with biophysical and biochemical characterizations and molecular dynamics simulations. TH presents a tetrameric structure with dimerized regulatory domains that are separated 15 Å from the catalytic domains. Upon DA binding, a 20-residue α-helix in the flexible N-terminal tail of the regulatory domain is fixed in the active site, blocking it, while S40-phosphorylation forces its egress. The structures reveal the molecular basis of the inhibitory and stabilizing effects of DA and its counteraction by S40-phosphorylation, key regulatory mechanisms for homeostasis of DA and TH.
History
DepositionJul 6, 2020-
Header (metadata) releaseDec 8, 2021-
Map releaseDec 8, 2021-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6zn2
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11309.png

Downloads & links

-
Map

FileDownload / File: emd_11309.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 180 pix.
= 189. Å		1.05 Å/pix.
x 180 pix.
= 189. Å		1.05 Å/pix.
x 180 pix.
= 189. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.076005965 - 0.1365582
Average (Standard dev.)0.00052892324 (±0.0005746861)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 188.99998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z189.000189.000189.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS180180180
D min/max/mean-0.0760.1370.001

-
Supplemental data

-
Half map: #2

Fileemd_11309_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_11309_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Tyrosine Hydroxylase

EntireName: Tyrosine Hydroxylase
Components
  • Complex: Tyrosine Hydroxylase
    • Protein or peptide: Tyrosine 3-monooxygenase
    • Protein or peptide: SER-LEU-ILE-GLU-ASP-ALA-ARG-LYS-GLU-ARG-GLU-ALA-ALA-VAL-ALA-ALA-ALA-ALA
  • Ligand: L-DOPAMINE
  • Ligand: FE (III) ION

-
Supramolecule #1: Tyrosine Hydroxylase

SupramoleculeName: Tyrosine Hydroxylase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Tyrosine 3-monooxygenase

MacromoleculeName: Tyrosine 3-monooxygenase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: tyrosine 3-monooxygenase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 38.087766 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: VPWFPRKVSE LDKCHHLVTK FDPDLDLDHP GFSDQVYRQR RKLIAEIAFQ YRHGDPIPRV EYTAEEIATW KEVYTTLKGL YATHACGEH LEAFALLERF SGYREDNIPQ LEDVSRFLKE RTGFQLRPVA GLLSARDFLA SLAFRVFQCT QYIRHASSPM H SPEPDCCH ...String:
VPWFPRKVSE LDKCHHLVTK FDPDLDLDHP GFSDQVYRQR RKLIAEIAFQ YRHGDPIPRV EYTAEEIATW KEVYTTLKGL YATHACGEH LEAFALLERF SGYREDNIPQ LEDVSRFLKE RTGFQLRPVA GLLSARDFLA SLAFRVFQCT QYIRHASSPM H SPEPDCCH ELLGHVPMLA DRTFAQFSQD IGLASLGASD EEIEKLSTLY WFTVEFGLCK QNGEVKAYGA GLLSSYGELL HC LSEEPEI RAFDPEAAAV QPYQDQTYQS VYFVSESFSD AKDKLRSYAS RIQRPFSVKF DPYTLAIDVL DSPQAVRRSL EGV QDELDT LAHALSAIG

UniProtKB: Tyrosine 3-monooxygenase

-
Macromolecule #2: SER-LEU-ILE-GLU-ASP-ALA-ARG-LYS-GLU-ARG-GLU-ALA-ALA-VAL-ALA-ALA-A...

MacromoleculeName: SER-LEU-ILE-GLU-ASP-ALA-ARG-LYS-GLU-ARG-GLU-ALA-ALA-VAL-ALA-ALA-ALA-ALA
type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.874081 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SLIEDARKER EAAVAAAA

-
Macromolecule #3: L-DOPAMINE

MacromoleculeName: L-DOPAMINE / type: ligand / ID: 3 / Number of copies: 4 / Formula: LDP
Molecular weightTheoretical: 153.178 Da
Chemical component information

ChemComp-LDP:
L-DOPAMINE / medication*YM

-
Macromolecule #4: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 4 / Number of copies: 4 / Formula: FE
Molecular weightTheoretical: 55.845 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 125033
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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