[English] 日本語
Yorodumi
- PDB-2mda: The Solution Structure of the Regulatory Domain of Tyrosine Hydro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2mda
TitleThe Solution Structure of the Regulatory Domain of Tyrosine Hydroxylase
ComponentsTyrosine 3-monooxygenase
KeywordsOXIDOREDUCTASE / Tyrosine hydroxylase / regulation / ACT domain
Function / homology
Function and homology information


Catecholamine biosynthesis / 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 / response to insecticide ...Catecholamine biosynthesis / 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 / response to insecticide / norepinephrine biosynthetic process / embryonic camera-type eye morphogenesis / hyaloid vascular plexus regression / epinephrine biosynthetic process / circadian sleep/wake cycle / aminergic neurotransmitter loading into synaptic vesicle / dopamine binding / catecholamine biosynthetic process / response to pyrethroid / eye photoreceptor cell development / response to isolation stress / melanosome membrane / sphingolipid metabolic process / response to ether / response to growth factor / synaptic transmission, dopaminergic / tetrahydrobiopterin binding / response to metal ion / response to herbicide / mating behavior / response to steroid hormone / dopamine biosynthetic process / amino acid binding / regulation of heart contraction / eating behavior / response to corticosterone / response to zinc ion / cellular response to alkaloid / social behavior / response to immobilization stress / smooth endoplasmic reticulum / response to light stimulus / small molecule binding / cellular response to manganese ion / response to electrical stimulus / response to salt stress / response to amphetamine / monooxygenase activity / visual perception / response to nutrient levels / ferric iron binding / fatty acid metabolic process / learning / response to activity / locomotory behavior / cellular response to glucose stimulus / animal organ morphogenesis / response to nicotine / cytoplasmic vesicle membrane / ferrous iron binding / response to organic cyclic compound / terminal bouton / cytoplasmic side of plasma membrane / cerebral cortex development / memory / cognition / cellular response to growth factor stimulus / response to peptide hormone / oxygen binding / cellular response to nicotine / cellular response to xenobiotic stimulus / synaptic vesicle / response to estradiol / heart development / cytoplasmic vesicle / perikaryon / response to ethanol / response to lipopolysaccharide / response to hypoxia / response to xenobiotic stimulus / neuron projection / protein domain specific binding / axon / neuronal cell body / dendrite / perinuclear region of cytoplasm / enzyme binding / mitochondrion / identical protein binding / nucleus / 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 domain / ACT-like domain / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Tyrosine 3-monooxygenase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / simulated annealing
AuthorsZhang, S. / Huang, T. / Hinck, A. / Fitzpatrick, P.
CitationJournal: J.Mol.Biol. / Year: 2014
Title: The solution structure of the regulatory domain of tyrosine hydroxylase.
Authors: Zhang, S. / Huang, T. / Ilangovan, U. / Hinck, A.P. / Fitzpatrick, P.F.
History
DepositionSep 8, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 1, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2014Group: Database references
Revision 1.2Mar 26, 2014Group: Database references
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tyrosine 3-monooxygenase
B: Tyrosine 3-monooxygenase


Theoretical massNumber of molelcules
Total (without water)20,9722
Polymers20,9722
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Tyrosine 3-monooxygenase / Tyrosine 3-hydroxylase / TH


Mass: 10485.864 Da / Num. of mol.: 2 / Fragment: Regulatory Domain (UNP residues 65-159)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Th / Plasmid: pETNTERM / Production host: Escherichia coli (E. coli) / References: UniProt: P04177

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-15N HSQC
1322D 1H-13C HSQC
1423D CBCA(CO)NH
1523D C(CO)NH
1623D HNCO
1723D HNCA
1823D HN(CA)CB
1923D HBHA(CO)NH
11023D HN(CO)CA
11123D H(CCO)NH
11223D (H)CCH-TOCSY
11323D HNHA
11413D 1H-15N NOESY
11533D 1H-15N NOESY
11623D 1H-13C NOESY
11742D IPAP-HSQC
1181T1
1191T2
1201Relax NOE

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.8 mM [U-95% 15N] RDTyrH65, 50 mM sodium phosphate, 95% H2O/5% D2O95% H2O/5% D2O
21.0-1.2 mM [U-95% 13C; U-95% 15N] RDTyrH65, 50 mM sodium phosphate, 95% H2O/5% D2O95% H2O/5% D2O
30.9 mM RDTyrH65, 0.9 mM [U-2H;U-15N] RDTyrH65, 50 mM sodium phosphate, 95% H2O/5% D2O95% H2O/5% D2O
40.8 mM [U-95% 15N] RDTyrH65, 50 mM sodium phosphate, 8 mg/mL Pf1 phage, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
0.8 mMRDTyrH65-159-1[U-95% 15N]1
50 mMsodium phosphate-21
mMRDTyrH65-159-3[U-95% 13C; U-95% 15N]1.0-1.22
50 mMsodium phosphate-42
0.9 mMRDTyrH65-159-53
0.9 mMRDTyrH65-159-6[U-2H;U-15N]3
50 mMsodium phosphate-73
0.8 mMRDTyrH65-159-8[U-95% 15N]4
50 mMsodium phosphate-94
8 mg/mLPf1 phage-104
Sample conditionsIonic strength: 0.11 / pH: 7.0 / Pressure: ambient / Temperature: 300 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE7001
Bruker AvanceBrukerAVANCE6002
Bruker AvanceBrukerAVANCE5003

-
Processing

NMR software
NameDeveloperClassification
ARIALinge, O'Donoghue and Nilgesstructure solution
ModelFreePalmerdata analysis
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
NMRViewJohnson, One Moon Scientificdata analysis
PECANEghbalnia, Wang, Bahrami, Assadi, and Markleychemical shift calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
ProcheckNMRLaskowski and MacArthurdata analysis
TALOSCornilescu, Delaglio and Baxdata analysis
TopSpinBruker Biospincollection
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 3070 / NOE intraresidue total count: 1154 / NOE long range total count: 644 / NOE medium range total count: 414 / NOE sequential total count: 830
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

+
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://pdbjlvh1.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