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- EMDB-18058: TH-DNAJC12 (108-198) -

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Basic information

Entry
Database: EMDB / ID: EMD-18058
TitleTH-DNAJC12 (108-198)
Map dataTH-DNAJC12D107 3DR
Sample
  • Complex: TH-DNAJC12 (108-198) Complex
    • Protein or peptide: Tyrosine Hydroxylate
    • Protein or peptide: DNAJC12 (108-198)
KeywordsDNAJC12 Hsp40 Hsp70 Tyrosine hydroxylate deficiency / CHAPERONE
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
J domain-containing protein 1-like / 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. ...J domain-containing protein 1-like / 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. / DnaJ domain / ACT-like domain / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain
Similarity search - Domain/homology
Tyrosine 3-monooxygenase / DnaJ homolog subfamily C member 12
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.05 Å
AuthorsOchoa L / Tai MDS / Muntaner J / Santiago C / Valpuesta JM / Martinez A / Cuellar J
Funding support Spain, Norway, 2 items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPID2019-105872GB-I00/AEI/10.13039/ 501100011033 Spain
Research Council of NorwayFRIMEDBIO 261826 Norway
CitationJournal: To Be Published
Title: 3D Reconstruction of TH-DNAJC12 (108-198) Complex
Authors: Tai MDS / Ochoa L / Flydal MI / Velasco L / Muntaner J / Santiago C / Jung-KC K / Stove SI / Moro F / Kallio JP / Muga A / Valpuesta JM / Cuellar J / Martinez A
History
DepositionJul 28, 2023-
Header (metadata) releaseFeb 5, 2025-
Map releaseFeb 5, 2025-
UpdateFeb 5, 2025-
Current statusFeb 5, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18058.png

Downloads & links

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Map

FileDownload / File: emd_18058.map.gz / Format: CCP4 / Size: 1.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTH-DNAJC12D107 3DR
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.46 Å/pix.
x 76 pix.
= 186.998 Å		2.46 Å/pix.
x 76 pix.
= 186.998 Å		2.46 Å/pix.
x 76 pix.
= 186.998 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.4605 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0221
Minimum - Maximum-0.09117123 - 0.19730619
Average (Standard dev.)0.000857063 (±0.0123573)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions767676
Spacing767676
CellA=B=C: 186.998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: TH-DNAJC12D107 3D halfmap 1

Fileemd_18058_half_map_1.map
AnnotationTH-DNAJC12D107 3D halfmap 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: TH-DNAJC12D107 3D halfmap 2

Fileemd_18058_half_map_2.map
AnnotationTH-DNAJC12D107 3D halfmap 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : TH-DNAJC12 (108-198) Complex

EntireName: TH-DNAJC12 (108-198) Complex
Components
  • Complex: TH-DNAJC12 (108-198) Complex
    • Protein or peptide: Tyrosine Hydroxylate
    • Protein or peptide: DNAJC12 (108-198)

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Supramolecule #1: TH-DNAJC12 (108-198) Complex

SupramoleculeName: TH-DNAJC12 (108-198) Complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 265 KDa

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Macromolecule #1: Tyrosine Hydroxylate

MacromoleculeName: Tyrosine Hydroxylate / type: protein_or_peptide / ID: 1 / Enantiomer: DEXTRO / EC number: tyrosine 3-monooxygenase
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GAMGPTPDAT TPQAKGFRRA VSELDAKQAE AIMSPRFIGR RQSLIEDARK EREAAVAAAA AAVPSEPGDP LEAVAFEEKE GKAMLNLLFS PRATKPSALS RAVKVFETFE AKIHHLETRP AQRPRAGGPH LEYFVRLEVR RGDLAALLSG VRQVSEDVRS PAGPKVPWFP ...String:
GAMGPTPDAT TPQAKGFRRA VSELDAKQAE AIMSPRFIGR RQSLIEDARK EREAAVAAAA AAVPSEPGDP LEAVAFEEKE GKAMLNLLFS PRATKPSALS RAVKVFETFE AKIHHLETRP AQRPRAGGPH LEYFVRLEVR RGDLAALLSG VRQVSEDVRS PAGPKVPWFP RKVSELDKCH HLVTKFDPDL DLDHPGFSDQ VYRQRRKLIA EIAFQYRHGD PIPRVEYTAE EIATWKEVYT TLKGLYATHA CGEHLEAFAL LERFSGYRED NIPQLEDVSR FLKERTGFQL RPVAGLLSAR DFLASLAFRV FQCTQYIRHA SSPMHSPEPD CCHELLGHVP MLADRTFAQF SQDIGLASLG ASDEEIEKLS TLYWFTVEFG LCKQNGEVKA YGAGLLSSYG ELLHCLSEEP EIRAFDPEAA AVQPYQDQTY QSVYFVSESF SDAKDKLRSY ASRIQRPFSV KFDPYTLAID VLDSPQAVRR SLEGVQDELD TLAHALSAIG

UniProtKB: Tyrosine 3-monooxygenase

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Macromolecule #2: DNAJC12 (108-198)

MacromoleculeName: DNAJC12 (108-198) / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GKKDLMLEES DKTHTTKMEN EECNEQRERK KEELASTAEK TEQKEPKPLE KSVSPQNSDS SGFADVNGWH LRFRWSKDAP SELLRKFRNY EI

UniProtKB: DnaJ homolog subfamily C member 12

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.85 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
30.0 mMC8H18N2O4SHepes
200.0 mMNaClSodium chloride
2.0 %C3H8O3Glycerol
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 295.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 3456 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 12996 / Average exposure time: 2.1 sec. / Average electron dose: 41.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1283996
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7a2g


Details: Cryosparc, RANSAC initial model and filtered atomic structures
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.05 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 128537
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software: (Name: RELION (ver. 3.0), cryoSPARC (ver. 3.0)) / Details: Relion and Cryosparc
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0) / Details: Relion
Final 3D classificationNumber classes: 3 / Software - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

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