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- EMDB-66270: Structure of dimeric Tribolium castaneum (Tc) PINK1 L552R mutant ... -

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Basic information

Entry
Database: EMDB / ID: EMD-66270
TitleStructure of dimeric Tribolium castaneum (Tc) PINK1 L552R mutant in prime-activation conformation
Map data
Sample
  • Complex: Structure of dimeric Tribolium castaneum (Tc) PINK1 L552R mutant in prime-activation conformation
    • Protein or peptide: Serine/threonine-protein kinase Pink1, mitochondrial
  • Ligand: CALCIUM ION
  • Ligand: water
Keywordskinase / location / TRANSFERASE
Function / homology
Function and homology information


positive regulation of free ubiquitin chain polymerization / autophagy of mitochondrion / positive regulation of mitochondrial fission / positive regulation of protein ubiquitination / protein autophosphorylation / regulation of apoptotic process / mitochondrial outer membrane / non-specific serine/threonine protein kinase / mitochondrial inner membrane / ubiquitin protein ligase binding ...positive regulation of free ubiquitin chain polymerization / autophagy of mitochondrion / positive regulation of mitochondrial fission / positive regulation of protein ubiquitination / protein autophosphorylation / regulation of apoptotic process / mitochondrial outer membrane / non-specific serine/threonine protein kinase / mitochondrial inner membrane / ubiquitin protein ligase binding / protein serine/threonine kinase activity / mitochondrion / metal ion binding / ATP binding / cytosol
Similarity search - Function
: / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Serine/threonine-protein kinase Pink1, mitochondrial
Similarity search - Component
Biological speciesTribolium castaneum (red flour beetle)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.04 Å
AuthorsXu HQ / Liu XY / Xue JR / Li BX / Yu XR / Chen C / Qin XH / Mi LZ / Liu Z
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)#31670738, # 31470730 China
CitationJournal: To Be Published
Title: Structure of dimeric Tribolium castaneum (Tc) PINK1 L552R mutant in prime-activation conformation
Authors: Xu HQ / Liu XY / Xue JR / Li BX / Yu XR / Chen C / Qin XH / Mi LZ / Liu Z
History
DepositionSep 19, 2025-
Header (metadata) releaseSep 23, 2026-
Map releaseSep 23, 2026-
UpdateSep 23, 2026-
Current statusSep 23, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_66270.png

Downloads & links

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Map

FileDownload / File: emd_66270.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.67 Å/pix.
x 400 pix.
= 267.2 Å		0.67 Å/pix.
x 400 pix.
= 267.2 Å		0.67 Å/pix.
x 400 pix.
= 267.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.668 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-3.273905 - 4.867976
Average (Standard dev.)0.00025132782 (±0.06538266)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 267.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_66270_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_66270_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Structure of dimeric Tribolium castaneum (Tc) PINK1 L552R mutant ...

EntireName: Structure of dimeric Tribolium castaneum (Tc) PINK1 L552R mutant in prime-activation conformation
Components
  • Complex: Structure of dimeric Tribolium castaneum (Tc) PINK1 L552R mutant in prime-activation conformation
    • Protein or peptide: Serine/threonine-protein kinase Pink1, mitochondrial
  • Ligand: CALCIUM ION
  • Ligand: water

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Supramolecule #1: Structure of dimeric Tribolium castaneum (Tc) PINK1 L552R mutant ...

SupramoleculeName: Structure of dimeric Tribolium castaneum (Tc) PINK1 L552R mutant in prime-activation conformation
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Tribolium castaneum (red flour beetle)

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Macromolecule #1: Serine/threonine-protein kinase Pink1, mitochondrial

MacromoleculeName: Serine/threonine-protein kinase Pink1, mitochondrial / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase
Source (natural)Organism: Tribolium castaneum (red flour beetle)
Molecular weightTheoretical: 51.40859 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: HHHHHHENLY FQGGGSEAIS KIKWQYYDID ESRFESNPIT LNDLSLGKPI AKGTNGVVYS AKVKDDETDD NKYPFALKMM FNYDIQSNS MEILKAMYRE TVPARMYYSN HDLNNWEIEL ANRRKHLPPH PNIVAIFSVF TDLIQELEGS KDLYPAALPP R LHPEGEGR ...String:
HHHHHHENLY FQGGGSEAIS KIKWQYYDID ESRFESNPIT LNDLSLGKPI AKGTNGVVYS AKVKDDETDD NKYPFALKMM FNYDIQSNS MEILKAMYRE TVPARMYYSN HDLNNWEIEL ANRRKHLPPH PNIVAIFSVF TDLIQELEGS KDLYPAALPP R LHPEGEGR NMSLFLLMKR YDCNLQSFLS TAPSTRTSLL LLAQLLEGVA HMTAHGIAHR DLKSDNLLLD TSEPESPILV IS DFGCCLA DKTNGLSLPY TSYEMDKGGN TALMAPEIIC QKPGTFSVLN YSKADLWAVG AIAYEIFNCH NPFYGPSRLK NFN YKEGDL PKLPDEVPTV IQALVANLLK RNPNKRLDPE VAANVCQLFL WAPSTWLKPG LKVPTSGEIL QWLLSLTTKV LCEG KINNK SFGEKFTRNW RRTYPEYLLI SSFLCRAKRA NVRNALHWIQ ENLPELD

UniProtKB: Serine/threonine-protein kinase Pink1, mitochondrial

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Macromolecule #2: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 1 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 2 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 407577
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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