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- PDB-9wuu: Structure of dimeric autoinhibited Tribolium castaneum (Tc) PINK1... -

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Basic information

Entry
Database: PDB / ID: 9wuu
TitleStructure of dimeric autoinhibited Tribolium castaneum (Tc) PINK1 L552R mutant in complex with Ca2+
Components(Serine/threonine-protein kinase Pink1, mitochondrial) x 2
KeywordsTRANSFERASE / kinase / complex
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.35 Å
AuthorsXu, H.Q. / Liu, X.Y. / Xue, J.R. / Li, B.X. / Yu, X.R. / Chen, C. / Qin, X.H. / Mi, L.Z. / LIu, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)#31670738, # 31470730 China
CitationJournal: To Be Published
Title: Structure of dimeric autoinhibited Tribolium castaneum (Tc) PINK1 L552R mutant in complex with Ca2+
Authors: Xu, H.Q. / Liu, X.Y. / Xue, J.R. / Li, B.X. / Yu, X.R. / Chen, C. / Qin, X.H. / Mi, L.Z. / LIu, Z.
History
DepositionSep 19, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 23, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 23, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Serine/threonine-protein kinase Pink1, mitochondrial
A: Serine/threonine-protein kinase Pink1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,9373
Polymers102,8972
Non-polymers401
Water181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Serine/threonine-protein kinase Pink1, mitochondrial / PTEN-induced putative kinase 1


Mass: 51488.566 Da / Num. of mol.: 1 / Mutation: L552R
Source method: isolated from a genetically manipulated source
Details: A,B subunits were not simultaneously phosphorylated.
Source: (gene. exp.) Tribolium castaneum (red flour beetle) / Gene: Pink1, TcasGA2_TC013202 / Production host: Escherichia coli (E. coli)
References: UniProt: D6WMX4, non-specific serine/threonine protein kinase
#2: Protein Serine/threonine-protein kinase Pink1, mitochondrial / PTEN-induced putative kinase 1


Mass: 51408.590 Da / Num. of mol.: 1 / Mutation: L552R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tribolium castaneum (red flour beetle) / Gene: Pink1, TcasGA2_TC013202 / Production host: Escherichia coli (E. coli)
References: UniProt: D6WMX4, non-specific serine/threonine protein kinase
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Structure of dimeric autoinhibited Tribolium castaneum (Tc) PINK1 L552R mutant in complex with Ca2+
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Tribolium castaneum (red flour beetle)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
1Topazparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.35 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 71484 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0025759
ELECTRON MICROSCOPYf_angle_d0.4897832
ELECTRON MICROSCOPYf_dihedral_angle_d4.905762
ELECTRON MICROSCOPYf_chiral_restr0.04883
ELECTRON MICROSCOPYf_plane_restr0.005992

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