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- PDB-9xip: Structure of dodecameric Apo TpkB from Thermus thermophilus -

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Basic information

Entry
Database: PDB / ID: 9xip
TitleStructure of dodecameric Apo TpkB from Thermus thermophilus
ComponentsSerine protein kinase
KeywordsSTRUCTURAL GENOMICS / HYPOTHETICAL PROTEIN / ATP-BINDING / PRK/YEAG FAMILY
Function / homologyPrkA C-terminal domain / PrkA AAA domain / Serine-protein kinase, PrkA / PrkA serine protein kinase C-terminal domain / PrkA AAA domain / PrkA AAA domain / protein kinase activity / P-loop containing nucleoside triphosphate hydrolase / Serine protein kinase
Function and homology information
Biological speciesThermus thermophilus HB8 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsTorri, M. / Kanno, R. / Mizoguchi, A. / Humbel, B. / Tani, K. / Masui, R.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)21am0101118 Japan
Japan Agency for Medical Research and Development (AMED)21am0101116 Japan
CitationJournal: J.Biochem. / Year: 2026
Title: Structure and biochemical analyses suggest that PrkA/YeaG protein of Thermus thermophilus functions as a putative molecular chaperone.
Authors: Torii, M. / Kanno, R. / Mizoguchi, A. / Humbel, B.M. / Tani, K. / Masui, R.
History
DepositionNov 3, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 1, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine protein kinase
B: Serine protein kinase
C: Serine protein kinase
D: Serine protein kinase
E: Serine protein kinase
F: Serine protein kinase
G: Serine protein kinase
H: Serine protein kinase
I: Serine protein kinase
J: Serine protein kinase
K: Serine protein kinase
L: Serine protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)960,51342
Polymers958,55112
Non-polymers1,96230
Water23,1311284
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Serine protein kinase / TpkB


Mass: 79879.211 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Gene: TTHA0843 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SK09
#2: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1284 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: Dodecameric TpkB / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Thermus thermophilus HB8 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMtris(hydroxymethyl)aminomethaneTris-HCl1
20.5 %3-[(3-Cholamidopropyl)dimethylammonio]-1-propanesulfonateCHAPS1
3200 mMsodium chlorideNaCl1
SpecimenConc.: 5.6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 80 % / Chamber temperature: 277 K

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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: 3000 nm / Nominal defocus min: 400 nm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 1 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1crYOLO1.7particle selection
4RELION3.1CTF correction
9RELION3.1initial Euler assignment
10RELION3.1final Euler assignment
11RELION3.1classification
12RELION3.13D reconstruction
13PHENIX1.19.2_4158model refinement
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 146086
SymmetryPoint symmetry: D6 (2x6 fold dihedral)
3D reconstructionResolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 100913 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
RefinementHighest resolution: 2.3 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00448888
ELECTRON MICROSCOPYf_angle_d0.6165964
ELECTRON MICROSCOPYf_dihedral_angle_d13.25619104
ELECTRON MICROSCOPYf_chiral_restr0.0467152
ELECTRON MICROSCOPYf_plane_restr0.0058580

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