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- EMDB-66913: Structure of dodecameric TpkB bound to AMP-PNP from Thermus therm... -

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Basic information

Entry
Database: EMDB / ID: EMD-66913
TitleStructure of dodecameric TpkB bound to AMP-PNP from Thermus thermophilus
Map datafull map
Sample
  • Complex: Dodecameric TpkB
    • Protein or peptide: Serine protein kinase
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
KeywordsHYPOTHETICAL PROTEIN / ATP-BINDING / PRK/YEAG FAMILY / STRUCTURAL GENOMICS
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsTorri M / Kanno R / Mizoguchi A / Humbel B / Tani K / Masui R
Funding support Japan, 2 items
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: Masayuki Torii / Ryo Kanno / Akira Mizoguchi / Bruno M Humbel / Kazutoshi Tani / Ryoji Masui /
Abstract: Protein phosphorylation, a key post-translational modification, is mediated by various protein kinases. The bacterial PrkA/YeaG is recognized as an atypical protein kinase, but its activity remains ...Protein phosphorylation, a key post-translational modification, is mediated by various protein kinases. The bacterial PrkA/YeaG is recognized as an atypical protein kinase, but its activity remains elusive. This study investigated the structural and functional characteristics of a PrkA/YeaG homologue, TpkB, from Thermus thermophilus HB8. Using cryo-electron microscopy, the structures of TpkB in apo and AMPPNP-bound forms were determined, revealing a hexameric ring architecture characteristic of AAA + superfamily proteins. The TpkB protomer is comprised of an N-terminal domain, an ATPase domain, and a LID domain. The ATPase domain contains conserved sequence motifs associated with ATPase activity, whereas the other domains present a novel fold. TpkB exhibits structural similarity to MoxR family proteins, which possess chaperone-like functions in conjunction with von Willebrand factor A (vWA) domain proteins. Structural and gene neighborhood analyses suggested a functional link between PrkA/YeaG proteins and vWA domain proteins. Biochemical analyses demonstrated that TpkB exhibited ATPase activity and chaperone-like activity, but lacked detectable protein kinase activity. These findings establish TpkB as a novel member of the AAA+ superfamily with potential chaperone functions, providing new insights into the PrkA/YeaG family.
History
DepositionNov 3, 2025-
Header (metadata) releaseJul 1, 2026-
Map releaseJul 1, 2026-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_66913.png

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Map

FileDownload / File: emd_66913.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationfull map
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 500 pix.
= 410. Å		0.82 Å/pix.
x 500 pix.
= 410. Å		0.82 Å/pix.
x 500 pix.
= 410. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.017
Minimum - Maximum-0.0620104 - 0.110955365
Average (Standard dev.)0.000048585232 (±0.003757701)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 410.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: odd half map

Fileemd_66913_half_map_1.map
Annotationodd half map
Projections & Slices
AxesZYX

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Histogram

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Half map: even half map

Fileemd_66913_half_map_2.map
Annotationeven half map
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Histogram

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Sample components

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Entire : Dodecameric TpkB

EntireName: Dodecameric TpkB
Components
  • Complex: Dodecameric TpkB
    • Protein or peptide: Serine protein kinase
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

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Supramolecule #1: Dodecameric TpkB

SupramoleculeName: Dodecameric TpkB / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Thermus thermophilus HB8 (bacteria)

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Macromolecule #1: Serine protein kinase

MacromoleculeName: Serine protein kinase / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus HB8 (bacteria)
Molecular weightTheoretical: 79.879211 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SSGENLYFQG GLNHMSELDF VRRGQDLKAY RALNWEGSFA DYLRLLKEDP RPLRTSFQRV HDMILAHGVE EYTRFKEKL LHYRFFDDPF EGGKDAVFGL DKPLMRLVAT LKAAAHRLGP ERRILLLHGP VGSAKSTIAR LLKKGLEAYS R TEEGKLFT ...String:
MGSSHHHHHH SSGENLYFQG GLNHMSELDF VRRGQDLKAY RALNWEGSFA DYLRLLKEDP RPLRTSFQRV HDMILAHGVE EYTRFKEKL LHYRFFDDPF EGGKDAVFGL DKPLMRLVAT LKAAAHRLGP ERRILLLHGP VGSAKSTIAR LLKKGLEAYS R TEEGKLFT FYWKTEEGPL PCPMHEEPLH LLPQDLREAF LEELRALHPD YPYPLEVEGD LCPVCRFQMR EGLRKYEGDL AA LLEHEVV VKRLVLSEKD RVGIGTFQPK DEKNQDSTEL TGDINYRKVA LYGSDSDPRA FNFDGELNIA NRGIVEFIEI LKL DVAFLY DLLTASQEHK IKSKKFAQTD IDEIVLGHTN EPEYRKLQAN EYMEALRDRT IKIDVPYILR VSDEVRIYQR DFAK VRGKH IAPHTLEMAA TWAVLTRLEP PKRAGLTLMQ KLKLYDGKLL PGWTEEAVRE LMGEAKREGL EGISPRYIQD KISNV LVTS EEPCINPFMV MNELEEGLKH HSLISDERTR ERYRALLQEV KAEYAEIVKN EVQRAIAADE EALNRLFHNY IDHVKA YVL GEKVKNPYTG APEPPNERLM RSIEERIDIP ESRKDDFRRE IMNYIGALAL EGKPFTYKDN DRLRRALELK LFDDQKD TI RLSALVSGVV DPETQAKIDV VKARLIRDYG YCEHCASGVL EFAASLFARS

UniProtKB: Serine protein kinase

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Macromolecule #2: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 2 / Number of copies: 12 / Formula: ANP
Molecular weightTheoretical: 506.196 Da
Chemical component information

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

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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

Concentration5.6 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
50.0 mMTris-HCltris(hydroxymethyl)aminomethane
0.5 %CHAPS3-[(3-Cholamidopropyl)dimethylammonio]-1-propanesulfonate
200.0 mMNaClsodium chloride
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 277 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.3000000000000003 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 132545
CTF correctionSoftware - Name: RELION (ver. 3.1) / Type: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: D6 (2x6 fold dihedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 16347
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-9xir:
Structure of dodecameric TpkB bound to AMP-PNP from Thermus thermophilus

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