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- PDB-9hjx: Structure of the Thermus termophillus transhydrogenase -

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Basic information

Entry
Database: PDB / ID: 9hjx
TitleStructure of the Thermus termophillus transhydrogenase
Components
  • (proton-translocating NAD(P)(+) transhydrogenase) x 2
  • NAD(P) transhydrogenase subunit beta
KeywordsMEMBRANE PROTEIN / Transhydrogenase / complex
Function / homology
Function and homology information


proton-translocating NAD(P)+ transhydrogenase activity / proton-translocating NAD(P)+ transhydrogenase / NADPH regeneration / NADP binding / oxidoreductase activity / plasma membrane
Similarity search - Function
NAD(P) transhydrogenase, alpha subunit, C-terminal / 4TM region of pyridine nucleotide transhydrogenase, mitoch / NADP transhydrogenase, beta subunit / NADP transhydrogenase beta-like domain / NAD(P) transhydrogenase beta subunit / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, conserved site-2 / Alanine dehydrogenase & pyridine nucleotide transhydrogenase signature 2. / Alanine dehydrogenase/PNT, C-terminal domain / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, N-terminal / Alanine dehydrogenase/PNT, N-terminal domain ...NAD(P) transhydrogenase, alpha subunit, C-terminal / 4TM region of pyridine nucleotide transhydrogenase, mitoch / NADP transhydrogenase, beta subunit / NADP transhydrogenase beta-like domain / NAD(P) transhydrogenase beta subunit / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, conserved site-2 / Alanine dehydrogenase & pyridine nucleotide transhydrogenase signature 2. / Alanine dehydrogenase/PNT, C-terminal domain / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, N-terminal / Alanine dehydrogenase/PNT, N-terminal domain / Alanine dehydrogenase/PNT, C-terminal domain / Alanine dehydrogenase/PNT, N-terminal domain / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, NAD(H)-binding domain / DHS-like NAD/FAD-binding domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / proton-translocating NAD(P)(+) transhydrogenase / proton-translocating NAD(P)(+) transhydrogenase / NAD(P) transhydrogenase subunit beta
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.39 Å
AuthorsTrasnea, P.I. / Sazanov, L.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)101020697European Union
CitationJournal: To Be Published
Title: Structure of the Thermus termophillus transhydrogenase
Authors: Trasnea, P.I. / Sazanov, L.
History
DepositionDec 2, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 17, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 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: proton-translocating NAD(P)(+) transhydrogenase
B: NAD(P) transhydrogenase subunit beta
C: proton-translocating NAD(P)(+) transhydrogenase
D: proton-translocating NAD(P)(+) transhydrogenase
E: NAD(P) transhydrogenase subunit beta
F: proton-translocating NAD(P)(+) transhydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,0957
Polymers194,3526
Non-polymers7431
Water00
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 proton-translocating NAD(P)(+) transhydrogenase


Mass: 9909.746 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: TthAA11_01930, TthHB5018_01710 / Production host: Thermus thermophilus (bacteria)
References: UniProt: A0A510HPH9, proton-translocating NAD(P)+ transhydrogenase
#2: Protein NAD(P) transhydrogenase subunit beta / Nicotinamide nucleotide transhydrogenase subunit beta


Mass: 47371.906 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The region from 264PHE to 273VAL was deleted from the model because of no density present in the map
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: TthHB5018_01700 / Production host: Thermus thermophilus (bacteria)
References: UniProt: A0A7R7TBV0, proton-translocating NAD(P)+ transhydrogenase
#3: Protein proton-translocating NAD(P)(+) transhydrogenase


Mass: 39894.332 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The region from SER219 to LEU230 and ALA 256 to ARG262 was deleted from the model because of no density present in the map
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: TthHB5018_01720 / Production host: Thermus thermophilus (bacteria)
References: UniProt: A0A7R7TBU1, proton-translocating NAD(P)+ transhydrogenase
#4: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
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: The entitre structure of transhydrogenase from Thermus termophillus, with the NADP ligand in the DIII subunit
Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightValue: 0.21 MDa / Experimental value: YES
Source (natural)Organism: Thermus thermophilus (bacteria) / Cellular location: Membrane
Source (recombinant)Organism: Thermus thermophilus (bacteria)
Buffer solutionpH: 7.2
Details: 150mM NaCl, 50mM HEPES, 0.02% DDM and CHAPS was added right before vitrification
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMsodium chlorideNaCl1
250 mMHEPESHEPES1
30.02 %N-Dodecyl-beta-D-maltosideDDM1
40.1 %CHAPSCHAPS1
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R0.6/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Details: Vitrification carried out

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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 magnification: 105000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 2.4 sec. / Electron dose: 89.6 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4772

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Processing

EM software
IDNameVersionCategory
1RELIONparticle selection
4RELIONCTF correction
19PHENIXdev_4933model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.39 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 114749 / Symmetry type: POINT
Atomic model buildingAccession code: 4O9U / Details: 4O9U / Source name: Other / Type: other
RefinementHighest resolution: 3.39 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00413392
ELECTRON MICROSCOPYf_angle_d0.70618189
ELECTRON MICROSCOPYf_dihedral_angle_d14.6294810
ELECTRON MICROSCOPYf_chiral_restr0.0472176
ELECTRON MICROSCOPYf_plane_restr0.0082289

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