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- PDB-9n4y: CryoEM structure of a filamentous soluble pyridine nucleotide tra... -

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Basic information

Entry
Database: PDB / ID: 9n4y
TitleCryoEM structure of a filamentous soluble pyridine nucleotide transhydrogenase
ComponentsSoluble pyridine nucleotide transhydrogenase
KeywordsFLAVOPROTEIN / transhydrogenase
Function / homology
Function and homology information


NAD(P)+ transhydrogenase (Si-specific) / NAD(P)+ transhydrogenase (Si-specific) activity / dihydrolipoyl dehydrogenase (NADH) activity / NADP+ metabolic process / 2-oxoglutarate metabolic process / flavin adenine dinucleotide binding / cytosol
Similarity search - Function
Soluble pyridine nucleotide transhydrogenase / : / Pyridine nucleotide-disulphide oxidoreductase, class I / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Soluble pyridine nucleotide transhydrogenase
Similarity search - Component
Biological speciesAzotobacter vinelandii (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsWarmack, R.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM143836-01 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM152765 United States
CitationJournal: To Be Published
Title: CryoEM-enabled visual proteomics reveals de novo structures of oligomeric protein complexes
Authors: Warmack, R.A.
History
DepositionFeb 3, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
a: Soluble pyridine nucleotide transhydrogenase
d: Soluble pyridine nucleotide transhydrogenase
g: Soluble pyridine nucleotide transhydrogenase
j: Soluble pyridine nucleotide transhydrogenase
m: Soluble pyridine nucleotide transhydrogenase
p: Soluble pyridine nucleotide transhydrogenase
s: Soluble pyridine nucleotide transhydrogenase
v: Soluble pyridine nucleotide transhydrogenase
y: Soluble pyridine nucleotide transhydrogenase
b: Soluble pyridine nucleotide transhydrogenase
e: Soluble pyridine nucleotide transhydrogenase
h: Soluble pyridine nucleotide transhydrogenase
k: Soluble pyridine nucleotide transhydrogenase
n: Soluble pyridine nucleotide transhydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)730,48528
Polymers719,48714
Non-polymers10,99814
Water00
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
Soluble pyridine nucleotide transhydrogenase / STH / NAD(P)(+) transhydrogenase [B-specific]


Mass: 51391.930 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii (bacteria) / Strain: DJ
References: UniProt: C1DR10, NAD(P)+ transhydrogenase (Si-specific)
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Filamentous assembly of the soluble pyridine nucleotide transhydrogenase
Type: COMPLEX / Entity ID: #1 / Source: NATURAL
Source (natural)Organism: Azotobacter vinelandii (bacteria) / Strain: DJ
Buffer solutionpH: 7.5
SpecimenConc.: 0.75 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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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: -2500 nm / Nominal defocus min: -800 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -108.13 ° / Axial rise/subunit: 38.23 Å / Axial symmetry: C1
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 88454 / Symmetry type: HELICAL
RefinementHighest resolution: 3.7 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00251769
ELECTRON MICROSCOPYf_angle_d0.44970257
ELECTRON MICROSCOPYf_dihedral_angle_d7.2577118
ELECTRON MICROSCOPYf_chiral_restr0.0427723
ELECTRON MICROSCOPYf_plane_restr0.0029057

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