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- EMDB-48915: CryoEM structure of a filamentous soluble pyridine nucleotide tra... -

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Basic information

Entry
Database: EMDB / ID: EMD-48915
TitleCryoEM structure of a filamentous soluble pyridine nucleotide transhydrogenase
Map data
Sample
  • Complex: Filamentous assembly of the soluble pyridine nucleotide transhydrogenase
    • Protein or peptide: Soluble pyridine nucleotide transhydrogenase
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
Keywordstranshydrogenase / FLAVOPROTEIN
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
Soluble pyridine nucleotide transhydrogenase
Similarity search - Component
Biological speciesAzotobacter vinelandii (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsWarmack RA
Funding support United States, 2 items
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: Structure / Year: 2025
Title: CryoEM-enabled visual proteomics reveals de novo structures of oligomeric protein complexes.
Authors: Yuanbo Shen / Ailiena O Maggiolo / Tianzheng Zhang / Rebeccah A Warmack /
Abstract: Single particle cryoelectron microscopy (cryoEM) and cryoelectron tomography (cryoET) are powerful methods for unveiling unique and functionally relevant structural states. Aided by mass spectrometry ...Single particle cryoelectron microscopy (cryoEM) and cryoelectron tomography (cryoET) are powerful methods for unveiling unique and functionally relevant structural states. Aided by mass spectrometry and machine learning, they promise to facilitate the visual exploration of proteomes. Leveraging visual proteomics, we interrogate structures isolated from a complex cellular milieu by cryoEM to identify and classify molecular structures and complexes de novo. By comparing three automated model building programs, CryoID, DeepTracer, and ModelAngelo, we determine the identity of six distinct oligomeric protein complexes from partially purified extracts of the nitrogen-fixing bacterium Azotobacter vinelandii using both anaerobic and aerobic cryoEM, including two original oligomeric structures. Overall, by allowing the study of near-native oligomeric protein states, cryoEM-enabled visual proteomics reveals unique structures that correspond to relevant species observed in situ.
History
DepositionFeb 3, 2025-
Header (metadata) releaseJul 16, 2025-
Map releaseJul 16, 2025-
UpdateSep 17, 2025-
Current statusSep 17, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48915.png

Downloads & links

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Map

FileDownload / File: emd_48915.map.gz / Format: CCP4 / Size: 2.4 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 864 pix.
= 561.6 Å		0.65 Å/pix.
x 864 pix.
= 561.6 Å		0.65 Å/pix.
x 864 pix.
= 561.6 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.65 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.167
Minimum - Maximum-0.23673472 - 0.58030623
Average (Standard dev.)-0.00019049934 (±0.019319763)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions864864864
Spacing864864864
CellA=B=C: 561.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_48915_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_48915_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Filamentous assembly of the soluble pyridine nucleotide transhydr...

EntireName: Filamentous assembly of the soluble pyridine nucleotide transhydrogenase
Components
  • Complex: Filamentous assembly of the soluble pyridine nucleotide transhydrogenase
    • Protein or peptide: Soluble pyridine nucleotide transhydrogenase
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE

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Supramolecule #1: Filamentous assembly of the soluble pyridine nucleotide transhydr...

SupramoleculeName: Filamentous assembly of the soluble pyridine nucleotide transhydrogenase
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Azotobacter vinelandii (bacteria) / Strain: DJ

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Macromolecule #1: Soluble pyridine nucleotide transhydrogenase

MacromoleculeName: Soluble pyridine nucleotide transhydrogenase / type: protein_or_peptide / ID: 1 / Number of copies: 14 / Enantiomer: LEVO / EC number: NAD(P)+ transhydrogenase (Si-specific)
Source (natural)Organism: Azotobacter vinelandii (bacteria) / Strain: DJ
Molecular weightTheoretical: 51.39193 KDa
SequenceString: MAVYNYDVVV IGTGPAGEGA AMNAVKAGRK VAVVDDRPQV GGNCTHLGTI PSKALRHSVR QIMQYNNNPL FRQIGEPRWF SFADVLKSA EQVIAKQVSS RTGYYARNRI DTFFGTASFC DEHTIEVVHL NGMVETLVAK QFVIATGSRP YRPADVDFTH P RIYDSDTI ...String:
MAVYNYDVVV IGTGPAGEGA AMNAVKAGRK VAVVDDRPQV GGNCTHLGTI PSKALRHSVR QIMQYNNNPL FRQIGEPRWF SFADVLKSA EQVIAKQVSS RTGYYARNRI DTFFGTASFC DEHTIEVVHL NGMVETLVAK QFVIATGSRP YRPADVDFTH P RIYDSDTI LSLGHTPRRL IIYGAGVIGC EYASIFSGLG VLVDLIDNRD QLLSFLDDEI SDSLSYHLRN NNVLIRHNEE YE RVEGLDN GVILHLKSGK KIKADAFLWS NGRTGNTDKL GLENIGLKAN GRGQIQVDEH YRTEVSNIYA AGDVIGWPSL ASA AYDQGR SAAGSITEND SWRFVDDVPT GIYTIPEISS VGKTERELTQ AKVPYEVGKA FFKGMARAQI AVEKAGMLKI LFHR ETLEI LGVHCFGYQA SEIVHIGQAI MNQKGEANTL KYFINTTFNY PTMAEAYRVA AYDGLNRLF

UniProtKB: Soluble pyridine nucleotide transhydrogenase

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Macromolecule #2: FLAVIN-ADENINE DINUCLEOTIDE

MacromoleculeName: FLAVIN-ADENINE DINUCLEOTIDE / type: ligand / ID: 2 / Number of copies: 14 / Formula: FAD
Molecular weightTheoretical: 785.55 Da
Chemical component information

ChemComp-FAD:
FLAVIN-ADENINE DINUCLEOTIDE / FAD*YM

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

Concentration0.75 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: -2.5 µm / Nominal defocus min: -0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 38.23 Å
Applied symmetry - Helical parameters - Δ&Phi: -108.13 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 88454
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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