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- EMDB-66321: Wild-type Escherichia coli transhydrogenase single dIII attached ... -

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Basic information

Entry
Database: EMDB / ID: EMD-66321
TitleWild-type Escherichia coli transhydrogenase single dIII attached to dII in the presence of both NADP+ and NAD+.
Map data
Sample
  • Complex: The E. coli transhydrogenase complex.
    • Protein or peptide: NAD(P) transhydrogenase subunit alpha
    • Protein or peptide: NAD(P) transhydrogenase subunit beta
  • Ligand: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Keywordsnicotinamide nucleotide transhydrogenase / hydride transfer / proton pump / conformational dynamics / NADPH production / MEMBRANE PROTEIN
Function / homology
Function and homology information


proton export across plasma membrane / proton-translocating NAD(P)+ transhydrogenase activity / proton-translocating NAD(P)+ transhydrogenase / NADPH regeneration / NADP binding / oxidoreductase activity / protein dimerization activity / plasma membrane
Similarity search - Function
NAD(P) transhydrogenase, alpha subunit / NADP transhydrogenase, beta subunit / NAD(P) transhydrogenase, alpha subunit, C-terminal / 4TM region of pyridine nucleotide transhydrogenase, mitoch / NADP transhydrogenase beta-like domain / NAD(P) transhydrogenase beta subunit / Alanine dehydrogenase/NAD(P) transhydrogenase, conserved site-1 / Alanine dehydrogenase & pyridine nucleotide transhydrogenase signature 1. / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, conserved site-2 / Alanine dehydrogenase & pyridine nucleotide transhydrogenase signature 2. ...NAD(P) transhydrogenase, alpha subunit / NADP transhydrogenase, beta subunit / NAD(P) transhydrogenase, alpha subunit, C-terminal / 4TM region of pyridine nucleotide transhydrogenase, mitoch / NADP transhydrogenase beta-like domain / NAD(P) transhydrogenase beta subunit / Alanine dehydrogenase/NAD(P) transhydrogenase, conserved site-1 / Alanine dehydrogenase & pyridine nucleotide transhydrogenase signature 1. / 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
NAD(P) transhydrogenase subunit alpha / NAD(P) transhydrogenase subunit beta
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.42 Å
AuthorsZhu JP / Zhang K / Li J / Zheng W / Gu M
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Wild-type Escherichia coli transhydrogenase single dIII attached to dII in the presence of both NADP+ and NAD+.
Authors: Zhu JP / Zhang K / Li J
History
DepositionSep 24, 2025-
Header (metadata) releaseSep 30, 2026-
Map releaseSep 30, 2026-
UpdateSep 30, 2026-
Current statusSep 30, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_66321.png

Downloads & links

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Map

FileDownload / File: emd_66321.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 360 pix.
= 299.52 Å		0.83 Å/pix.
x 360 pix.
= 299.52 Å		0.83 Å/pix.
x 360 pix.
= 299.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.109
Minimum - Maximum-0.4094992 - 0.6726513
Average (Standard dev.)-0.00022136277 (±0.014027352)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 299.52002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_66321_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_66321_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : The E. coli transhydrogenase complex.

EntireName: The E. coli transhydrogenase complex.
Components
  • Complex: The E. coli transhydrogenase complex.
    • Protein or peptide: NAD(P) transhydrogenase subunit alpha
    • Protein or peptide: NAD(P) transhydrogenase subunit beta
  • Ligand: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

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Supramolecule #1: The E. coli transhydrogenase complex.

SupramoleculeName: The E. coli transhydrogenase complex. / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Escherichia coli K-12 (bacteria)

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Macromolecule #1: NAD(P) transhydrogenase subunit alpha

MacromoleculeName: NAD(P) transhydrogenase subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: proton-translocating NAD(P)+ transhydrogenase
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 11.747049 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
YALMALAIIL FGWMASVAPK EFLGHFTVFA LACVVGYYVV WNVSHALHTP LMSVTNAISG IIVVGALLQI GQGGWVSFLS FIAVLIASI NIFGGFTVTQ RMLKMFRKN

UniProtKB: NAD(P) transhydrogenase subunit alpha

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Macromolecule #2: NAD(P) transhydrogenase subunit beta

MacromoleculeName: NAD(P) transhydrogenase subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: proton-translocating NAD(P)+ transhydrogenase
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 48.762746 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSGGLVTAAY IVAAILFIFS LAGLSKHETS RQGNNFGIAG MAIALIATIF GPDTGNVGWI LLAMVIGGAI GIRLAKKVEM TEMPELVAI LHSFVGLAAV LVGFNSYLHH DAGMAPILVN IHLTEVFLGI FIGAVTFTGS VVAFGKLCGK ISSKPLMLPN R HKMNLAAL ...String:
MSGGLVTAAY IVAAILFIFS LAGLSKHETS RQGNNFGIAG MAIALIATIF GPDTGNVGWI LLAMVIGGAI GIRLAKKVEM TEMPELVAI LHSFVGLAAV LVGFNSYLHH DAGMAPILVN IHLTEVFLGI FIGAVTFTGS VVAFGKLCGK ISSKPLMLPN R HKMNLAAL VVSFLLLIVF VRTDSVGLQV LALLIMTAIA LVFGWHLVAS IGGADMPVVV SMLNSYSGWA AAAAGFMLSN DL LIVTGAL VGSSGAILSY IMCKAMNRSF ISVIAGGFGT DGSSTGDDQE VGEHREITAE ETAELLKNSH SVIITPGYGM AVA QAQYPV AEITEKLRAR GINVRFGIHP VAGRLPGHMN VLLAEAKVPY DIVLEMDEIN DDFADTDTVL VIGANDTVNP AAQD DPKSP IAGMPVLEVW KAQNVIVFKR SMNTGYAGVQ NPLFFKENTH MLFGDAKASV DAILKAL

UniProtKB: NAD(P) transhydrogenase subunit beta

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Macromolecule #3: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

MacromoleculeName: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / type: ligand / ID: 3 / Number of copies: 1 / Formula: NAP
Molecular weightTheoretical: 743.405 Da
Chemical component information

ChemComp-NAP:
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

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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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.378 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.42 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 96595
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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