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- EMDB-62870: Structures and mechanism of the nicotinamide nucleotide transhydr... -

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Basic information

Entry
Database: EMDB / ID: EMD-62870
TitleStructures and mechanism of the nicotinamide nucleotide transhydrogenase from E. coli
Map data
Sample
  • Complex: The E. coli nicotinamide nucleotide transhydrogenase complex
    • Protein or peptide: NAD(P) transhydrogenase subunit alpha
    • Protein or peptide: NAD(P) transhydrogenase subunit beta
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: Palmitoyl-CoA
KeywordsNicotinamide nucleotide transhydrogenase / Mitochondrial inner membrane / E. coli transhydrogenase / Hydride transfer / Proton motive force / NAD+ / NADH / NADP+ / NADPH / 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 / 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/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 / 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/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/pyridine nucleotide transhydrogenase, N-terminal / Alanine dehydrogenase/PNT, C-terminal domain / 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: 2.88 Å
AuthorsZhu J / Zhang K / Gennis RB / Li J
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32201038 China
CitationJournal: To Be Published
Title: Structures and mechanism of the nicotinamide nucleotide transhydrogenase from E. coli
Authors: Zhu J / Zhang K / Gennis RB / Li J
History
DepositionDec 25, 2024-
Header (metadata) releaseJan 7, 2026-
Map releaseJan 7, 2026-
UpdateJan 7, 2026-
Current statusJan 7, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62870.png

Downloads & links

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Map

FileDownload / File: emd_62870.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 320 pix.
= 262.4 Å		0.82 Å/pix.
x 320 pix.
= 262.4 Å		0.82 Å/pix.
x 320 pix.
= 262.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.22565874 - 0.5155926
Average (Standard dev.)0.0003709001 (±0.014299385)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 262.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_62870_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_62870_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : The E. coli nicotinamide nucleotide transhydrogenase complex

EntireName: The E. coli nicotinamide nucleotide transhydrogenase complex
Components
  • Complex: The E. coli nicotinamide nucleotide transhydrogenase complex
    • Protein or peptide: NAD(P) transhydrogenase subunit alpha
    • Protein or peptide: NAD(P) transhydrogenase subunit beta
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: Palmitoyl-CoA

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Supramolecule #1: The E. coli nicotinamide nucleotide transhydrogenase complex

SupramoleculeName: The E. coli nicotinamide nucleotide transhydrogenase complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 200 KDa

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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: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 3 / Number of copies: 1 / Formula: PC1
Molecular weightTheoretical: 790.145 Da
Chemical component information

ChemComp-PC1:
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / phospholipid*YM

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Macromolecule #4: Palmitoyl-CoA

MacromoleculeName: Palmitoyl-CoA / type: ligand / ID: 4 / Number of copies: 2 / Formula: PKZ
Molecular weightTheoretical: 1.005943 KDa
Chemical component information

ChemComp-PKZ:
Palmitoyl-CoA

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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: 1.2 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: 2.88 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 210838
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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