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- EMDB-64527: Single-subunit apo Escherichia coli nicotinamide nucleotide trans... -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-64527
TitleSingle-subunit apo Escherichia coli nicotinamide nucleotide transhydrogenase
Map data
Sample
  • Complex: The E. coli transhydrogenase complex.
    • Protein or peptide: NAD(P) transhydrogenase subunit beta
    • Protein or peptide: NAD(P) transhydrogenase subunit alpha
    • Protein or peptide: NAD(P) transhydrogenase subunit alpha
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 / protein dimerization activity / oxidoreductase 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/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: 3.43 Å
AuthorsZhu J / Gennis RB / Zhang K / Li J
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32201038 China
CitationJournal: To Be Published
Title: Single-subunit apo Escherichia coli nicotinamide nucleotide transhydrogenase
Authors: Zhu J / Gennis RB / Zhang K / Li J
History
DepositionMay 9, 2025-
Header (metadata) releaseMay 27, 2026-
Map releaseMay 27, 2026-
UpdateMay 27, 2026-
Current statusMay 27, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64527.png

Downloads & links

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Map

FileDownload / File: emd_64527.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.)
0.82 Å/pix.
x 360 pix.
= 295.2 Å		0.82 Å/pix.
x 360 pix.
= 295.2 Å		0.82 Å/pix.
x 360 pix.
= 295.2 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: 0.156
Minimum - Maximum-0.079741694 - 1.4425137
Average (Standard dev.)0.001827321 (±0.022425966)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 295.2 Å
α=β=γ: 90.0 °

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Supplemental data

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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 beta
    • Protein or peptide: NAD(P) transhydrogenase subunit alpha
    • Protein or peptide: NAD(P) transhydrogenase subunit alpha

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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: all
Source (natural)Organism: Escherichia coli K-12 (bacteria)

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Macromolecule #1: NAD(P) transhydrogenase subunit beta

MacromoleculeName: NAD(P) transhydrogenase subunit beta / 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) / Strain: K-12
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 #2: NAD(P) transhydrogenase subunit alpha

MacromoleculeName: NAD(P) transhydrogenase subunit alpha / 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) / Strain: K-12
Molecular weightTheoretical: 10.742778 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ILFGWMASVA PKEFLGHFTV FALACVVGYY VVWNVSHALH TPLMSVTNAI SGIIVVGALL QIGQGGWVSF LSFIAVLIAS INIFGGFTV TQRMLKMFKN

UniProtKB: NAD(P) transhydrogenase subunit alpha

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Macromolecule #3: NAD(P) transhydrogenase subunit alpha

MacromoleculeName: NAD(P) transhydrogenase subunit alpha / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO / EC number: proton-translocating NAD(P)+ transhydrogenase
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K-12
Molecular weightTheoretical: 40.183902 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: HHGRIGIPRE RLTNETRVAA TPKTVEQLLK LGFTVAVESG AGQLASFDDK AFVQAGAEIV EGNSVWQSEI ILKVNAPLDD EIALLNPGT TLVSFIWPAQ NPELMQKLAE RNVTVMAMDS VPRISRAQSL DALSSMANIA GYRAIVEAAH EFGRFFTGQI T AAGKVPPA ...String:
HHGRIGIPRE RLTNETRVAA TPKTVEQLLK LGFTVAVESG AGQLASFDDK AFVQAGAEIV EGNSVWQSEI ILKVNAPLDD EIALLNPGT TLVSFIWPAQ NPELMQKLAE RNVTVMAMDS VPRISRAQSL DALSSMANIA GYRAIVEAAH EFGRFFTGQI T AAGKVPPA KVMVIGAGVA GLAAIGAANS LGAIVRAFDT RPEVKEQVQS MGAEFLELDF KEEAGSGDGY AKVMSDAFIK AE MELFAAQ AKEVDIIVTT ALIPGKPAPK LITREMVDSM KAGSVIVDLA AQNGGNCEYT VPGEIFTTEN GVKVIGYTDL PGR LPTQSS QLYGTNLVNL LKLLCKEKDG NITVDFDDVV IRGVTVIRAG EITWPAPPIQ V

UniProtKB: NAD(P) transhydrogenase subunit alpha

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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: 1.25 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: 3.43 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 42826
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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