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- EMDB-38098: CryoEM structure of the trifunctional NAD biosynthesis/regulator ... -

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Basic information

Entry
Database: EMDB / ID: EMD-38098
TitleCryoEM structure of the trifunctional NAD biosynthesis/regulator protein NadR in complex with NAD
Map data
Sample
  • Complex: the trifunctional NAD biosynthesis/regulator protein NadR in complex with NAD
    • Protein or peptide: Trifunctional NAD biosynthesis/regulator protein NadR
  • Ligand: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
  • Ligand: PHOSPHATE ION
Keywordsthe trifunctional NAD biosynthesis/regulator protein NadR / CELL INVASION
Function / homology
Function and homology information


response to alkaline pH / adenylyltransferase complex / ribosylnicotinamide kinase / ribosylnicotinamide kinase activity / nicotinamide-nucleotide adenylyltransferase / cellular response to metal ion / nicotinamide-nucleotide adenylyltransferase activity / NAD+ biosynthetic process / catalytic complex / cis-regulatory region sequence-specific DNA binding ...response to alkaline pH / adenylyltransferase complex / ribosylnicotinamide kinase / ribosylnicotinamide kinase activity / nicotinamide-nucleotide adenylyltransferase / cellular response to metal ion / nicotinamide-nucleotide adenylyltransferase activity / NAD+ biosynthetic process / catalytic complex / cis-regulatory region sequence-specific DNA binding / protein homotetramerization / magnesium ion binding / ATP binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
: / Nicotinamide-nucleotide adenylyltransferase / NAD biosynthesis/regulator protein NadR / NadR/Ttd14, AAA domain / NadR, nicotinamide/nicotinate mononucleotide adenylyltransferase domain / AAA domain / Helix-turn-helix / Cytidyltransferase-like domain / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. ...: / Nicotinamide-nucleotide adenylyltransferase / NAD biosynthesis/regulator protein NadR / NadR/Ttd14, AAA domain / NadR, nicotinamide/nicotinate mononucleotide adenylyltransferase domain / AAA domain / Helix-turn-helix / Cytidyltransferase-like domain / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / Lambda repressor-like, DNA-binding domain superfamily / Rossmann-like alpha/beta/alpha sandwich fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Trifunctional NAD biosynthesis/regulator protein NadR
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria) / Escherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.66 Å
AuthorsJiang WX / Dong X / Cheng XQ / Ma LX / Xing Q
Funding support China, 1 items
OrganizationGrant numberCountry
National Basic Research Program of China (973 Program)2021YFC2100100 China
CitationJournal: To Be Published
Title: CryoEM structure of the trifunctional NAD biosynthesis/regulator protein NadR in complex with NAD
Authors: Jiang WX / Dong X / Cheng XQ / Ma LX / Xing Q
History
DepositionNov 24, 2023-
Header (metadata) releaseDec 4, 2024-
Map releaseDec 4, 2024-
UpdateDec 4, 2024-
Current statusDec 4, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_38098.png

Downloads & links

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Map

FileDownload / File: emd_38098.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.)
0.57 Å/pix.
x 360 pix.
= 203.76 Å		0.57 Å/pix.
x 360 pix.
= 203.76 Å		0.57 Å/pix.
x 360 pix.
= 203.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.566 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0408
Minimum - Maximum-0.09234191 - 0.19109856
Average (Standard dev.)0.00015232326 (±0.010201069)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 203.76 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_38098_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_38098_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 trifunctional NAD biosynthesis/regulator protein NadR in comp...

EntireName: the trifunctional NAD biosynthesis/regulator protein NadR in complex with NAD
Components
  • Complex: the trifunctional NAD biosynthesis/regulator protein NadR in complex with NAD
    • Protein or peptide: Trifunctional NAD biosynthesis/regulator protein NadR
  • Ligand: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
  • Ligand: PHOSPHATE ION

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Supramolecule #1: the trifunctional NAD biosynthesis/regulator protein NadR in comp...

SupramoleculeName: the trifunctional NAD biosynthesis/regulator protein NadR in complex with NAD
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)

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Macromolecule #1: Trifunctional NAD biosynthesis/regulator protein NadR

MacromoleculeName: Trifunctional NAD biosynthesis/regulator protein NadR / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: nicotinamide-nucleotide adenylyltransferase
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 40.393555 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: KTIGVVFGKF YPLHTGHIYL IQRACSQVDE LHIIMGFDDT RDRALFEDSA MSQQPTVPDR LRWLLQTFKY QKNIRIHAFN EEGMEPYPH GWDVWSNGIK KFMAEKGIQP DLIYTSEEAD APQYMEHLGI ETVLVDPKRT FMSISGAQIR ENPFRYWEYI P TEVKPFFV ...String:
KTIGVVFGKF YPLHTGHIYL IQRACSQVDE LHIIMGFDDT RDRALFEDSA MSQQPTVPDR LRWLLQTFKY QKNIRIHAFN EEGMEPYPH GWDVWSNGIK KFMAEKGIQP DLIYTSEEAD APQYMEHLGI ETVLVDPKRT FMSISGAQIR ENPFRYWEYI P TEVKPFFV RTVAILGGES SGKSTLVNKL ANIFNTTSAW EYGRDYVFSH LGGDEIALQY SDYDKIALGH AQYIDFAVKY AN KVAFIDT DFVTTQAFCK KYEGREHPFV QALIDEYRFD LVILLENNTP WVADGLRSLG SSVDRKEFQN LLVEMLEENN IEF VRVEEE DYDSRFLRCV ELVREMMGEQ R

UniProtKB: Trifunctional NAD biosynthesis/regulator protein NadR

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Macromolecule #2: NICOTINAMIDE-ADENINE-DINUCLEOTIDE

MacromoleculeName: NICOTINAMIDE-ADENINE-DINUCLEOTIDE / type: ligand / ID: 2 / Number of copies: 4 / Formula: NAD
Molecular weightTheoretical: 663.425 Da
Chemical component information

ChemComp-NAD:
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD*YM

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Macromolecule #3: PHOSPHATE ION

MacromoleculeName: PHOSPHATE ION / type: ligand / ID: 3 / Number of copies: 4 / Formula: PO4
Molecular weightTheoretical: 94.971 Da
Chemical component information

ChemComp-PO4:
PHOSPHATE ION

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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

Concentration3.5 mg/mL
BufferpH: 7.2
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 38.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.66 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 484976
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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