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- EMDB-37217: Cryo-EM structure of human NADK tetramer -

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Basic information

Entry
Database: EMDB / ID: EMD-37217
TitleCryo-EM structure of human NADK tetramer
Map dataThis map is reconstructed from cryo-EM images collected from K3 camera of TITAN KRIOSg3i and is analysised mainly by the cryoSPARC and Relion.
Sample
  • Organelle or cellular component: Tetrameric cytoplasm NADK
    • Protein or peptide: NAD kinase
KeywordsNAD kinase / NADP / Nucleotide-binding / CYTOSOLIC PROTEIN
Function / homology
Function and homology information


NAD+ kinase / NAD+ kinase activity / NADP+ biosynthetic process / Nicotinate metabolism / NAD+ metabolic process / phosphorylation / positive regulation of insulin secretion involved in cellular response to glucose stimulus / ATP metabolic process / ATP binding / metal ion binding / cytosol
Similarity search - Function
ATP-NAD kinase C-terminal domain / NAD kinase / ATP-NAD kinase, PpnK-type, C-terminal / ATP-NAD kinase N-terminal domain / NAD kinase/diacylglycerol kinase-like domain superfamily / Inorganic polyphosphate/ATP-NAD kinase, N-terminal
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.54 Å
AuthorsZhang P / Hu M / Liu Z
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)8227110337 China
CitationJournal: To Be Published
Title: Regulation of NADK tetramer conformation and activity by cancer-associated mutants
Authors: Zhang P / Hu M / Liu Z
History
DepositionAug 18, 2023-
Header (metadata) releaseAug 21, 2024-
Map releaseAug 21, 2024-
UpdateAug 21, 2024-
Current statusAug 21, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37217.png

Downloads & links

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Map

FileDownload / File: emd_37217.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis map is reconstructed from cryo-EM images collected from K3 camera of TITAN KRIOSg3i and is analysised mainly by the cryoSPARC and Relion.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 256 pix.
= 212.48 Å		0.83 Å/pix.
x 256 pix.
= 212.48 Å		0.83 Å/pix.
x 256 pix.
= 212.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.25200695 - 0.5018305
Average (Standard dev.)-0.000014236033 (±0.015014578)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 212.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: The half maps were reconstructed by cryoSPARC from...

Fileemd_37217_half_map_1.map
AnnotationThe half maps were reconstructed by cryoSPARC from half of the particles.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_37217_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 : Tetrameric cytoplasm NADK

EntireName: Tetrameric cytoplasm NADK
Components
  • Organelle or cellular component: Tetrameric cytoplasm NADK
    • Protein or peptide: NAD kinase

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Supramolecule #1: Tetrameric cytoplasm NADK

SupramoleculeName: Tetrameric cytoplasm NADK / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 200 KDa

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Macromolecule #1: NAD kinase

MacromoleculeName: NAD kinase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: NAD+ kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 49.914773 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GHMASGSMEM EQEKMTMNKE LSPDAAAYCC SACHGDETWS YNHPIRGRAK SRSLSASPAL GSTKEFRRTR SLHGPCPVTT FGPKACVLQ NPQTIMHIQD PASQRLTWNK SPKSVLVIKK MRDASLLQPF KELCTHLMEE NMIVYVEKKV LEDPAIASDE S FGAVKKKF ...String:
GHMASGSMEM EQEKMTMNKE LSPDAAAYCC SACHGDETWS YNHPIRGRAK SRSLSASPAL GSTKEFRRTR SLHGPCPVTT FGPKACVLQ NPQTIMHIQD PASQRLTWNK SPKSVLVIKK MRDASLLQPF KELCTHLMEE NMIVYVEKKV LEDPAIASDE S FGAVKKKF CTFREDYDDI SNQIDFIICL GGDGTLLYAS SLFQGSVPPV MAFHLGSLGF LTPFSFENFQ SQVTQVIEGN AA VVLRSRL KVRVVKELRG KKTAVHNGLG ENGSQAAGLD MDVGKQAMQY QVLNEVVIDR GPSSYLSNVD VYLDGHLITT VQG DGVIVS TPTGSTAYAA AAGASMIHPN VPAIMITPIC PHSLSFRPIV VPAGVELKIM LSPEARNTAW VSFDGRKRQE IRHG DSISI TTSCYPLPSI CVRDPVSDWF ESLAQCLHWN VRKKQAHFEE EEEEEEEG

UniProtKB: NAD kinase

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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

Concentration10 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.1 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3pfn

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.54 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1564310
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: PROJECTION MATCHING

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