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- PDB-8kgc: Cryo-EM structure of human NADK tetramer -

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Basic information

Entry
Database: PDB / ID: 8kgc
TitleCryo-EM structure of human NADK tetramer
ComponentsNAD kinase
KeywordsCYTOSOLIC PROTEIN / NAD kinase / NADP / Nucleotide-binding
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.54 Å
AuthorsZhang, P. / Hu, M. / Liu, Z.
Funding support China, 1items
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, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 21, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NAD kinase
B: NAD kinase
C: NAD kinase
D: NAD kinase


Theoretical massNumber of molelcules
Total (without water)199,6594
Polymers199,6594
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
NAD kinase / Poly(P)/ATP NAD kinase


Mass: 49914.773 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NADK / Production host: Escherichia coli (E. coli) / References: UniProt: O95544, NAD+ kinase

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Tetrameric cytoplasm NADK / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.2 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenConc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1100 nm
Image recordingElectron dose: 55 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21rc1_5127 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.54 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1564310 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 134.77 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00249231
ELECTRON MICROSCOPYf_angle_d0.445412619
ELECTRON MICROSCOPYf_chiral_restr0.0461523
ELECTRON MICROSCOPYf_plane_restr0.00421601
ELECTRON MICROSCOPYf_dihedral_angle_d10.33293172

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