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- PDB-8zsi: CryoEM Helical Structure of HAM-SIR2 with dITP and NAD fragment -

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Basic information

Entry
Database: PDB / ID: 8zsi
TitleCryoEM Helical Structure of HAM-SIR2 with dITP and NAD fragment
Components
  • Non-canonical purine NTP pyrophosphatase
  • Sir2 family NAD-dependent protein deacetylase
KeywordsIMMUNE SYSTEM / NADase / Filament / CryoEM
Function / homologyNICOTINAMIDE-ADENINE-DINUCLEOTIDE / 2'-deoxyinosine 5'-triphosphate
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsHao, F. / Eddie, T. / Bin, W. / Min, L.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Ministry of Education (MoE, Singapore) Singapore
CitationJournal: To Be Published
Title: CryoEM Helical Structure of HAM-SIR2 with dITP and NAD fragment
Authors: Hao, F. / Eddie, T. / Bin, W. / Min, L.
History
DepositionJun 5, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 10, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Non-canonical purine NTP pyrophosphatase
B: Non-canonical purine NTP pyrophosphatase
C: Non-canonical purine NTP pyrophosphatase
D: Non-canonical purine NTP pyrophosphatase
E: Sir2 family NAD-dependent protein deacetylase
F: Sir2 family NAD-dependent protein deacetylase
G: Sir2 family NAD-dependent protein deacetylase
H: Sir2 family NAD-dependent protein deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)209,36714
Polymers206,0728
Non-polymers3,2966
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Non-canonical purine NTP pyrophosphatase


Mass: 20929.131 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: GRW56_02065, GRW57_01900 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43
#2: Protein
Sir2 family NAD-dependent protein deacetylase


Mass: 30588.818 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: GRW56_02060, GRW57_01895 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43
#3: Chemical
ChemComp-Y43 / 2'-deoxyinosine 5'-triphosphate


Mass: 492.166 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N4O13P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Filament of HAM-SIR2 with dITP with NAD fragment / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 206 kDa/nm / Experimental value: YES
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding 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: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 80.62 ° / Axial rise/subunit: 48.69 Å / Axial symmetry: D2
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 188609 / Symmetry type: HELICAL

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