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- PDB-8zsh: Cryo-EM Helical Structure of dITP-activated KomBC complex -

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Basic information

Entry
Database: PDB / ID: 8zsh
TitleCryo-EM Helical Structure of dITP-activated KomBC complex
Components
  • KomB, HAM-like protein, Non-canonical purine NTP pyrophosphatase
  • KomC, SIR2 domain protein, NADase
KeywordsIMMUNE SYSTEM / Bacterial immunity / NADase / Filament / CryoEM.
Function / homology2'-deoxyinosine 5'-triphosphate
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3 Å
AuthorsHao, F. / Eddie, T. / Kai, S. / Bin, W. / Min, L.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Ministry of Education (MoE, Singapore) Singapore
CitationJournal: To Be Published
Title: Cryo-EM Helical Structure of dITP-activated KomBC complex
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: KomB, HAM-like protein, Non-canonical purine NTP pyrophosphatase
B: KomB, HAM-like protein, Non-canonical purine NTP pyrophosphatase
C: KomB, HAM-like protein, Non-canonical purine NTP pyrophosphatase
D: KomB, HAM-like protein, Non-canonical purine NTP pyrophosphatase
E: KomC, SIR2 domain protein, NADase
F: KomC, SIR2 domain protein, NADase
G: KomC, SIR2 domain protein, NADase
H: KomC, SIR2 domain protein, NADase
J: KomB, HAM-like protein, Non-canonical purine NTP pyrophosphatase
I: KomB, HAM-like protein, Non-canonical purine NTP pyrophosphatase
K: KomB, HAM-like protein, Non-canonical purine NTP pyrophosphatase
L: KomB, HAM-like protein, Non-canonical purine NTP pyrophosphatase
M: KomC, SIR2 domain protein, NADase
N: KomC, SIR2 domain protein, NADase
O: KomC, SIR2 domain protein, NADase
P: KomC, SIR2 domain protein, NADase
Y: KomB, HAM-like protein, Non-canonical purine NTP pyrophosphatase
e: KomB, HAM-like protein, Non-canonical purine NTP pyrophosphatase
W: KomB, HAM-like protein, Non-canonical purine NTP pyrophosphatase
U: KomB, HAM-like protein, Non-canonical purine NTP pyrophosphatase
g: KomC, SIR2 domain protein, NADase
i: KomC, SIR2 domain protein, NADase
k: KomC, SIR2 domain protein, NADase
m: KomC, SIR2 domain protein, NADase
f: KomB, HAM-like protein, Non-canonical purine NTP pyrophosphatase
Z: KomB, HAM-like protein, Non-canonical purine NTP pyrophosphatase
V: KomB, HAM-like protein, Non-canonical purine NTP pyrophosphatase
X: KomB, HAM-like protein, Non-canonical purine NTP pyrophosphatase
h: KomC, SIR2 domain protein, NADase
j: KomC, SIR2 domain protein, NADase
l: KomC, SIR2 domain protein, NADase
n: KomC, SIR2 domain protein, NADase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)833,62464
Polymers825,36032
Non-polymers8,26432
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
KomB, HAM-like protein, Non-canonical purine NTP pyrophosphatase


Mass: 20929.131 Da / Num. of mol.: 16
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
KomC, SIR2 domain protein, NADase


Mass: 30655.889 Da / Num. of mol.: 16
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.: 16 / Source method: obtained synthetically / Formula: C10H15N4O13P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
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 octomeric HAM-SIR2 with dITP / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 824 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: TFS 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: 78.41 ° / Axial rise/subunit: 47.48 Å / Axial symmetry: D2
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 335058 / Symmetry type: HELICAL
RefinementHighest resolution: 3 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00760032
ELECTRON MICROSCOPYf_angle_d1.07781072
ELECTRON MICROSCOPYf_dihedral_angle_d18.15722400
ELECTRON MICROSCOPYf_chiral_restr0.0628736
ELECTRON MICROSCOPYf_plane_restr0.01310224

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