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- PDB-8wof: Cryo-EM structure of SIR2/HerA complex -

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Basic information

Entry
Database: PDB / ID: 8wof
TitleCryo-EM structure of SIR2/HerA complex
Components
  • Helicase HerA central domain-containing protein
  • SIR2-like domain-containing protein
KeywordsIMMUNE SYSTEM / bacterial immune proteins
Function / homologySIR2-like domain / SIR2-like domain / DHS-like NAD/FAD-binding domain superfamily / SIR2-like domain-containing protein
Function and homology information
Biological speciesPaenibacillus sp. 453mf (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsYu, G. / Liao, F. / Li, X. / Li, Z. / Zhang, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32200496 China
CitationJournal: To Be Published
Title: Cryo-EM structure of a bacterial protein
Authors: Yu, G. / Liao, F. / Li, X. / Li, Z. / Zhang, H.
History
DepositionOct 7, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release
Revision 1.0Sep 11, 2024Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 11, 2024Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Sep 11, 2024Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 11, 2024Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 11, 2024Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 11, 2024Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jun 18, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Helicase HerA central domain-containing protein
J: SIR2-like domain-containing protein
K: SIR2-like domain-containing protein
L: Helicase HerA central domain-containing protein
M: Helicase HerA central domain-containing protein
N: Helicase HerA central domain-containing protein
O: Helicase HerA central domain-containing protein
P: SIR2-like domain-containing protein
Q: SIR2-like domain-containing protein
R: SIR2-like domain-containing protein
S: SIR2-like domain-containing protein
T: SIR2-like domain-containing protein
B: Helicase HerA central domain-containing protein


Theoretical massNumber of molelcules
Total (without water)771,02413
Polymers771,02413
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Helicase HerA central domain-containing protein


Mass: 77626.344 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: WP_091160506.1 / Source: (gene. exp.) Paenibacillus sp. 453mf (bacteria) / Gene: SAMN04488601_104156 / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Protein
SIR2-like domain-containing protein


Mass: 43609.480 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillus sp. 453mf (bacteria) / Gene: SAMN04488601_104157 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1I6T0R8
Has protein modificationN

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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: Cryo-EM structure of a bacterial protein / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.4 MDa / Experimental value: YES
Source (natural)Organism: Paenibacillus sp. 453mf (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 40 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 43232 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00244940
ELECTRON MICROSCOPYf_angle_d0.50561404
ELECTRON MICROSCOPYf_dihedral_angle_d12.08615145
ELECTRON MICROSCOPYf_chiral_restr0.0437339
ELECTRON MICROSCOPYf_plane_restr0.0037958

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