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- PDB-8yqf: Structure of PsSIR2 tetradecamer -

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Basic information

Entry
Database: PDB / ID: 8yqf
TitleStructure of PsSIR2 tetradecamer
ComponentsSIR2-like domain-containing protein
KeywordsIMMUNE SYSTEM / cell growth inhibition
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: 5.5 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: Structure of a bacterial protein
Authors: Yu, G. / Liao, F. / Li, X. / Li, Z. / Zhang, H.
History
DepositionMar 19, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SIR2-like domain-containing protein
B: SIR2-like domain-containing protein
C: SIR2-like domain-containing protein
D: SIR2-like domain-containing protein
E: SIR2-like domain-containing protein
F: SIR2-like domain-containing protein
G: SIR2-like domain-containing protein
H: SIR2-like domain-containing protein
I: SIR2-like domain-containing protein
J: SIR2-like domain-containing protein
K: SIR2-like domain-containing protein
L: SIR2-like domain-containing protein
M: SIR2-like domain-containing protein
N: SIR2-like domain-containing protein


Theoretical massNumber of molelcules
Total (without water)610,53314
Polymers610,53314
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
SIR2-like domain-containing protein


Mass: 43609.480 Da / Num. of mol.: 14
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

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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: PsSIR2 tetradecamer / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
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: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 5.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 50000 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00238808
ELECTRON MICROSCOPYf_angle_d0.42952836
ELECTRON MICROSCOPYf_dihedral_angle_d10.03213986
ELECTRON MICROSCOPYf_chiral_restr0.0386174
ELECTRON MICROSCOPYf_plane_restr0.0036846

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