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- PDB-8xhs: Cryo-EM structure of free-state KmAgo -

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Basic information

Entry
Database: PDB / ID: 8xhs
TitleCryo-EM structure of free-state KmAgo
ComponentsKmAgo
KeywordsDNA BINDING PROTEIN / Mesophilic prokaryotic Argonaute
Biological speciesKurthia massiliensis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.85 Å
AuthorsXin, T. / Hui, D. / Shaowen, W.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2021YFC2100100 China
CitationJournal: To Be Published
Title: Structural and mechanistic insights into a mesophilic prokaryotic Argonaute
Authors: Xin, T. / Hui, D. / Shaowen, W.
History
DepositionDec 18, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 25, 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: KmAgo


Theoretical massNumber of molelcules
Total (without water)85,4851
Polymers85,4851
Non-polymers00
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein KmAgo


Mass: 85485.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kurthia massiliensis (bacteria) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O
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: KmAgo / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Kurthia massiliensis (bacteria)
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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 54 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 386173 / Symmetry type: POINT
RefinementHighest resolution: 2.85 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0025164
ELECTRON MICROSCOPYf_angle_d0.4876981
ELECTRON MICROSCOPYf_dihedral_angle_d4.128673
ELECTRON MICROSCOPYf_chiral_restr0.042774
ELECTRON MICROSCOPYf_plane_restr0.003882

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