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- PDB-8xih: protein-DNA complex -

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Basic information

Entry
Database: PDB / ID: 8xih
Titleprotein-DNA complex
Components
  • DNA (5'-D(P*AP*TP*AP*AP*AP*AP*A)-3')
  • DNA (5'-D(P*TP*GP*AP*GP*GP*TP*AP*A)-3')
  • DNA (5'-D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*AP*TP*TP*TP*GP*T)-3')
  • Piwi domain-containing protein
KeywordsDNA BINDING PROTEIN/DNA / DNA / protein / DNA BINDING PROTEIN-DNA complex
Function / homologyRibonuclease H superfamily / nucleic acid binding / Ribonuclease H-like superfamily / DNA / DNA (> 10) / Piwi domain-containing protein
Function and homology information
Biological speciesMucilaginibacter paludis DSM 18603 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsLi, Z.
Funding support1items
OrganizationGrant numberCountry
Not fundedNA
CitationJournal: To Be Published
Title: protein-DNA complex
Authors: Zhuang, L.
History
DepositionDec 19, 2023Deposition site: PDBJ / Processing site: PDBC
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: Piwi domain-containing protein
B: Piwi domain-containing protein
G: DNA (5'-D(P*TP*GP*AP*GP*GP*TP*AP*A)-3')
H: DNA (5'-D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*AP*TP*TP*TP*GP*T)-3')
E: DNA (5'-D(P*AP*TP*AP*AP*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,5337
Polymers193,4845
Non-polymers492
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 Piwi domain-containing protein


Mass: 91915.383 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mucilaginibacter paludis DSM 18603 (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: H1YCU5
#2: DNA chain DNA (5'-D(P*TP*GP*AP*GP*GP*TP*AP*A)-3')


Mass: 2490.666 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Mucilaginibacter paludis DSM 18603 (bacteria)
#3: DNA chain DNA (5'-D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*AP*TP*TP*TP*GP*T)-3')


Mass: 5024.260 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Mucilaginibacter paludis DSM 18603 (bacteria)
#4: DNA chain DNA (5'-D(P*AP*TP*AP*AP*AP*AP*A)-3')


Mass: 2138.476 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Mucilaginibacter paludis DSM 18603 (bacteria)
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / 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: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: protein-DNA complex / Type: COMPLEX / Entity ID: #1-#4 / Source: MULTIPLE SOURCES
Source (natural)Organism: Mucilaginibacter paludis DSM 18603 (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7
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: 2200 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 54 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 274970 / Symmetry type: POINT

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