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- PDB-7xlt: Cryo-EM Structure of R-loop monoclonal antibody S9.6 in recognizi... -

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Basic information

Entry
Database: PDB / ID: 7xlt
TitleCryo-EM Structure of R-loop monoclonal antibody S9.6 in recognizing RNA:DNA hybrids
Components
  • DNA
  • RNA
  • S9.6 Fab HC
  • S9.6 Fab LC
KeywordsDNA-RNA HYBRID / RNA:DNA hybrid / S9.6 fab
Function / homologyDNA / DNA (> 10) / RNA / RNA (> 10)
Function and homology information
Biological speciesMus musculus (house mouse)
Arabidopsis (plant)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsLi, Q. / Lin, C. / Luo, Z. / Li, H. / Li, X. / Sun, Q.
Funding support China, 1items
OrganizationGrant numberCountry
Other private041301470 China
CitationJournal: J Genet Genomics / Year: 2022
Title: Cryo-EM structure of R-loop monoclonal antibody S9.6 in recognizing RNA:DNA hybrids.
Authors: Qin Li / Chao Lin / Zhipu Luo / Haitao Li / Xueming Li / Qianwen Sun /
History
DepositionApr 22, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 25, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2022Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 3, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: S9.6 Fab HC
L: S9.6 Fab LC
A: DNA
B: RNA


Theoretical massNumber of molelcules
Total (without water)73,3054
Polymers73,3054
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Antibody S9.6 Fab HC


Mass: 23856.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody S9.6 Fab LC


Mass: 24182.803 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Igkc, Igk-C / Production host: Mus musculus (house mouse)
#3: DNA chain DNA


Mass: 12142.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis (plant) / Production host: Arabidopsis (plant)
#4: RNA chain RNA


Mass: 13123.080 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis (plant) / Production host: Arabidopsis (plant)
Has protein modificationY

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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 R-loop monoclonal antibody S9.6 in recognizing RNA:DNA hybrids
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Mus musculus (house mouse)
Buffer solutionpH: 7.2
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: 2400 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 64305 / Symmetry type: POINT

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