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- EMDB-33286: Cryo-EM Structure of R-loop monoclonal antibody S9.6 in recognizi... -

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Basic information

Entry
Database: EMDB / ID: EMD-33286
TitleCryo-EM Structure of R-loop monoclonal antibody S9.6 in recognizing RNA:DNA hybrids
Map data
Sample
  • Complex: Cryo-EM Structure of R-loop monoclonal antibody S9.6 in recognizing RNA:DNA hybrids
    • Protein or peptide: S9.6 Fab HC
    • Protein or peptide: S9.6 Fab LC
    • DNA: DNA
    • RNA: RNA
KeywordsRNA:DNA hybrid / S9.6 fab / DNA-RNA HYBRID
Biological speciesMus musculus (house mouse) / Arabidopsis (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsLi Q / Lin C / Luo Z / Li H / Li X / Sun Q
Funding support China, 1 items
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, 2022-
Header (metadata) releaseMay 25, 2022-
Map releaseMay 25, 2022-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33286.png

Downloads & links

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Map

FileDownload / File: emd_33286.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 180 pix.
= 196.38 Å		1.09 Å/pix.
x 180 pix.
= 196.38 Å		1.09 Å/pix.
x 180 pix.
= 196.38 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.091 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.2175915 - 1.1302297
Average (Standard dev.)-0.0010193274 (±0.04647635)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 196.37999 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_33286_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_33286_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM Structure of R-loop monoclonal antibody S9.6 in recognizi...

EntireName: Cryo-EM Structure of R-loop monoclonal antibody S9.6 in recognizing RNA:DNA hybrids
Components
  • Complex: Cryo-EM Structure of R-loop monoclonal antibody S9.6 in recognizing RNA:DNA hybrids
    • Protein or peptide: S9.6 Fab HC
    • Protein or peptide: S9.6 Fab LC
    • DNA: DNA
    • RNA: RNA

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Supramolecule #1: Cryo-EM Structure of R-loop monoclonal antibody S9.6 in recognizi...

SupramoleculeName: Cryo-EM Structure of R-loop monoclonal antibody S9.6 in recognizing RNA:DNA hybrids
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: S9.6 Fab HC

MacromoleculeName: S9.6 Fab HC / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.85675 KDa
SequenceString: EVQLQQSGPE LVKPGASVKM SCKASGYTFT SYVMHWVKQK PGQGLEWIGF INLYNDGTKY NEKFKGKATL TSDKSSSTAY MELSSLTSK DSAVYYCARD YYGSRWFDYW GQGTTLTVSS AKTTAPSVYP LAPVCGDTTG SSVTLGCLVK GYFPEPVTLT W NSGSLSSG ...String:
EVQLQQSGPE LVKPGASVKM SCKASGYTFT SYVMHWVKQK PGQGLEWIGF INLYNDGTKY NEKFKGKATL TSDKSSSTAY MELSSLTSK DSAVYYCARD YYGSRWFDYW GQGTTLTVSS AKTTAPSVYP LAPVCGDTTG SSVTLGCLVK GYFPEPVTLT W NSGSLSSG VHTFPAVLQS DLYTLSSSVT VTSSTWPSQS ITCNVAHPAS STKVDKKIEP RV

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Macromolecule #2: S9.6 Fab LC

MacromoleculeName: S9.6 Fab LC / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 24.182803 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString: DVLMTQTPLS LPVSLGDQAS ISCRSSQSIV HSNGNTYLEW YLQKPGQSPK LLIYKVSNRF SGVPDRFSGS GSGTDFTLKI SRVEAEDLG VYYCFQGSHV PYTFGGGTKL EIKRADAAPT VSIFPPSSEQ LTSGGASVVC FLNNFYPKDI NVKWKIDGSE R QNGVLNSW ...String:
DVLMTQTPLS LPVSLGDQAS ISCRSSQSIV HSNGNTYLEW YLQKPGQSPK LLIYKVSNRF SGVPDRFSGS GSGTDFTLKI SRVEAEDLG VYYCFQGSHV PYTFGGGTKL EIKRADAAPT VSIFPPSSEQ LTSGGASVVC FLNNFYPKDI NVKWKIDGSE R QNGVLNSW TDQDSKDSTY SMSSTLTLTK DEYERHNSYT CEATHKTSTS PIVKSFNRNE C

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Macromolecule #3: DNA

MacromoleculeName: DNA / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Arabidopsis (plant)
Molecular weightTheoretical: 12.142727 KDa
SequenceString:
(DT)(DC)(DT)(DG)(DT)(DT)(DC)(DT)(DT)(DC) (DG)(DT)(DG)(DT)(DT)(DC)(DC)(DT)(DC)(DG) (DT)(DC)(DT)(DG)(DT)(DT)(DC)(DT)(DT) (DC)(DG)(DT)(DG)(DT)(DT)(DC)(DC)(DT)(DC) (DG)

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Macromolecule #4: RNA

MacromoleculeName: RNA / type: rna / ID: 4 / Number of copies: 1
Source (natural)Organism: Arabidopsis (plant)
Molecular weightTheoretical: 13.12308 KDa
SequenceString:
CGAGGAACAC GAAGAACAGA CGAGGAACAC GAAGAACAGA

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 64305
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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