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- EMDB-33286: Cryo-EM Structure of R-loop monoclonal antibody S9.6 in recognizi... -
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Open data
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Basic information
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Title | Cryo-EM Structure of R-loop monoclonal antibody S9.6 in recognizing RNA:DNA hybrids | |||||||||
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Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.4 Å | |||||||||
![]() | Li Q / Lin C / Luo Z / Li H / Li X / Sun Q | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 20.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 15.8 KB 15.8 KB | Display Display | ![]() |
Images | ![]() | 30.5 KB | ||
Others | ![]() ![]() | 20.6 MB 20.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 625 KB | Display | ![]() |
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Full document | ![]() | 624.6 KB | Display | |
Data in XML | ![]() | 10.1 KB | Display | |
Data in CIF | ![]() | 11.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.091 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_33286_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_33286_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Cryo-EM Structure of R-loop monoclonal antibody S9.6 in recognizi...
Entire | Name: Cryo-EM Structure of R-loop monoclonal antibody S9.6 in recognizing RNA:DNA hybrids |
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Components |
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-Supramolecule #1: Cryo-EM Structure of R-loop monoclonal antibody S9.6 in recognizi...
Supramolecule | Name: Cryo-EM Structure of R-loop monoclonal antibody S9.6 in recognizing RNA:DNA hybrids type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() ![]() |
-Macromolecule #1: S9.6 Fab HC
Macromolecule | Name: S9.6 Fab HC / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 23.85675 KDa |
Sequence | String: 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 |
-Macromolecule #2: S9.6 Fab LC
Macromolecule | Name: S9.6 Fab LC / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 24.182803 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: 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 |
-Macromolecule #3: DNA
Macromolecule | Name: DNA / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 12.142727 KDa |
Sequence | String: (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) |
-Macromolecule #4: RNA
Macromolecule | Name: RNA / type: rna / ID: 4 / Number of copies: 1 |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 13.12308 KDa |
Sequence | String: CGAGGAACAC GAAGAACAGA CGAGGAACAC GAAGAACAGA |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.2 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination 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
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 64305 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |