+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17362 | ||||||||||||
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Title | Homotypic interacting B1 fab bound to Chondroitin Sulfate A | ||||||||||||
Map data | |||||||||||||
Sample |
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Keywords | Chondroitin Sulfate A / SUGAR BINDING PROTEIN | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||||||||
Authors | Raghavan SSR / Dagil R / Wang KT / Salanti A | ||||||||||||
Funding support | Denmark, 3 items
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Citation | Journal: To Be Published Title: Structure of homotypic B1 fabs bound to Chondroiting Sulfate A Authors: Raghavan SSR / Vidal-Calvo EE / Dagil R / Wang KT / Salanti A | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_17362.map.gz | 91.3 MB | EMDB map data format | |
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Header (meta data) | emd-17362-v30.xml emd-17362.xml | 14.3 KB 14.3 KB | Display Display | EMDB header |
Images | emd_17362.png | 82.6 KB | ||
Filedesc metadata | emd-17362.cif.gz | 5.2 KB | ||
Others | emd_17362_half_map_1.map.gz emd_17362_half_map_2.map.gz | 165.1 MB 165.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17362 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17362 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_17362.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.832 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_17362_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_17362_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : B1 fabs bound to chondroitin sulphate A
Entire | Name: B1 fabs bound to chondroitin sulphate A |
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Components |
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-Supramolecule #1: B1 fabs bound to chondroitin sulphate A
Supramolecule | Name: B1 fabs bound to chondroitin sulphate A / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 50 kDa/nm |
-Macromolecule #1: B1 fab light
Macromolecule | Name: B1 fab light / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 23.662383 KDa |
Recombinant expression | Organism: Cricetulus griseus (Chinese hamster) |
Sequence | String: MEVQLLESGG GLVQPGGSLR LSCAASGFTF TSYAMSWVRQ APGKGLEWVS GISYGSGDTY YADSVKGRFT ISRDNSKNTL YLQMNSLRA EDTAVYYCAR SRGSQTFDYW GQGTLVTVSS ASTKGPSVFP LAPSSKSTSG GTAALGCLVK DYFPEPVTVS W NSGALTSG ...String: MEVQLLESGG GLVQPGGSLR LSCAASGFTF TSYAMSWVRQ APGKGLEWVS GISYGSGDTY YADSVKGRFT ISRDNSKNTL YLQMNSLRA EDTAVYYCAR SRGSQTFDYW GQGTLVTVSS ASTKGPSVFP LAPSSKSTSG GTAALGCLVK DYFPEPVTVS W NSGALTSG VHTFPAVLQS SGLYSLSSVV TVPSSSLGTQ TYICNVNHKP SNTKVDKKVE PKSEF |
-Macromolecule #2: B1 fab heavy
Macromolecule | Name: B1 fab heavy / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 26.419492 KDa |
Recombinant expression | Organism: Cricetulus griseus (Chinese hamster) |
Sequence | String: DIVLTQSPAT LSLSPGERAT LSCRASQSVS RSLAWYQQKP GQAPRLLIYG SSNRATGIPA RFSGSGSGTD FTLTISSLEP EDFAVYYCQ QRIHTSWTFG QGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String: DIVLTQSPAT LSLSPGERAT LSCRASQSVS RSLAWYQQKP GQAPRLLIYG SSNRATGIPA RFSGSGSGTD FTLTISSLEP EDFAVYYCQ QRIHTSWTFG QGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEAGKPI PNPLLGLDST GGSAHIVMVD AY KPTK |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 1.0 µm |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 40.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: INSILICO MODEL |
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Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1250000 |