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Yorodumi- EMDB-41809: A mechanistic understanding of protective influenza B neuraminida... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41809 | |||||||||
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Title | A mechanistic understanding of protective influenza B neuraminidase mAbs at the airway interface | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Neuraminidase Sialidase / HYDROLASE | |||||||||
Function / homology | Function and homology information : / : / : / exo-alpha-sialidase / carbohydrate metabolic process / host cell plasma membrane / virion membrane / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Influenza B virus (B/Iowa/06/2017) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.89 Å | |||||||||
Authors | Ferguson JA / Oeverdieck S / Ward AB | |||||||||
Funding support | United States, 1 items
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Citation | Journal: To Be Published Title: A mechanistic understanding of protective influenza B neuraminidase mAbs at the airway interface Authors: Ferguson JA / Oeverdieck S / Ward AB | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_41809.map.gz | 483.6 MB | EMDB map data format | |
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Header (meta data) | emd-41809-v30.xml emd-41809.xml | 20.8 KB 20.8 KB | Display Display | EMDB header |
Images | emd_41809.png | 40.8 KB | ||
Filedesc metadata | emd-41809.cif.gz | 6.7 KB | ||
Others | emd_41809_additional_1.map.gz emd_41809_half_map_1.map.gz emd_41809_half_map_2.map.gz | 93 MB 474 MB 474 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41809 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41809 | HTTPS FTP |
-Validation report
Summary document | emd_41809_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_41809_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_41809_validation.xml.gz | 19 KB | Display | |
Data in CIF | emd_41809_validation.cif.gz | 22.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41809 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41809 | HTTPS FTP |
-Related structure data
Related structure data | 8u1cMC 8u1qC 8u1sC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_41809.map.gz / Format: CCP4 / Size: 512 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: 0.725 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Downsampled map used for Rosetta relax
File | emd_41809_additional_1.map | ||||||||||||
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Annotation | Downsampled map used for Rosetta_relax | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_41809_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_41809_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Complex of human donor mAb-fv domain bound to influenza B neurami...
Entire | Name: Complex of human donor mAb-fv domain bound to influenza B neuraminidase |
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Components |
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-Supramolecule #1: Complex of human donor mAb-fv domain bound to influenza B neurami...
Supramolecule | Name: Complex of human donor mAb-fv domain bound to influenza B neuraminidase type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: mAb-400 heavy chain
Macromolecule | Name: mAb-400 heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 14.438196 KDa |
Recombinant expression | Organism: Cricetulus griseus (Chinese hamster) |
Sequence | String: GLQLVQSGAE LKKPGESLKI SCQGSGYTFP IYWIGWVRQI PGKGLEWMGI IYPGDSDTRY SPSFEGQVTI SADKSVTTAY LQWSSLKAS DTAMYYCARH SEPWYPDHRF WPPYPFDIWG QGTMVTVSS |
-Macromolecule #2: mAb-400 light chain
Macromolecule | Name: mAb-400 light chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 11.529794 KDa |
Recombinant expression | Organism: Cricetulus griseus (Chinese hamster) |
Sequence | String: EIVLTQSPGT LSLSPGERAT LSCRSSQTVS SGYLAWYQQK RGQAPRLLIY GASSRATGIP DRFSGSGSGT DFTLTISRLE PEDFAVYFC QHHGTSPGTF GGGTKVEIK |
-Macromolecule #3: Neuraminidase
Macromolecule | Name: Neuraminidase / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Influenza B virus (B/Iowa/06/2017) |
Molecular weight | Theoretical: 51.104258 KDa |
Recombinant expression | Organism: Drosophila melanogaster (fruit fly) |
Sequence | String: MLPSTIQTLT LFLTSGGVLL SLYVSASLSY LLYSDILLKF SPTEITAPTM PLDCANASNV QAVNRSATKG VTLLLPGPEW TYPRLSCPG STFQKALLIS PHRFGETKGN SAPLIIREPF VACGPNECKH FALTHYAAQP GGYYNGTRGD RNKLRHLISV K LGKIPTVE ...String: MLPSTIQTLT LFLTSGGVLL SLYVSASLSY LLYSDILLKF SPTEITAPTM PLDCANASNV QAVNRSATKG VTLLLPGPEW TYPRLSCPG STFQKALLIS PHRFGETKGN SAPLIIREPF VACGPNECKH FALTHYAAQP GGYYNGTRGD RNKLRHLISV K LGKIPTVE NSIFHMAAWS GSACHDGKEW TYIGVDGPDN NALLKVKYGE AYTDTYHSYA NNILRTQESA CNCIGGNCYL MI TDGSASG VSECRFLKIR EGRIIKEIFP TGRVKHTEEC TCGFASNKTI ECACRDNRYT AKRPFVKLNV ETDTAEIRLM CTD TYLDTP RPNDGSITGP CESDGDKGSG GIKGGFVHQR MKSKIGRWYS RTMSKTERMG MGLYVKYGGD PWADSDALAF SGVM VPMKE PGWYSFGFEI KDKKCDVPCI GIEMVHDGGK ETWHSAATAI YCLMGSGQLL WDTVTGVDMA L UniProtKB: Neuraminidase |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.4 mg/mL |
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Buffer | pH: 7.4 / Details: TBS |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 25 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK III |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4048 pixel / Digitization - Dimensions - Height: 4048 pixel / Number grids imaged: 1 / Number real images: 5958 / Average electron dose: 49.87 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Calibrated defocus max: 1.5 µm / Calibrated defocus min: 1.5 µm / Calibrated magnification: 190000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 0.7000000000000001 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 190000 |
Sample stage | Specimen holder model: OTHER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model |
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Output model | PDB-8u1c: |