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- EMDB-41809: A mechanistic understanding of protective influenza B neuraminida... -
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Open data
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Basic information
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Title | A mechanistic understanding of protective influenza B neuraminidase mAbs at the airway interface | |||||||||
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![]() | Neuraminidase Sialidase / ![]() | |||||||||
Function / homology | ![]() exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Ferguson JA / Oeverdieck S / Ward AB | |||||||||
Funding support | ![]()
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![]() | ![]() 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 | ![]() | 483.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 20.8 KB 20.8 KB | Display Display | ![]() |
Images | ![]() | 40.8 KB | ||
Filedesc metadata | ![]() | 6.7 KB | ||
Others | ![]() ![]() ![]() | 93 MB 474 MB 474 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8u1cMC ![]() 8u1qC ![]() 8u1sC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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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 |
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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: ![]() ![]() |
-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: ![]() ![]() |
Molecular weight | Theoretical: 14.438196 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
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: ![]() ![]() |
Molecular weight | Theoretical: 11.529794 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
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: ![]() |
Molecular weight | Theoretical: 51.104258 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
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: ![]() |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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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 |
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Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
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![]() |
Sample stage | Specimen holder model: OTHER / Cooling holder cryogen: NITROGEN |
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 |
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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Image processing
Particle selection | Number selected: 1096437 |
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Startup model | Type of model: INSILICO MODEL |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC |
Final 3D classification | Number classes: 1 |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC |
Final reconstruction | Applied symmetry - Point group: C4 (4 fold cyclic![]() |
-Atomic model buiding 1
Initial model |
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Output model | ![]() PDB-8u1c: |