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- EMDB-50546: Cryo-EM structure of Influenza B/Washington/02/2019 virus hemaggl... -
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Open data
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Basic information
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Title | Cryo-EM structure of Influenza B/Washington/02/2019 virus hemagglutinin in complex with single-domain antibody hVHH-69. | ||||||||||||
![]() | Anisotropic sharpened map of Influenza B/Washington/02/2019 hemagglutinin in complex with hVHH-69, used for model refinement in Phenix. | ||||||||||||
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![]() | hemagglutinin / single-domain antibody / complex / ANTIVIRAL PROTEIN | ||||||||||||
Function / homology | ![]() viral budding from plasma membrane / host cell surface receptor binding / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.93 Å | ||||||||||||
![]() | Felix J / Matthys A / Savvides SN / Saelens X | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Single-domain antibodies directed against hemagglutinin and neuraminidase protect against influenza B viruses Authors: Matthys A / Felix J / Catani JPP / Roose K / Nerinckx W / Van Buyten B / Fijalkowska D / Callewaert N / Savvides SN / Saelens X | ||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 165.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 24.4 KB 24.4 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 11.9 KB | Display | ![]() |
Images | ![]() | 93.5 KB | ||
Masks | ![]() | 178 MB | ![]() | |
Filedesc metadata | ![]() | 7 KB | ||
Others | ![]() ![]() ![]() ![]() | 165.1 MB 151.4 MB 165 MB 165 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 963.4 KB | Display | ![]() |
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Full document | ![]() | 963 KB | Display | |
Data in XML | ![]() | 20.7 KB | Display | |
Data in CIF | ![]() | 26.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9fm1MC ![]() 9fm2C 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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Annotation | Anisotropic sharpened map of Influenza B/Washington/02/2019 hemagglutinin in complex with hVHH-69, used for model refinement in Phenix. | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.72 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Additional map: Unsharpened, unfiltered full map of Influenza B/Washington/02/2019 hemagglutinin...
File | emd_50546_additional_1.map | ||||||||||||
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Annotation | Unsharpened, unfiltered full map of Influenza B/Washington/02/2019 hemagglutinin in complex with hVHH-69, used for map and model validation. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: DeepEMhancer sharpened map of Influenza B/Washington/02/2019 hemagglutinin in...
File | emd_50546_additional_2.map | ||||||||||||
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Annotation | DeepEMhancer sharpened map of Influenza B/Washington/02/2019 hemagglutinin in complex with hVHH-69, used for model building and map visualization. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 2 of Influenza B/Washington/02/2019 hemagglutinin in...
File | emd_50546_half_map_1.map | ||||||||||||
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Annotation | Half map 2 of Influenza B/Washington/02/2019 hemagglutinin in complex with hVHH-69. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 1 of Influenza B/Washington/02/2019 hemagglutinin in...
File | emd_50546_half_map_2.map | ||||||||||||
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Annotation | Half map 1 of Influenza B/Washington/02/2019 hemagglutinin in complex with hVHH-69. | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Complex between Influenza B/Washington/02/2019 virus hemagglutini...
Entire | Name: Complex between Influenza B/Washington/02/2019 virus hemagglutinin and single-domain antibody hVHH-69 |
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Components |
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-Supramolecule #1: Complex between Influenza B/Washington/02/2019 virus hemagglutini...
Supramolecule | Name: Complex between Influenza B/Washington/02/2019 virus hemagglutinin and single-domain antibody hVHH-69 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 270 KDa |
-Macromolecule #1: Hemagglutinin
Macromolecule | Name: Hemagglutinin / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 65.530621 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MPMGSLQPLA TLYLLGMLVA SVLGDRICTG ITSSNSPHVV KTATQGEVNV TGVIPLTTTP TKSHFANLKG TETRGKLCPK CLNCTDLDV ALGRPKCTGK IPSARVSILH EVRPVTSGCF PIMHDRTKIR QLPNLLRGYE HVRLSTHNVI NAEDAPGRPY E IGTSGSCP ...String: MPMGSLQPLA TLYLLGMLVA SVLGDRICTG ITSSNSPHVV KTATQGEVNV TGVIPLTTTP TKSHFANLKG TETRGKLCPK CLNCTDLDV ALGRPKCTGK IPSARVSILH EVRPVTSGCF PIMHDRTKIR QLPNLLRGYE HVRLSTHNVI NAEDAPGRPY E IGTSGSCP NITNGNGFFA TMAWAVPKNK TATNPLTIEV PYICTEGEDQ ITVWGFHSDN ETQMAKLYGD SKPQKFTSSA NG VTTHYVS QIGGFPNQTE DGGLPQSGRI VVDYMVQKSG KTGTITYQRG ILLPQKVWCA SGRSKVIKGS LPLIGEADCL HEK YGGLNK SKPYYTGEHA KAIGNCPIWV KTPLKLANGT KYRPPAKLLK ERGFFGAIAG FLEGGWEGMI AGWHGYTSHG AHGV AVAAD LKSTQEAINK ITKNLNSLSE LEVKNLQRLS GAMDELHNEI LELDEKVDDL RADTISSQIE LAVLLSNEGI INSED EHLL ALERKLKKML GPSAVEIGNG CFETKHKCNQ TCLDRIAAGT FDAGEFSLPT FDSLNITAAS LNDDGLDNHT ISGKRM KQI EDKIEEIESK QKKIENEIAR IKKLIGERSA WSHPQFEK UniProtKB: Hemagglutinin |
-Macromolecule #2: Single-domain antibody hVHH-69
Macromolecule | Name: Single-domain antibody hVHH-69 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 13.521857 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: DVQLVESGGG LVQPGGSLRL SCAASGLVDS ANVAWFRQAP GKEREFVAAV KWRSGSTIYA DSVEGRFTIS RDNAKSTVYL QMNSLRPED TAVYYCAANQ WYSGGYYGEK NYDYWGQGTL VTVSS |
-Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 6 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ![]() ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.4 mg/mL | ||||||||||
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Buffer | pH: 7.4 Component:
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE | ||||||||||
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | JEOL CRYO ARM 300 |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 4352 / Average electron dose: 60.0 e/Å2 Details: Images were collected at 40 degree tilt to overcome preferred orientations. |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm |