+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-35733 | |||||||||
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Title | H7N9 HA-1H9 Fab | |||||||||
Map data | The cryoEM structure of HA-1H9 complex | |||||||||
Sample |
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Keywords | H7N9 / HA / Neutralizing antibody / complex / MEMBRANE PROTEIN / MEMBRANE PROTEIN-IMMUNE SYSTEM complex | |||||||||
Function / homology | Function and homology information viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / apical plasma membrane / 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 Similarity search - Function | |||||||||
Biological species | H7N9 subtype (virus) / Mus musculus (house mouse) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
Authors | Zhao BB / Sun ZZ | |||||||||
Funding support | China, 1 items
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Citation | Journal: To Be Published Title: H7N9 HA-1H9 Fab Authors: Zhao BB / Sun ZZ | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_35733.map.gz | 230.3 MB | EMDB map data format | |
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Header (meta data) | emd-35733-v30.xml emd-35733.xml | 15.2 KB 15.2 KB | Display Display | EMDB header |
Images | emd_35733.png | 66.9 KB | ||
Filedesc metadata | emd-35733.cif.gz | 5.7 KB | ||
Others | emd_35733_half_map_1.map.gz emd_35733_half_map_2.map.gz | 226.3 MB 226.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-35733 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-35733 | HTTPS FTP |
-Validation report
Summary document | emd_35733_validation.pdf.gz | 966 KB | Display | EMDB validaton report |
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Full document | emd_35733_full_validation.pdf.gz | 965.6 KB | Display | |
Data in XML | emd_35733_validation.xml.gz | 16 KB | Display | |
Data in CIF | emd_35733_validation.cif.gz | 19.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35733 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35733 | HTTPS FTP |
-Related structure data
Related structure data | 8iuyMC 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_35733.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | The cryoEM structure of HA-1H9 complex | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.076 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: The half A map of HA-1H9 complex
File | emd_35733_half_map_1.map | ||||||||||||
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Annotation | The half A map of HA-1H9 complex | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: The half B map of HA-1H9 complex
File | emd_35733_half_map_2.map | ||||||||||||
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Annotation | The half B map of HA-1H9 complex | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : The complex of H7N9 HA-1H9 Fab
Entire | Name: The complex of H7N9 HA-1H9 Fab |
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Components |
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-Supramolecule #1: The complex of H7N9 HA-1H9 Fab
Supramolecule | Name: The complex of H7N9 HA-1H9 Fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: H7N9 subtype (virus) |
-Macromolecule #1: Hemagglutinin
Macromolecule | Name: Hemagglutinin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: H7N9 subtype (virus) |
Molecular weight | Theoretical: 54.963367 KDa |
Recombinant expression | Organism: Baculovirus expression vector pFastBac1-HM |
Sequence | String: DKICLGHHAV SNGTKVNTLT ERGVEVVNAT ETVERTNTPR ICSKGKRTVD LGQCGLLGTI TGPPQCDQFL EFSADLIIER REGSDVCYP GKFVNEEALR QILRESGGID KESMGFTYNG IRTNGVTSAC RRSGSSFYAE MKWLLSNTDN AAFPQMTKSY K NTRESPAI ...String: DKICLGHHAV SNGTKVNTLT ERGVEVVNAT ETVERTNTPR ICSKGKRTVD LGQCGLLGTI TGPPQCDQFL EFSADLIIER REGSDVCYP GKFVNEEALR QILRESGGID KESMGFTYNG IRTNGVTSAC RRSGSSFYAE MKWLLSNTDN AAFPQMTKSY K NTRESPAI IVWGIHHSVS TAEQTKLYGS GNKLVTVGSS NYQQSFVPSP GARPQVNGLS GRIDFHWLIL NPNDTVTFSF NG AFIAPDR ASFLRGKSMG IQSGVQVDAN CEGDCYHSGG TIISNLPFQN IDSRAVGKCP RYVKQRSLLL ATGMKNVPEV PKG KRTARG LFGAIAGFIE NGWEGLIDGW YGFRHQNAQG EGTAADYKST QSAIDQITGK LNRLIAKTNQ QFKLIDNEFN EVEK QIGNV INWTRDSITE VWSYNAELLV AMENQHTIDL ADSEMDKLYE RVKRQLRENA EEDGTGCFEI FHKCDDDCMA SIRNN TYDH RKYREEAMQN UniProtKB: Hemagglutinin |
-Macromolecule #2: 1H9 Fab heavy chain
Macromolecule | Name: 1H9 Fab heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 13.339751 KDa |
Recombinant expression | Organism: Mus musculus (house mouse) |
Sequence | String: MVQLQESGPG LVKPSQSLSL TCTVTGYSIT SDYTWNWIRQ FPGNKLEWMG YITYSDTTSY NPSLKSRISI TRDTSKNQFF LQLNSVTTE DTATYYCARS DGWYGFAYWG QGTLVTVSA |
-Macromolecule #3: 1H9 Fab light chain
Macromolecule | Name: 1H9 Fab light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 11.661016 KDa |
Recombinant expression | Organism: Mus musculus (house mouse) |
Sequence | String: DIQMNQSPSS LSASLGDTIT ITCHASQNIN VWLSWYQQKP GNIPKLLIYK AFDLHTGVPS RFSGSGSGTG FTLTISSLQP EDIATYYCQ QGQTYPFTFG GGTKLEIK |
-Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 3 / 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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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: NITROGEN |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 179237 |
Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: NOT APPLICABLE |