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Yorodumi- EMDB-41441: CryoEM structure of H7 hemagglutinin from A/Shanghai2/2013 H7N9 i... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41441 | |||||||||
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Title | CryoEM structure of H7 hemagglutinin from A/Shanghai2/2013 H7N9 in complex with a human neutralizing antibody H7.HK2 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | virus / antibody / influenza / VIRAL PROTEIN / VIRAL 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 | Homo sapiens (human) / Influenza A virus (A/Shanghai/02/2013(H7N9)) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.69 Å | |||||||||
Authors | Morano NC / Becker JE / Wu X / Shapiro L | |||||||||
Funding support | United States, 1 items
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Citation | Journal: To Be Published Title: CryoEM structure of H7 hemagglutinin from A/Shanghai2/2013 H7N9 in complex with a human neutralizing antibody H7.HK1 Authors: Morano NC / Wu X / Shapiro L | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_41441.map.gz | 203.8 MB | EMDB map data format | |
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Header (meta data) | emd-41441-v30.xml emd-41441.xml | 15.5 KB 15.5 KB | Display Display | EMDB header |
Images | emd_41441.png | 138.8 KB | ||
Filedesc metadata | emd-41441.cif.gz | 5.7 KB | ||
Others | emd_41441_half_map_1.map.gz emd_41441_half_map_2.map.gz | 200.8 MB 200.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41441 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41441 | HTTPS FTP |
-Validation report
Summary document | emd_41441_validation.pdf.gz | 851.6 KB | Display | EMDB validaton report |
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Full document | emd_41441_full_validation.pdf.gz | 851.2 KB | Display | |
Data in XML | emd_41441_validation.xml.gz | 15.6 KB | Display | |
Data in CIF | emd_41441_validation.cif.gz | 18.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41441 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41441 | HTTPS FTP |
-Related structure data
Related structure data | 8toaMC 8tnlC 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_41441.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.83 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_41441_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_41441_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : H7 hemagglutinin from A/Shanghai2/2013 H7N9 in complex with a hum...
Entire | Name: H7 hemagglutinin from A/Shanghai2/2013 H7N9 in complex with a human neutralizing antibody H7.HK1 |
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Components |
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-Supramolecule #1: H7 hemagglutinin from A/Shanghai2/2013 H7N9 in complex with a hum...
Supramolecule | Name: H7 hemagglutinin from A/Shanghai2/2013 H7N9 in complex with a human neutralizing antibody H7.HK1 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: H7.HK2 Neutralizing Antibody Heavy Chain
Macromolecule | Name: H7.HK2 Neutralizing Antibody Heavy Chain / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 13.104523 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: QVQLQGSGPG LLRPSETLSL TCSVSGVSIN SYYWSWVRQP PGKALEWIGY IYYSGNTNYN PSLESRVTIS VDRSKNQFSL KMTSVTAAD TARYFCARQG IFGDYGSDYW GPGTLVTVSS |
-Macromolecule #2: H7.HK2 Neutralizing Antibody Light Chain
Macromolecule | Name: H7.HK2 Neutralizing Antibody Light Chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 12.18963 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: DIVMTQSPLS LPVTPGEPAS ISCRSNQSLQ HSNGYVHLDW YRQKPGQSPH LLIYLGFNRA SGVPDRFSGG GSGTDFTLKI SRVEAEDVG VYYCMQGLQT PFTFGPGTTV DLK |
-Macromolecule #3: Hemagglutinin
Macromolecule | Name: Hemagglutinin / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Influenza A virus (A/Shanghai/02/2013(H7N9)) |
Molecular weight | Theoretical: 63.075688 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MNTQILVFAL IAIIPTNADK ICLGHHAVSN GTKVNTLCER GVEVVNATET VERTNIPRIC SKGKRTVDLG QCGLLGTITG PPQCDQFLE FSADLIIERR EGSDVCYPGK FVNEEALRQI LRESGGIDKE AMGFTYSGIR TNGATSSCRR SGSSFYAEMK W LLSNTDNA ...String: MNTQILVFAL IAIIPTNADK ICLGHHAVSN GTKVNTLCER GVEVVNATET VERTNIPRIC SKGKRTVDLG QCGLLGTITG PPQCDQFLE FSADLIIERR EGSDVCYPGK FVNEEALRQI LRESGGIDKE AMGFTYSGIR TNGATSSCRR SGSSFYAEMK W LLSNTDNA AFPQMTKSYK NTRKNPALIV WGIHHSGSTA EQTKLYGSGN KLVTVGSSNY QQSFVPSPGA RTQVNGQSGR ID FHWLMLN PNDTVTFSFN GAFIAPDRAS FLRGKSMGIQ SGVQVDADCE GDCYYSGGTI ISNLPFQNID SRAVGKCPRY VKQ RSLLLA TGMKNVPEIP KGRRRRRRGL FGAIAGFIEN GWEGLIDGWY GFRHQNAQGE GTAADYKSTQ SAIDCITGKL NRLI EKTNQ QFELIDNEFT EVEKQIGNVI NWTRDSITEV WSYNAELLVA MENQHTIDLA DSEMDKLYER VKRQLRENAE EDGTG CFEI FHKCDDDCMA SIRNNTYDHS KYREEAMQNR IQIDGVSGRL VPRGSPGSGY IPEAPRDGQA YVRKDGEWVL LSTFLG HHH HHH UniProtKB: Hemagglutinin |
-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: 11 / 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: 7 |
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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 K3 BIOQUANTUM (6k x 4k) / Average electron dose: 58.06 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: 2.0 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.69 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 191469 |
Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: NOT APPLICABLE |