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Yorodumi- EMDB-30707: Hemagglutinin Influenza A virus (A/Okuda/1957(H2N2) bound with a ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30707 | |||||||||
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Title | Hemagglutinin Influenza A virus (A/Okuda/1957(H2N2) bound with a neutralizing antibody | |||||||||
Map data | ||||||||||
Sample |
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Keywords | neutralizing antibody / Influenza A virus / Hemagglutinin / Fv-clasp / Okuda / VIRAL PROTEIN | |||||||||
Function / homology | Function and homology information viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / 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 | Influenza A virus (A/Okuda/1957(H2N2)) / Mus musculus (house mouse) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
Authors | Shirouzu M | |||||||||
Citation | Journal: To Be Published Title: Hemagglutinin Influenza A virus (A/Okuda/1957(H2N2) bound with a neutralizing antibody Authors: Makino-Okamura C / Hata H / Watanabe T / Kim S / Hebrard M / Sato R / Yan M / Onodera T / Takahashi Y / Li Q / Taylor T / Okuno Y / Kurosaki T / Tomabechi Y / Uchikubo-Kamo T / Kamada K / Shirouzu M / Fukuyama H | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_30707.map.gz | 12.1 MB | EMDB map data format | |
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Header (meta data) | emd-30707-v30.xml emd-30707.xml | 19.7 KB 19.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_30707_fsc.xml | 5.4 KB | Display | FSC data file |
Images | emd_30707.png | 65.9 KB | ||
Others | emd_30707_half_map_1.map.gz emd_30707_half_map_2.map.gz | 9.8 MB 9.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30707 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30707 | HTTPS FTP |
-Validation report
Summary document | emd_30707_validation.pdf.gz | 886.5 KB | Display | EMDB validaton report |
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Full document | emd_30707_full_validation.pdf.gz | 886.1 KB | Display | |
Data in XML | emd_30707_validation.xml.gz | 10.9 KB | Display | |
Data in CIF | emd_30707_validation.cif.gz | 14.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30707 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30707 | HTTPS FTP |
-Related structure data
Related structure data | 7dkjMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_30707.map.gz / Format: CCP4 / Size: 12.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.47 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: #1
File | emd_30707_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_30707_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Hemagglutinin Influenza A virus (A/Okuda/1957(H2N2) bound with a ...
Entire | Name: Hemagglutinin Influenza A virus (A/Okuda/1957(H2N2) bound with a neutralizing antibody |
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Components |
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-Supramolecule #1: Hemagglutinin Influenza A virus (A/Okuda/1957(H2N2) bound with a ...
Supramolecule | Name: Hemagglutinin Influenza A virus (A/Okuda/1957(H2N2) bound with a neutralizing antibody type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Influenza A virus (A/Okuda/1957(H2N2)) |
Molecular weight | Theoretical: 290 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: Influenza A virus (A/Okuda/1957(H2N2)) / Strain: A/Okuda/1957(H2N2) |
Molecular weight | Theoretical: 67.423797 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MLLVNQSHQG FNKEHTSKMV SAIVLYVLLA AAAHSAFADQ ICIGYHANNS TEKVDTICER NVTVTHAKDI LEKTHNGKLC KLNGIPPLE LGDCSIAGWL LGNPKCDRLL SVPEWSYIME KENPRDGLCF PGSFSDYEEL KHLLSSVKHF EKVKILPKDR W TQHTTTGG ...String: MLLVNQSHQG FNKEHTSKMV SAIVLYVLLA AAAHSAFADQ ICIGYHANNS TEKVDTICER NVTVTHAKDI LEKTHNGKLC KLNGIPPLE LGDCSIAGWL LGNPKCDRLL SVPEWSYIME KENPRDGLCF PGSFSDYEEL KHLLSSVKHF EKVKILPKDR W TQHTTTGG SRACAVSGNP SFFRNMVWLT EKGSNYPVAK GSYNNTSGEQ MLIIWGVHHP NDETEQRTLY QNVGTYVSVS TS TLNKRST PETATRPKVN GQGGRMEFFW TLLDMWDTIN FESTGNLIAP EYGFKISKRG SSGIIKTEGT LENCETKCQT PLG AINTTL PFHNVHPLTI GECPKYVKSE KLVLATGLRN VPQIESRGLF GAIAGFIEGG WQGMVDGWYG YHHSNDQGSG YAAD KESTQ KAFDCITNKV NSVIEKINTQ FEAVGKEFGN LEKRLENLNK KMEDGFIDVW TYNAELLVLM ENERTLDFHD SNVKN LYSK VRMQLRDNVK ELGNGCFEFY HKCDDECMNS VKNGTYDYPK YEEESKLNRN EIKGVLVPRG SPGSGYIPEA PRDGQA YVR KDGEWVLLST FLGSGLNDIF EAQKIEWHEG HHHHHH |
-Macromolecule #2: Fv-clasp heavy chain
Macromolecule | Name: Fv-clasp heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 23.083908 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MKDHLIHNHH KHEHAHAEHL YFQGSSGSSG EVKLVESGGG LVQPGGSLRL SCGTSGFTLT DDYMTWVRQP PGKALEWLGF IRDRANGYT TEYSASVKGR FTISRDNSQS IVYLQMNTLR VEDSATYYCA RPKGYFPYAM DYWGQGTSVI VCSGSDYEFL K SWTVEDLQ ...String: MKDHLIHNHH KHEHAHAEHL YFQGSSGSSG EVKLVESGGG LVQPGGSLRL SCGTSGFTLT DDYMTWVRQP PGKALEWLGF IRDRANGYT TEYSASVKGR FTISRDNSQS IVYLQMNTLR VEDSATYYCA RPKGYFPYAM DYWGQGTSVI VCSGSDYEFL K SWTVEDLQ KRLLALDPMM EQEIEEIRQK YQSKRQPILD AIEAK |
-Macromolecule #3: Fv-clasp light chain
Macromolecule | Name: Fv-clasp light chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 21.287729 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MKDHLIHNHH KHEHAHAEHL YFQGSSGSSG DIQMTQSPAS LSVSVGETVT ITCRASENIY SNLAWYQQKQ GKSPQLLVYA ATNLADGVP SRFSGSGSGT QYSLKINSLQ SEDFGSYYCQ HFWGTPWTFG GGTKLEIKAG SDYEFLKSWT VEDLQKRLLA L DPMMEQEI EEIRQKYQCK RQPILDAIEA K |
-Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 9 / 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
Concentration | 0.03 mg/mL |
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Buffer | pH: 7.5 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy
Microscope | FEI TECNAI ARCTICA |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 2043 / Average exposure time: 12.0 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm |
Sample stage | Specimen holder model: OTHER |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model | (Chain: PDB, experimental model, PDB, experimental model) |
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Refinement | Space: REAL / Protocol: AB INITIO MODEL / Overall B value: 141.37 / Target criteria: Corelation coefficient |
Output model | PDB-7dkj: |