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- EMDB-30707: Hemagglutinin Influenza A virus (A/Okuda/1957(H2N2) bound with a ... -
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Open data
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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 | |||||||||
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Function / homology | ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Shirouzu M | |||||||||
![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 12.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19.7 KB 19.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 5.4 KB | Display | ![]() |
Images | ![]() | 65.9 KB | ||
Others | ![]() ![]() | 9.8 MB 9.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7dkjMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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 |
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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: ![]() ![]() |
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: ![]() ![]() |
Molecular weight | Theoretical: 67.423797 KDa |
Recombinant expression | Organism: ![]() ![]() |
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: ![]() ![]() ![]() |
Molecular weight | Theoretical: 23.083908 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
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: ![]() ![]() ![]() |
Molecular weight | Theoretical: 21.287729 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
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 | ![]() |
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Aggregation state | particle |
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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 |
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Electron microscopy
Microscope | FEI TECNAI ARCTICA |
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Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Sample stage | Specimen holder model: OTHER |
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 |
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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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: |