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Yorodumi- EMDB-17724: CryoEM reconstruction of hemagglutinin HK68 of Influenza A virus ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17724 | |||||||||
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Title | CryoEM reconstruction of hemagglutinin HK68 of Influenza A virus bound to an Affimer reagent | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Complex / Inhibitor / CryoEM / Antiviral / ANTIVIRAL PROTEIN | |||||||||
Function / homology | Function and homology information viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / 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 | Influenza A virus / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Debski-Antoniak O / Flynn A / Klebl DP / Tiede C / Muench S / Tomlinson D / Fontana J | |||||||||
Funding support | 1 items
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Citation | Journal: To Be Published Title: Exploiting the Affimer platform against influenza A virus Authors: Debski-Antoniak O / Flynn A / Klebl DP / Tiede C / Muench S / Tomlinson D / Fontana J | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_17724.map.gz | 214.6 MB | EMDB map data format | |
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Header (meta data) | emd-17724-v30.xml emd-17724.xml | 19.4 KB 19.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17724_fsc.xml | 13.2 KB | Display | FSC data file |
Images | emd_17724.png | 67 KB | ||
Filedesc metadata | emd-17724.cif.gz | 5.8 KB | ||
Others | emd_17724_additional_1.map.gz emd_17724_additional_2.map.gz emd_17724_half_map_1.map.gz emd_17724_half_map_2.map.gz | 230.3 MB 121.6 MB 226.5 MB 226.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17724 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17724 | HTTPS FTP |
-Validation report
Summary document | emd_17724_validation.pdf.gz | 772.1 KB | Display | EMDB validaton report |
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Full document | emd_17724_full_validation.pdf.gz | 771.7 KB | Display | |
Data in XML | emd_17724_validation.xml.gz | 22.2 KB | Display | |
Data in CIF | emd_17724_validation.cif.gz | 28.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17724 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17724 | HTTPS FTP |
-Related structure data
Related structure data | 8pk3MC 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_17724.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.86 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: #1
File | emd_17724_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: #2
File | emd_17724_additional_2.map | ||||||||||||
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Density Histograms |
-Half map: #1
File | emd_17724_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_17724_half_map_2.map | ||||||||||||
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Density Histograms |
-Sample components
-Entire : CryoEM reconstruction of hemagglutinin HK68 of Influenza A virus ...
Entire | Name: CryoEM reconstruction of hemagglutinin HK68 of Influenza A virus bound to an Affimer reagent |
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Components |
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-Supramolecule #1: CryoEM reconstruction of hemagglutinin HK68 of Influenza A virus ...
Supramolecule | Name: CryoEM reconstruction of hemagglutinin HK68 of Influenza A virus bound to an Affimer reagent type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2-#3 |
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Source (natural) | Organism: Influenza A virus |
-Macromolecule #1: Hemagglutinin HA1 chain
Macromolecule | Name: Hemagglutinin HA1 chain / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Influenza A virus |
Molecular weight | Theoretical: 35.349754 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: ADPGATLCLG HHAVPNGTLV KTITDDQIEV TNATELVQSS STGKICNNPH RILDGIDCTL IDALLGDPHC DVFQNETWDL FVERSKAFS NCYPYDVPDY ASLRSLVASS GTLEFITEGF TWTGVTQNGG SNACKRGPGS GFFSRLNWLT KSGSTYPVLN V TMPNNDNF ...String: ADPGATLCLG HHAVPNGTLV KTITDDQIEV TNATELVQSS STGKICNNPH RILDGIDCTL IDALLGDPHC DVFQNETWDL FVERSKAFS NCYPYDVPDY ASLRSLVASS GTLEFITEGF TWTGVTQNGG SNACKRGPGS GFFSRLNWLT KSGSTYPVLN V TMPNNDNF DKLYIWGVHH PSTNQEQTSL YVQASGRVTV STRRSQQTII PNIGSRPWVR GLSSRISIYW TIVKPGDVLV IN SNGNLIA PRGYFKMRTG KSSIMRSDAP IDTCISECIT PNGSIPNDKP FQNVNKITYG ACPKYVKQNT LKLATGMRNV PEK QT UniProtKB: Hemagglutinin |
-Macromolecule #2: Hemagglutinin HA2 chain
Macromolecule | Name: Hemagglutinin HA2 chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Influenza A virus |
Molecular weight | Theoretical: 20.21235 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: GLFGAIAGFI ENGWEGMIDG WYGFRHQNSE GTGQAADLKS TQAAIDQING KLNRVIEKTN EKFHQIEKEF SEVEGRIQDL EKYVEDTKI DLWSYNAELL VALENQHTID LTDSEMNKLF EKTRRQLREN AEEMGNGCFK IYHKCDNACI ESIRNGTYDH D VYRDEALN NRFQIKG UniProtKB: Hemagglutinin |
-Macromolecule #3: Affimer molecule (A31)
Macromolecule | Name: Affimer molecule (A31) / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 10.491819 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: SLEIEELARF AVDEHNKKEN ALLEFVRVVK AKEQFNYDQW QDYTMYYLTL EAKDGGKKKL YEAKVWVKFV DSAFETENFK ELQEFKP |
-Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / 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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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 56.2 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: OTHER / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |