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Yorodumi- EMDB-0235: Structure of Influenza Hemagglutinin ectodomain (A/duck/Alberta/3... -
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-Basic information
Entry | Database: EMDB / ID: EMD-0235 | ||||||||||||||||||||||||
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Title | Structure of Influenza Hemagglutinin ectodomain (A/duck/Alberta/35/76) in complex with FISW84 Fab Fragment | ||||||||||||||||||||||||
Map data | Sharpened Map of A/duck/Alberta/35/76 Hemagglutinin Ectodomain in Complex with FISW84 Fab | ||||||||||||||||||||||||
Sample |
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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 / membrane Similarity search - Function | ||||||||||||||||||||||||
Biological species | Influenza A virus (strain A/Duck/Alberta/35/1976 H1N1) / Homo sapiens (human) | ||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||||||||||||||||||||
Authors | Benton DJ / Rosenthal PB | ||||||||||||||||||||||||
Funding support | United Kingdom, 7 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2018 Title: Influenza hemagglutinin membrane anchor. Authors: Donald J Benton / Andrea Nans / Lesley J Calder / Jack Turner / Ursula Neu / Yi Pu Lin / Esther Ketelaars / Nicole L Kallewaard / Davide Corti / Antonio Lanzavecchia / Steven J Gamblin / ...Authors: Donald J Benton / Andrea Nans / Lesley J Calder / Jack Turner / Ursula Neu / Yi Pu Lin / Esther Ketelaars / Nicole L Kallewaard / Davide Corti / Antonio Lanzavecchia / Steven J Gamblin / Peter B Rosenthal / John J Skehel / Abstract: Viruses with membranes fuse them with cellular membranes, to transfer their genomes into cells at the beginning of infection. For Influenza virus, the membrane glycoprotein involved in fusion is the ...Viruses with membranes fuse them with cellular membranes, to transfer their genomes into cells at the beginning of infection. For Influenza virus, the membrane glycoprotein involved in fusion is the hemagglutinin (HA), the 3D structure of which is known from X-ray crystallographic studies. The soluble ectodomain fragments used in these studies lacked the "membrane anchor" portion of the molecule. Since this region has a role in membrane fusion, we have determined its structure by analyzing the intact, full-length molecule in a detergent micelle, using cryo-EM. We have also compared the structures of full-length HA-detergent micelles with full-length HA-Fab complex detergent micelles, to describe an infectivity-neutralizing monoclonal Fab that binds near the ectodomain membrane anchor junction. We determine a high-resolution HA structure which compares favorably in detail with the structure of the ectodomain seen by X-ray crystallography; we detect, clearly, all five carbohydrate side chains of HA; and we find that the ectodomain is joined to the membrane anchor by flexible, eight-residue-long, linkers. The linkers extend into the detergent micelle to join a central triple-helical structure that is a major component of the membrane anchor. | ||||||||||||||||||||||||
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_0235.map.gz | 475.7 MB | EMDB map data format | |
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Header (meta data) | emd-0235-v30.xml emd-0235.xml | 24.8 KB 24.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_0235_fsc.xml | 18.1 KB | Display | FSC data file |
Images | emd_0235.png | 51 KB | ||
Masks | emd_0235_msk_1.map | 512 MB | Mask map | |
Others | emd_0235_additional.map.gz emd_0235_half_map_1.map.gz emd_0235_half_map_2.map.gz | 475.7 MB 475 MB 475 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0235 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0235 | HTTPS FTP |
-Related structure data
Related structure data | 6hjpMC 0234C 0236C 0237C 6hjnC 6hjqC 6hjrC 6hkgC 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_0235.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Sharpened Map of A/duck/Alberta/35/76 Hemagglutinin Ectodomain in Complex with FISW84 Fab | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.078 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_0235_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Unsharpened Map of A/duck/Alberta/35/76 Hemagglutinin Ectodomain in Complex...
File | emd_0235_additional.map | ||||||||||||
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Annotation | Unsharpened Map of A/duck/Alberta/35/76 Hemagglutinin Ectodomain in Complex with FISW84 Fab | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 2 of A/duck/Alberta/35/76 Hemagglutinin Ectodomain in...
File | emd_0235_half_map_1.map | ||||||||||||
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Annotation | Half map 2 of A/duck/Alberta/35/76 Hemagglutinin Ectodomain in Complex with FISW84 Fab | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 1 of A/duck/Alberta/35/76 Hemagglutinin Ectodomain in...
File | emd_0235_half_map_2.map | ||||||||||||
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Annotation | Half map 1 of A/duck/Alberta/35/76 Hemagglutinin Ectodomain in Complex with FISW84 Fab | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Complex of A/duck/Alberta/35/76 Haemagglutinin and FISW84 Fab Fragment
Entire | Name: Complex of A/duck/Alberta/35/76 Haemagglutinin and FISW84 Fab Fragment |
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Components |
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-Supramolecule #1: Complex of A/duck/Alberta/35/76 Haemagglutinin and FISW84 Fab Fragment
Supramolecule | Name: Complex of A/duck/Alberta/35/76 Haemagglutinin and FISW84 Fab Fragment type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Molecular weight | Theoretical: 300 KDa |
-Supramolecule #2: A/duck/Alberta/35/76 Haemagglutinin
Supramolecule | Name: A/duck/Alberta/35/76 Haemagglutinin / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Influenza A virus (strain A/Duck/Alberta/35/1976 H1N1) |
-Supramolecule #3: FISW84 Fab Fragment
Supramolecule | Name: FISW84 Fab Fragment / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
-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 (strain A/Duck/Alberta/35/1976 H1N1) |
Molecular weight | Theoretical: 35.684852 KDa |
Sequence | String: DTICVGYHAN NSTDTVDTVL EKNVTVTHSV NLLEDSHNGK LCSLNGIAPL QLGKCNVAGW LLGNPECDLL LTANSWSYII ETSNSENGT CYPGEFIDYE ELREQLSSVS SFEKFEIFPK ASSWPNHETT KGVTAACSYS GASSFYRNLL WITKKGTSYP K LSKSYTNN ...String: DTICVGYHAN NSTDTVDTVL EKNVTVTHSV NLLEDSHNGK LCSLNGIAPL QLGKCNVAGW LLGNPECDLL LTANSWSYII ETSNSENGT CYPGEFIDYE ELREQLSSVS SFEKFEIFPK ASSWPNHETT KGVTAACSYS GASSFYRNLL WITKKGTSYP K LSKSYTNN KGKEVLVLWG VHHPPSVSEQ QSLYQNADAY VSVGSSKYNR RFAPEIAARP KVRGQAGRMN YYWTLLDQGD TI TFEATGN LIAPWYAFAL NKGSDSGIIT SDAPVHNCDT RCQTPHGALN SSLPFQNVHP ITIGECPKYV KSTKLRMATG LRN VPSI |
-Macromolecule #2: Hemagglutinin
Macromolecule | Name: Hemagglutinin / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Influenza A virus (strain A/Duck/Alberta/35/1976 H1N1) |
Molecular weight | Theoretical: 19.953924 KDa |
Sequence | String: GLFGAIAGFI EGGWTGMIDG WYGYHHQNEQ GSGYAADQKS TQNAIDGITS KVNSVIEKMN TQFTAVGKEF NNLERRIENL NKKVDDGFL DVWTYNAELL VLLENERTLD FHDSNVRNLY EKVKSQLRNN AKEIGNGCFE FYHKCDDECM ESVKNGTYDY P KYSEESKL NREEID |
-Macromolecule #3: Heavy chain of FISW84 Fab Fragment
Macromolecule | Name: Heavy chain of FISW84 Fab Fragment / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 22.925875 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: EVQLLESGGG LVQPGGSLRL SCAASGFTFS SYGMAWVRQA PGKGLEWVSF ISATGLSTYF ADSVKGRFTI SRDTTKNTLY LQMNSLRAD DTAVYFCARM RRTMIAFGGN DFWGQGTLVT VSSASTKGPS VFPLAPSGTA ALGCLVKDYF PEPVTVSWNS G ALTSGVHT ...String: EVQLLESGGG LVQPGGSLRL SCAASGFTFS SYGMAWVRQA PGKGLEWVSF ISATGLSTYF ADSVKGRFTI SRDTTKNTLY LQMNSLRAD DTAVYFCARM RRTMIAFGGN DFWGQGTLVT VSSASTKGPS VFPLAPSGTA ALGCLVKDYF PEPVTVSWNS G ALTSGVHT FPAVLQSSGL YSLSSVVTVP SSSLGTQTYI CNVNHKPSNT KVDKRVEP |
-Macromolecule #4: Light chain of FISW84 Fab Fragment
Macromolecule | Name: Light chain of FISW84 Fab Fragment / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 23.277766 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: EVVMTQSPAT LSVSPGEGAT LSCRASQSVN TNVAWYQQKP GQAPRLLIYG ASTRATGIPA RFSGSGSGTE FTLTISTLQS EDFAVYYCQ QYSNWPPITF GQGTRLEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String: EVVMTQSPAT LSVSPGEGAT LSCRASQSVN TNVAWYQQKP GQAPRLLIYG ASTRATGIPA RFSGSGSGTE FTLTISTLQS EDFAVYYCQ QYSNWPPITF GQGTRLEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGE |
-Macromolecule #9: UNKNOWN BRANCHED FRAGMENT OF PHOSPHOLIPID
Macromolecule | Name: UNKNOWN BRANCHED FRAGMENT OF PHOSPHOLIPID / type: ligand / ID: 9 / Number of copies: 3 / Formula: UPL |
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Molecular weight | Theoretical: 478.92 Da |
Chemical component information | ChemComp-UPL: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.5 mg/mL | ||||||||||||||
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Buffer | pH: 8 Component:
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Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 43.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |