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Yorodumi- EMDB-41874: CryoEM structure of A/Solomon Islands/3/2006 H1 HA in complex wit... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41874 | |||||||||
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Title | CryoEM structure of A/Solomon Islands/3/2006 H1 HA in complex with 05.GC.w2.3C10-H1_SI06 | |||||||||
Map data | CryoEM map of A/Solomon Islands/3/2006 H1 HA in complex with 3C10 mAb | |||||||||
Sample |
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Keywords | Influenza virus / hemagglutinin / H1 / monoclonal antibody / virus / 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 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.41 Å | |||||||||
Authors | Moore N / Han J / Ward AB / Wilson IA | |||||||||
Funding support | United States, 1 items
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Citation | Journal: To Be Published Title: Persistence of germinal center B cell responses after influenza virus vaccination in humans Authors: McIntire KM / Meng H / Lin TH / Kim W / Moore NE / Han J / McMahon M / Wang M / Malladi SK / Mohammed BM / Zhou JQ / Schmitz AJ / Hoehn K / Suessen T / Middleton WD / Teefey SA / Presti RM / ...Authors: McIntire KM / Meng H / Lin TH / Kim W / Moore NE / Han J / McMahon M / Wang M / Malladi SK / Mohammed BM / Zhou JQ / Schmitz AJ / Hoehn K / Suessen T / Middleton WD / Teefey SA / Presti RM / Krammer F / Turner JS / Ward AB / Wilson IA / Kleinstein SH / Ellebedy AH | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_41874.map.gz | 86.2 MB | EMDB map data format | |
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Header (meta data) | emd-41874-v30.xml emd-41874.xml | 21.2 KB 21.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_41874_fsc.xml | 9.5 KB | Display | FSC data file |
Images | emd_41874.png | 88.1 KB | ||
Masks | emd_41874_msk_1.map | 91.1 MB | Mask map | |
Filedesc metadata | emd-41874.cif.gz | 6.8 KB | ||
Others | emd_41874_half_map_1.map.gz emd_41874_half_map_2.map.gz | 84.6 MB 84.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41874 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41874 | HTTPS FTP |
-Validation report
Summary document | emd_41874_validation.pdf.gz | 1.2 MB | Display | EMDB validaton report |
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Full document | emd_41874_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | emd_41874_validation.xml.gz | 17.4 KB | Display | |
Data in CIF | emd_41874_validation.cif.gz | 22.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41874 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41874 | HTTPS FTP |
-Related structure data
Related structure data | 8u44MC 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_41874.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | CryoEM map of A/Solomon Islands/3/2006 H1 HA in complex with 3C10 mAb | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.045 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_41874_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: CryoEM half map A of A/Solomon Islands/3/2006 H1...
File | emd_41874_half_map_1.map | ||||||||||||
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Annotation | CryoEM half map A of A/Solomon Islands/3/2006 H1 HA in complex with 3C10 mAb | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: CryoEM half map B of A/Solomon Islands/3/2006 H1...
File | emd_41874_half_map_2.map | ||||||||||||
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Annotation | CryoEM half map B of A/Solomon Islands/3/2006 H1 HA in complex with 3C10 mAb | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Immune complex of A/Solomon Islands/3/2006 H1 HA with Fab 3C10
Entire | Name: Immune complex of A/Solomon Islands/3/2006 H1 HA with Fab 3C10 |
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Components |
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-Supramolecule #1: Immune complex of A/Solomon Islands/3/2006 H1 HA with Fab 3C10
Supramolecule | Name: Immune complex of A/Solomon Islands/3/2006 H1 HA with Fab 3C10 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #3-#4, #1-#2 |
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Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #2: Fab
Supramolecule | Name: Fab / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #3: HA
Supramolecule | Name: HA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: 05.GC.w2.3C10-H1_SI06 Heavy chain
Macromolecule | Name: 05.GC.w2.3C10-H1_SI06 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: 25.771057 KDa |
Recombinant expression | Organism: Cricetulus griseus (Chinese hamster) |
Sequence | String: METDTLLLWV LLLWVPGSTG DEVQLVQSGA EVKKPGSSVR VSCKASGGTF SAISWVRQAP GQGLEWMGGI IPVFGTANYA QKFQGRVTI TADDSTSTAY MEVSSLRSDD TAVYYCAREE TWKGATIGVM GIWGQGTMVT VSSASTKGPS VFPLAPSSKS T SGGTAALG ...String: METDTLLLWV LLLWVPGSTG DEVQLVQSGA EVKKPGSSVR VSCKASGGTF SAISWVRQAP GQGLEWMGGI IPVFGTANYA QKFQGRVTI TADDSTSTAY MEVSSLRSDD TAVYYCAREE TWKGATIGVM GIWGQGTMVT VSSASTKGPS VFPLAPSSKS T SGGTAALG CLVKDYFPEP VTVSWNSGAL TSGVHTFPAV LQSSGLYSLS SVVTVPSSSL GTQTYICNVN HKPSNTKVDK RV EPKSC |
-Macromolecule #2: 05.GC.w2.3C10-H1_SI06 Light chain
Macromolecule | Name: 05.GC.w2.3C10-H1_SI06 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: 25.706625 KDa |
Recombinant expression | Organism: Cricetulus griseus (Chinese hamster) |
Sequence | String: METDTLLLWV LLLWVPGSTG DDIQMTQSPS SLSASVGDRV TITCRASQSI SSYLNWYQHK PGKAPKLLIF TASNLQSGVP SRFSGGGSG TDFTLTISSL QPEDFATYYC QQSYTSPRTF GQGTKVEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN F YPREAKVQ ...String: METDTLLLWV LLLWVPGSTG DDIQMTQSPS SLSASVGDRV TITCRASQSI SSYLNWYQHK PGKAPKLLIF TASNLQSGVP SRFSGGGSG TDFTLTISSL QPEDFATYYC QQSYTSPRTF GQGTKVEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN F YPREAKVQ WKVDNALQSG NSQESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC |
-Macromolecule #3: Hemagglutinin HA1 chain
Macromolecule | Name: Hemagglutinin HA1 chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Influenza A virus |
Molecular weight | Theoretical: 40.835902 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MVLVNQSHQG FNKEHTSKMV SAIVLYVLLA AAAHSAFAAD PGDTICIGYH ANNSTDTVDT VLEKNVTVTH SVNLLEDSHN GKLCRLKGI APLQLGNCSV AGWILGNPEC ELLISRESWS YIVEKPNPEN GTCYPGHFAD YEELREQLSS VSSFERFEIF P KESSWPNH ...String: MVLVNQSHQG FNKEHTSKMV SAIVLYVLLA AAAHSAFAAD PGDTICIGYH ANNSTDTVDT VLEKNVTVTH SVNLLEDSHN GKLCRLKGI APLQLGNCSV AGWILGNPEC ELLISRESWS YIVEKPNPEN GTCYPGHFAD YEELREQLSS VSSFERFEIF P KESSWPNH TTTGVSASCS HNGESSFYKN LLWLTGKNGL YPNLSKSYAN NKEKEVLVLW GVHHPPNIGD QRALYHKENA YV SVVSSHY SRKFTPEIAK RPKVRDQEGR INYYWTLLEP GDTIIFEANG NLIAPRYAFA LSRGFGSGII NSNAPMDECD AKC QTPQGA INSSLPFQNV HPVTIGECPK YVRSAKLRMV TGLRNIPSIQ SR UniProtKB: Hemagglutinin |
-Macromolecule #4: Hemagglutinin HA2 chain
Macromolecule | Name: Hemagglutinin HA2 chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Influenza A virus |
Molecular weight | Theoretical: 26.988895 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: GLFGAIAGFI EGGWTGMVDG WYGYHHQNEQ GSGYAADQKS TQNAINGITN KVNSVIEKMN TQFTAVGKEF NKLERRMENL NKKVDDGFI DIWTYNAELL VLLENERTLD FHDSNVKNLY EKVKSQLKNN AKEIGNGCFE FYHKCNDECM ESVKNGTYDY P KYSEESKL ...String: GLFGAIAGFI EGGWTGMVDG WYGYHHQNEQ GSGYAADQKS TQNAINGITN KVNSVIEKMN TQFTAVGKEF NKLERRMENL NKKVDDGFI DIWTYNAELL VLLENERTLD FHDSNVKNLY EKVKSQLKNN AKEIGNGCFE FYHKCNDECM ESVKNGTYDY P KYSEESKL NREKIDSGGG GLNDIFEAQK IEWHERLVPR GSPGSGYIPE APRDGQAYVR KDGEWVLLST FLGHHHHHH UniProtKB: Hemagglutinin |
-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 | 0.6 mg/mL |
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Buffer | pH: 7.6 / Details: Tris-buffered saline |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 25 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 29000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |