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Yorodumi- EMDB-27440: CryoEM structure of Influenza A virus A/Ohio/09/2015 hemagglutini... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-27440 | |||||||||
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Title | CryoEM structure of Influenza A virus A/Ohio/09/2015 hemagglutinin bound to CR6261 Fab | |||||||||
Map data | ||||||||||
Sample |
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Keywords | NIAID / hemagglutinin stalk binding antibody / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex | |||||||||
Biological species | Influenza A virus / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.62 Å | |||||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | |||||||||
Funding support | United States, 1 items
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Citation | Journal: To Be Published Title: CryoEM structure of Influenza A virus A/Ohio/09/2015 hemagglutinin bound to CR6261 Fab Authors: Yang M / Edwards TE / Horanyi PS / Lorimer DD | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_27440.map.gz | 339.1 MB | EMDB map data format | |
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Header (meta data) | emd-27440-v30.xml emd-27440.xml | 19.2 KB 19.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_27440_fsc.xml | 19.4 KB | Display | FSC data file |
Images | emd_27440.png | 85.7 KB | ||
Filedesc metadata | emd-27440.cif.gz | 6.5 KB | ||
Others | emd_27440_half_map_1.map.gz emd_27440_half_map_2.map.gz | 614.7 MB 614.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-27440 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27440 | HTTPS FTP |
-Validation report
Summary document | emd_27440_validation.pdf.gz | 1022.1 KB | Display | EMDB validaton report |
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Full document | emd_27440_full_validation.pdf.gz | 1021.7 KB | Display | |
Data in XML | emd_27440_validation.xml.gz | 28.1 KB | Display | |
Data in CIF | emd_27440_validation.cif.gz | 37 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27440 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27440 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_27440.map.gz / Format: CCP4 / Size: 662.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.675 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_27440_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_27440_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Influenza A virus A/Ohio/09/2015 hemagglutinin bound to CR6261 Fab
Entire | Name: Influenza A virus A/Ohio/09/2015 hemagglutinin bound to CR6261 Fab |
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Components |
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-Supramolecule #1: Influenza A virus A/Ohio/09/2015 hemagglutinin bound to CR6261 Fab
Supramolecule | Name: Influenza A virus A/Ohio/09/2015 hemagglutinin bound to CR6261 Fab type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Molecular weight | Theoretical: 450 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 / Strain: A/Ohio/09/2015 |
Molecular weight | Theoretical: 64.428137 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MVLVNQSHQG FNKEHTSKMV SAIVLYVLLA AAAHSAFAGS DKICIGYHAN NSTDTVDTVL EKNVTVTHSV NLLENKHNGK LCKLRGVAP LHLGKCNIAG WLLGNPECES LATASSWSYI VETSSSNNGT CYPGDFINYE ELREQLSSVS SFEKFEIFPK T SSWPNHET ...String: MVLVNQSHQG FNKEHTSKMV SAIVLYVLLA AAAHSAFAGS DKICIGYHAN NSTDTVDTVL EKNVTVTHSV NLLENKHNGK LCKLRGVAP LHLGKCNIAG WLLGNPECES LATASSWSYI VETSSSNNGT CYPGDFINYE ELREQLSSVS SFEKFEIFPK T SSWPNHET NKGVTAACPH AGTNSFYKNL IWLVKKENSY PKINISYTNN RGKEVLVLWA IHHPPTSTDQ QSLYQNANSY VF VGSSRYS RKFEPEIATR PKVRGQAGRM NYYWTLVEPG DKITFEATGN LVVPRYAFAL KRNSGSGIII SETPVHDCDT TCQ TPNGAI NTSLPFQNIH PVTIGECPKY VKSTKLRMAT GLRNIPSIQS RGLFGAIAGF IEGGWTGMID GWYGYHHQNE QGSG YAADL KSTQNAIDGI TNKVNSVIEK MNTQFTAVGK EFSHLERRIE NLNKKVDDGF IDIWTYNAEL LVLLENERTL DYHDS NVKT LYEKVRSQLK NNAKEIGNGC FEFYHKCDDT CMESVKNGTY DYPKYSEEFL VPRGSPGSGY IPEAPRDGQA YVRKDG EWV LLSTFLGHHH HHH |
-Macromolecule #2: CR6261 Fab heavy chain
Macromolecule | Name: CR6261 Fab heavy 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: 27.066621 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MEWSWVFLFF LSVTTGVHSE VQLVESGAEV KKPGSSVKVS CKASGGPFRS YAISWVRQAP GQGPEWMGGI IPIFGTTKYA PKFQGRVTI TADDFAGTVY MELSSLRSED TAMYYCAKHM GYQVRETMDV WGKGTTVTVS SASTKGPSVF PLAPSSKSTS G GTAALGCL ...String: MEWSWVFLFF LSVTTGVHSE VQLVESGAEV KKPGSSVKVS CKASGGPFRS YAISWVRQAP GQGPEWMGGI IPIFGTTKYA PKFQGRVTI TADDFAGTVY MELSSLRSED TAMYYCAKHM GYQVRETMDV WGKGTTVTVS SASTKGPSVF PLAPSSKSTS G GTAALGCL VKDYFPEPVT VSWNSGALTS GVHTFPAVLQ SSGLYSLSSV VTVPSSSLGT QTYICNVNHK PSNTKVDKRV EP KSCDKHH HHHH |
-Macromolecule #3: CR6261 Fab light chain
Macromolecule | Name: CR6261 Fab light chain / 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: 25.514395 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MEWSWVFLFF LSVTTGVHSQ SVLTQPPSVS AAPGQKVTIS CSGSSSNIGN DYVSWYQQLP GTAPKLLIYD NNKRPSGIPD RFSGSKSGT SATLGITGLQ TGDEANYYCA TWDRRPTAYV VFGGGTKLTV LGAAAGQPKA APSVTLFPPS SEELQANKAT L VCLISDFY ...String: MEWSWVFLFF LSVTTGVHSQ SVLTQPPSVS AAPGQKVTIS CSGSSSNIGN DYVSWYQQLP GTAPKLLIYD NNKRPSGIPD RFSGSKSGT SATLGITGLQ TGDEANYYCA TWDRRPTAYV VFGGGTKLTV LGAAAGQPKA APSVTLFPPS SEELQANKAT L VCLISDFY PGAVTVAWKA DSSPVKAGVE TTTPSKQSNN KYAASSYLSL TPEQWKSHRS YSCQVTHEGS TVEKTVAPTE CS |
-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: |
-Macromolecule #6: water
Macromolecule | Name: water / type: ligand / ID: 6 / Number of copies: 18 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.5 mg/mL | |||||||||
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Buffer | pH: 8 Component:
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Grid | Model: EMS Lacey Carbon / Material: COPPER / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Support film - topology: LACEY | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 12095 / Average exposure time: 2.3 sec. / Average electron dose: 80.0 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: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |