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- EMDB-22652: Structure of full-length influenza HA with a head-binding antibod... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-22652 | |||||||||
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Title | Structure of full-length influenza HA with a head-binding antibody at pH 7.8 | |||||||||
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Function / homology | ![]() 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 | ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||
![]() | Gui M / Xiang Y / Gao J | |||||||||
![]() | ![]() Title: Structural intermediates in the low pH-induced transition of influenza hemagglutinin. Authors: Jingjing Gao / Miao Gui / Ye Xiang / ![]() Abstract: The hemagglutinin (HA) glycoproteins of influenza viruses play a key role in binding host cell receptors and in mediating virus-host cell membrane fusion during virus infection. Upon virus entry, HA ...The hemagglutinin (HA) glycoproteins of influenza viruses play a key role in binding host cell receptors and in mediating virus-host cell membrane fusion during virus infection. Upon virus entry, HA is triggered by low pH and undergoes large structural rearrangements from a prefusion state to a postfusion state. While structures of prefusion state and postfusion state of HA have been reported, the intermediate structures remain elusive. Here, we report two distinct low pH intermediate conformations of the influenza virus HA using cryo-electron microscopy (cryo-EM). Our results show that a decrease in pH from 7.8 to 5.2 triggers the release of fusion peptides from the binding pockets and then causes a dramatic conformational change in the central helices, in which the membrane-proximal ends of the central helices unwind to an extended form. Accompanying the conformational changes of the central helices, the stem region of the HA undergoes an anticlockwise rotation of 9.5 degrees and a shift of 15 Å. The HA head, after being stabilized by an antibody, remains unchanged compared to the neutral pH state. Thus, the conformational change of the HA stem region observed in our research is likely to be independent of the HA head. These results provide new insights into the structural transition of HA during virus entry. | |||||||||
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 | ![]() | 7.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 15.2 KB 15.2 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 10.6 KB | Display | ![]() |
Images | ![]() | 156.4 KB | ||
Masks | ![]() | 103 MB | ![]() | |
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7k37MC ![]() 7k39C ![]() 7k3aC ![]() 7k3bC 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
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Voxel size | X=Y=Z: 1.33 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : complex of hemagglutinin with antibody
Entire | Name: complex of hemagglutinin with antibody |
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Components |
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-Supramolecule #1: complex of hemagglutinin with antibody
Supramolecule | Name: complex of hemagglutinin with antibody / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() |
-Supramolecule #2: hemagglutinin
Supramolecule | Name: hemagglutinin / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2 |
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-Supramolecule #3: antigen-binding fragment
Supramolecule | Name: antigen-binding fragment / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4 |
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-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: ![]() Strain: A/Hong Kong/1/1968 H3N2 |
Molecular weight | Theoretical: 37.948812 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MKTIIALSYI FCLALGQDLP GNDNSTATLC LGHHAVPNGT LVKTITDDQI EVTNATELVQ SSSTGKICNN PHRILDGIDC TLIDALLGD PHCDVFQNET WDLFVERSKA FSNCYPYDVP DYASLRSLVA SSGTLEFITE GFTWTGVTQN GGSNACKRGP G SGFFSRLN ...String: MKTIIALSYI FCLALGQDLP GNDNSTATLC LGHHAVPNGT LVKTITDDQI EVTNATELVQ SSSTGKICNN PHRILDGIDC TLIDALLGD PHCDVFQNET WDLFVERSKA FSNCYPYDVP DYASLRSLVA SSGTLEFITE GFTWTGVTQN GGSNACKRGP G SGFFSRLN WLTKSGSTYP VLNVTMPNND NFDKLYIWGV HHPSTNQEQT SLYVQASGRV TVSTRRSQQT IIPNIGSRPW VR GLSSRIS IYWTIVKPGD VLVINSNGNL IAPRGYFKMR TGKSSIMRSD APIDTCISEC ITPNGSIPND KPFQNVNKIT YGA CPKYVK QNTLKLATGM RNVPEKQTR |
-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: ![]() Strain: A/Hong Kong/1/1968 H3N2 |
Molecular weight | Theoretical: 28.947525 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: GLFGAIAGFI ENGWEGMIDG WYGFRHQNSE GTGQAADLKS TQAAIDQING KLNRVIEKTN EKFHQIEKEF SEVEGRIQDL EKYVEDTKI DLWSYNAELL VALENQHTID LTDSEMNKLF EKTRRQLREN AEDMGNGCFK IYHKCDNACI ESIRNGTYDH D VYRDEALN ...String: GLFGAIAGFI ENGWEGMIDG WYGFRHQNSE GTGQAADLKS TQAAIDQING KLNRVIEKTN EKFHQIEKEF SEVEGRIQDL EKYVEDTKI DLWSYNAELL VALENQHTID LTDSEMNKLF EKTRRQLREN AEDMGNGCFK IYHKCDNACI ESIRNGTYDH D VYRDEALN NRFQIKGVEL KSGYKDWILW ISFAISCFLL CVVLLGFIMW ACQRGNIRCN ICISMGWSHP QFEKGGGARG GS GGGSWSH PQFEKGF |
-Macromolecule #3: antibody Fab light chain
Macromolecule | Name: antibody Fab light chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 23.11241 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: QSVLTQPPSV SGAPGQRVTI SCTGSSSNIG AGYAVHWYQQ LPGTAPKLLI SGNSNRPSGV PDRFSGSKSG TSASLAITGL QAEDEADYY CQSYDSSLSG SVFGGGTKLT VLGRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL Q SGNSQESV ...String: QSVLTQPPSV SGAPGQRVTI SCTGSSSNIG AGYAVHWYQQ LPGTAPKLLI SGNSNRPSGV PDRFSGSKSG TSASLAITGL QAEDEADYY CQSYDSSLSG SVFGGGTKLT VLGRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL Q SGNSQESV TEQDSKDSTY SLSSTLTLSK ADYEKHKVYA CEVTHQGLSS PVTKSFNRGE C |
-Macromolecule #4: antibody Fab heavy chain
Macromolecule | Name: antibody Fab heavy chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 25.278605 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: QVQLVQSGAE VKKPGASVTV SCQVSGYTLT SYGLSWVRQA PGQGLEWVGW INTYDGQTKY VKKFQGRVTM TTHTGTNTAY MEMKSLRSD DTAVYYCARV EGVRGVMGFH YYPMDVWGQG TMVTVSSKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA ...String: QVQLVQSGAE VKKPGASVTV SCQVSGYTLT SYGLSWVRQA PGQGLEWVGW INTYDGQTKY VKKFQGRVTM TTHTGTNTAY MEMKSLRSD DTAVYYCARV EGVRGVMGFH YYPMDVWGQG TMVTVSSKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYICNV NHKPSNTKVD KKVEPKSCDK GLEVLFQ |
-Macromolecule #8: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 8 / 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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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.8 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |