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- EMDB-22653: Structure of full-length influenza HA with a head-binding antibod... -

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Basic information

Entry
Database: EMDB / ID: EMD-22653
TitleStructure of full-length influenza HA with a head-binding antibody at pH 5.2, conformation A, neutral pH-like
Map data
Sample
  • Complex: complex of hemagglutinin with antibody
    • Complex: hemagglutinin
      • Protein or peptide: Hemagglutinin
      • Protein or peptide: Hemagglutinin
    • Complex: antigen-binding fragment
      • Protein or peptide: antibody Fab light chain
      • Protein or peptide: antibody Fab heavy chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsinfluenza / virus / hemagglutinin / antibody / low pH / VIRAL 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
Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein
Similarity search - Domain/homology
Hemagglutinin / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus (A/Hong Kong/1/1968(H3N2)) / Influenza A virus (strain A/Hong Kong/1/1968 H3N2) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsGui M / Gao J / Xiang Y
CitationJournal: PLoS Pathog / Year: 2020
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
DepositionSep 10, 2020-
Header (metadata) releaseNov 11, 2020-
Map releaseNov 11, 2020-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.06
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7k39
  • Surface level: 0.06
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22653.png

Downloads & links

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Map

FileDownload / File: emd_22653.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.33 Å/pix.
x 300 pix.
= 399. Å		1.33 Å/pix.
x 300 pix.
= 399. Å		1.33 Å/pix.
x 300 pix.
= 399. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.33 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06 / Movie #1: 0.06
Minimum - Maximum-0.31052062 - 0.5961899
Average (Standard dev.)0.0003238329 (±0.009329879)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 399.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.331.331.33
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z399.000399.000399.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.3110.5960.000

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Supplemental data

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Mask #1

Fileemd_22653_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : complex of hemagglutinin with antibody

EntireName: complex of hemagglutinin with antibody
Components
  • Complex: complex of hemagglutinin with antibody
    • Complex: hemagglutinin
      • Protein or peptide: Hemagglutinin
      • Protein or peptide: Hemagglutinin
    • Complex: antigen-binding fragment
      • Protein or peptide: antibody Fab light chain
      • Protein or peptide: antibody Fab heavy chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: complex of hemagglutinin with antibody

SupramoleculeName: complex of hemagglutinin with antibody / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Influenza A virus (A/Hong Kong/1/1968(H3N2))

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Supramolecule #2: hemagglutinin

SupramoleculeName: hemagglutinin / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2

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Supramolecule #3: antigen-binding fragment

SupramoleculeName: antigen-binding fragment / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4

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Macromolecule #1: Hemagglutinin

MacromoleculeName: Hemagglutinin / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus (strain A/Hong Kong/1/1968 H3N2)
Strain: A/Hong Kong/1/1968 H3N2
Molecular weightTheoretical: 37.948812 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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

UniProtKB: Hemagglutinin

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Macromolecule #2: Hemagglutinin

MacromoleculeName: Hemagglutinin / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus (strain A/Hong Kong/1/1968 H3N2)
Strain: A/Hong Kong/1/1968 H3N2
Molecular weightTheoretical: 28.947525 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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

UniProtKB: Hemagglutinin

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Macromolecule #3: antibody Fab light chain

MacromoleculeName: antibody Fab light chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.11241 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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

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Macromolecule #4: antibody Fab heavy chain

MacromoleculeName: antibody Fab heavy chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.278605 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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

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Macromolecule #8: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 8 / Number of copies: 9 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 5.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 227854
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
FSC plot (resolution estimation)

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