[English] 日本語
Yorodumi
- EMDB-45997: Hemagglutinin A/Hong Kong/1/68 produced in GnTI- cells -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-45997
TitleHemagglutinin A/Hong Kong/1/68 produced in GnTI- cells
Map datasharpen map of influenza hemagglutinin A/Hong Kong/1/1968 expressed in GNTI- cells
Sample
  • Complex: hemagglutinin A/Hong Kong/1/68 trimer
    • Protein or peptide: Hemagglutinin HA1 chain
    • Protein or peptide: Hemagglutinin HA2 chain,Green fluorescent protein fusion
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordshemagglutinin / glycoprotein / VIRAL PROTEIN
Function / homology
Function and homology information


bioluminescence / viral budding from plasma membrane / generation of precursor metabolites and energy / 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 ...bioluminescence / viral budding from plasma membrane / generation of precursor metabolites and energy / 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 / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein
Similarity search - Domain/homology
Green fluorescent protein / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus / Influenza A virus (strain A/Hong Kong/1/1968 H3N2) / Aequorea victoria (jellyfish)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsTorrents de la Pena A / de Paiva Froes Rocha R / Ward AB
Funding support United States, 1 items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationINV-004923 United States
CitationJournal: Nat Commun / Year: 2025
Title: Structural and immunological characterization of the H3 influenza hemagglutinin during antigenic drift.
Authors: Rebeca de Paiva Froes Rocha / Ilhan Tomris / Charles A Bowman / Emma Stevens / Jason Kantorow / Corinna M Plitt / Weiwei Peng / Svearike Oeverdieck / Thales Galdino Andrade / James A ...Authors: Rebeca de Paiva Froes Rocha / Ilhan Tomris / Charles A Bowman / Emma Stevens / Jason Kantorow / Corinna M Plitt / Weiwei Peng / Svearike Oeverdieck / Thales Galdino Andrade / James A Ferguson / Diana D Jung / Rafael Elias Marques / Sander Herfst / Joost Snijder / Srirupa Chakraborty / Alba Torrents de la Peña / Zachary T Berndsen / Robert P de Vries / Andrew B Ward /
Abstract: The quest for a universal influenza vaccine holds great promise for mitigating the global burden of influenza-related morbidity and mortality. However, challenges persist in identifying conserved ...The quest for a universal influenza vaccine holds great promise for mitigating the global burden of influenza-related morbidity and mortality. However, challenges persist in identifying conserved epitopes capable of eliciting robust and durable immune responses. In this study, we explore the influence of glycan evolution on H3 hemagglutinin from 1968 to present day and its impacts on protein structure, antigenicity and immunogenicity by using computational, biochemical and biophysical techniques. Structural characterization of HK/68 and Sing/16 by cryo-electron microscopy shows that while HK/68 is resistant to enzymatic deglycosylation, removal of glycans destabilizes the hyperglycosylated head and membrane-proximal region in Sing/16. Furthermore, the appearance of glycans in Sing/16 hemagglutinin head domain shifts the polyclonal immune response upon vaccination to target the esterase and stem. These insights expand our understanding of glycans beyond their role in protein folding and highlight the interplay among glycan integration and immune recognition to design a universal influenza vaccine.
History
DepositionJul 31, 2024-
Header (metadata) releaseAug 6, 2025-
Map releaseAug 6, 2025-
UpdateDec 24, 2025-
Current statusDec 24, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_45997.png

Downloads & links

-
Map

FileDownload / File: emd_45997.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpen map of influenza hemagglutinin A/Hong Kong/1/1968 expressed in GNTI- cells
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.15 Å/pix.
x 320 pix.
= 368. Å		1.15 Å/pix.
x 320 pix.
= 368. Å		1.15 Å/pix.
x 320 pix.
= 368. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.15 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.8400526 - 1.5075723
Average (Standard dev.)0.0002136096 (±0.025415923)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 368.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_45997_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: map of influenza hemagglutinin A/Hong Kong/1/1968 expressed in...

Fileemd_45997_additional_1.map
Annotationmap of influenza hemagglutinin A/Hong Kong/1/1968 expressed in GNTI- cells
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map of influenza hemagglutinin A/Hong Kong/1/1968 expressed...

Fileemd_45997_half_map_1.map
Annotationhalf map of influenza hemagglutinin A/Hong Kong/1/1968 expressed in GNTI- cells
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map of influenza hemagglutinin A/Hong Kong/1/1968 expressed...

Fileemd_45997_half_map_2.map
Annotationhalf map of influenza hemagglutinin A/Hong Kong/1/1968 expressed in GNTI- cells
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : hemagglutinin A/Hong Kong/1/68 trimer

EntireName: hemagglutinin A/Hong Kong/1/68 trimer
Components
  • Complex: hemagglutinin A/Hong Kong/1/68 trimer
    • Protein or peptide: Hemagglutinin HA1 chain
    • Protein or peptide: Hemagglutinin HA2 chain,Green fluorescent protein fusion
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: hemagglutinin A/Hong Kong/1/68 trimer

SupramoleculeName: hemagglutinin A/Hong Kong/1/68 trimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Influenza A virus / Strain: A/Hong Kong/1/1968 H3N2

-
Macromolecule #1: Hemagglutinin HA1 chain

MacromoleculeName: Hemagglutinin HA1 chain / 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: 38.523496 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MPMGSLQPLA TLYLLGMLVA SVLAQDLPGN DNSTATLCLG HHAVPNGTLV KTITDDQIEV TNATELVQSS STGKICNNPH RILDGIDCT LIDALLGDPH CDVFQNETWD LFVERSKAFS NCYPYDVPDY ASLRSLVASS GTLEFITEGF TWTGVTQNGG S NACKRGPG ...String:
MPMGSLQPLA TLYLLGMLVA SVLAQDLPGN DNSTATLCLG HHAVPNGTLV KTITDDQIEV TNATELVQSS STGKICNNPH RILDGIDCT LIDALLGDPH CDVFQNETWD LFVERSKAFS NCYPYDVPDY ASLRSLVASS GTLEFITEGF TWTGVTQNGG S NACKRGPG SGFFSRLNWL TKSGSTYPVL NVTMPNNDNF DKLYIWGVHH PSTNQEQTSL YVQASGRVTV STRRSQQTII PN IGSRPWV RGLSSRISIY WTIVKPGDVL VINSNGNLIA PRGYFKMRTG KSSIMRSDAP IDTCISECIT PNGSIPNDKP FQN VNKITY GACPKYVKQN TLKLATGMRN VPEKQT

UniProtKB: Hemagglutinin

-
Macromolecule #2: Hemagglutinin HA2 chain,Green fluorescent protein fusion

MacromoleculeName: Hemagglutinin HA2 chain,Green fluorescent protein fusion
type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Aequorea victoria (jellyfish)
Molecular weightTheoretical: 56.073738 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: RGLFGAIAGF IENGWEGMID GWYGFRHQNS EGTGQAADLK STQAAIDQIN GKLNRVIEKT NEKFHQIEKE FSEVEGRIQD LEKYVEDTK IDLWSYNAEL LVALENQHTI DLTDSEMNKL FEKTRRQLRE NAEDMGNGCF KIYHKCDNAC IESIRNGTYD H DVYRDEAL ...String:
RGLFGAIAGF IENGWEGMID GWYGFRHQNS EGTGQAADLK STQAAIDQIN GKLNRVIEKT NEKFHQIEKE FSEVEGRIQD LEKYVEDTK IDLWSYNAEL LVALENQHTI DLTDSEMNKL FEKTRRQLRE NAEDMGNGCF KIYHKCDNAC IESIRNGTYD H DVYRDEAL NNRFQIKGVE LKLELIKRMK QIEDKIEEIE SKQKKIENEI ARIKKIKLVP RGSVDENLYF QAMSKGEELF TG VVPILVE LDGDVNGHKF SVRGEGEGDA TNGKLTLKFI CTTGKLPVPW PTLVTTLTYG VQCFSRYPDH MKRHDFFKSA MPE GYVQER TISFKDDGTY KTRAEVKFEG DTLVNRIELK GIDFKEDGNI LGHKLEYNFN SHNVYITADK QKNGIKANFK IRHN VEDGS VQLADHYQQN TPIGDGPVLL PDNHYLSTQS VLSKDPNEKR DHMVLLEFVT AAGITHGMSS AWSHPQFEKG GGSGG GSGG SAWSHPQFEK

UniProtKB: Hemagglutinin, Green fluorescent protein

-
Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 18 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1 mg/mL
BufferpH: 7.4 / Details: TBS
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 5 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

+
Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4zcj

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 59301
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

4zcj


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-9cxt:
Hemagglutinin A/Hong Kong/1/68 produced in GnTI- cells

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more