[English] 日本語
Yorodumi
- EMDB-71796: Cryo-EM structure of stabilized H5N1 A/Texas/37/2024 hemagglutini... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-71796
TitleCryo-EM structure of stabilized H5N1 A/Texas/37/2024 hemagglutinin fused to foldon
Map dataCryo-EM structure of stabilized H5N1 A/Texas/37/2024 hemagglutinin fused to foldon
Sample
  • Virus: Influenza A virus
    • Protein or peptide: Hemagglutinin, foldon fusion
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHPAI H5N1 / Influenza Hemagglutinin / stabilization / VIRAL PROTEIN
Biological speciesInfluenza A virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsDosey A / King N
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19 AI181881 United States
CitationJournal: Sci Transl Med / Year: 2026
Title: Stabilization of the H5 clade 2.3.4.4b hemagglutinin improves vaccine-elicited neutralizing antibody responses in mice.
Authors: Annie Dosey / Bernadeta Dadonaite / Rebecca A Gillespie / Elizabeth M Leaf / Matthew J Vukovich / Jackson McGowan / Emily Grey / Hiromi Muramatsu / Rachel H J Jun / Norbert Pardi / Masaru ...Authors: Annie Dosey / Bernadeta Dadonaite / Rebecca A Gillespie / Elizabeth M Leaf / Matthew J Vukovich / Jackson McGowan / Emily Grey / Hiromi Muramatsu / Rachel H J Jun / Norbert Pardi / Masaru Kanekiyo / Jesse D Bloom / Neil P King /
Abstract: Transmission of highly pathogenic avian influenza from H5 clade 2.3.4.4b has expanded in recent years to infect large populations of birds and mammals, heightening the risk of a human pandemic. ...Transmission of highly pathogenic avian influenza from H5 clade 2.3.4.4b has expanded in recent years to infect large populations of birds and mammals, heightening the risk of a human pandemic. Influenza viruses that are adapted to transmission in birds and a variety of mammals tend to have a less stable hemagglutinin (HA) than seasonal influenza viruses, enabling membrane fusion at comparatively higher pH levels. Here, we combined five mutations in the H5 HA that increased its melting temperature and promoted stable closure of the HA trimer. Structural analysis by cryo-electron microscopy revealed that the stabilizing mutations create several new hydrophobic interactions while maintaining the local HA structure. We found that vaccinating mice with stabilized H5 HA immunogens resulted in higher hemagglutination inhibition and neutralization titers than nonstabilized comparators. Epitope mapping of vaccine-elicited polyclonal antibody responses using negative-stain electron microscopy and deep mutational scanning showed that site E on the side of the HA receptor binding domain was immunodominant across all groups; however, the stabilized immunogens shifted responses toward the receptor binding site, which elicited a higher proportion of neutralizing antibodies. Consistent with these findings, stabilized H5 HA immunogens delivered as messenger RNA-lipid nanoparticle (mRNA-LNP) vaccines protected mice against H5N1 challenge. These findings highlight that H5 HA-stabilizing mutations enhance the quality of antibody responses across different vaccine formats, underscoring their potential to improve pandemic preparedness vaccines targeting viruses from this widely circulating clade.
History
DepositionJul 23, 2025-
Header (metadata) releaseFeb 4, 2026-
Map releaseFeb 4, 2026-
UpdateAug 12, 2026-
Current statusAug 12, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_71796.png

Downloads & links

-
Map

FileDownload / File: emd_71796.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of stabilized H5N1 A/Texas/37/2024 hemagglutinin fused to foldon
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 400 pix.
= 337.2 Å		0.84 Å/pix.
x 400 pix.
= 337.2 Å		0.84 Å/pix.
x 400 pix.
= 337.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.843 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.5325549 - 0.8036606
Average (Standard dev.)0.0000043582086 (±0.021665672)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 337.2 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_71796_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Cryo-EM half map of stabilized H5N1 A/Texas/37/2024 hemagglutinin...

Fileemd_71796_half_map_1.map
AnnotationCryo-EM half map of stabilized H5N1 A/Texas/37/2024 hemagglutinin fused to foldon
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Cryo-EM half map of stabilized H5N1 A/Texas/37/2024 hemagglutinin...

Fileemd_71796_half_map_2.map
AnnotationCryo-EM half map of stabilized H5N1 A/Texas/37/2024 hemagglutinin fused to foldon
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Influenza A virus

EntireName: Influenza A virus
Components
  • Virus: Influenza A virus
    • Protein or peptide: Hemagglutinin, foldon fusion
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: Influenza A virus

SupramoleculeName: Influenza A virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: H5N1 ectodomain recombinantly expressed in HEK293F cells.
NCBI-ID: 11320 / Sci species name: Influenza A virus / Sci species strain: H5N1 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No

-
Macromolecule #1: Hemagglutinin, foldon fusion

MacromoleculeName: Hemagglutinin, foldon fusion / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus / Strain: A/Texas/37/2024
Molecular weightTheoretical: 63.09682 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DQICIGYHAN NSTEQVDTIM EKNVTVTHAQ DILEKTHNGK LCDLNGVKPL ILKDCSVAGW LLGNPMCDEF IRVPEWSYIV ERANPANDL CFPGSLNDYE ELKHMLSRIN HFEKIQIIPK SSWPNHETSL GVSAACPYQG APSFFRNVVW LIKKNDAYPT I KISYNNTN ...String:
DQICIGYHAN NSTEQVDTIM EKNVTVTHAQ DILEKTHNGK LCDLNGVKPL ILKDCSVAGW LLGNPMCDEF IRVPEWSYIV ERANPANDL CFPGSLNDYE ELKHMLSRIN HFEKIQIIPK SSWPNHETSL GVSAACPYQG APSFFRNVVW LIKKNDAYPT I KISYNNTN REDLLILWGI HHSNNAEEQT NLYKNPITYI SVGTSTLNQR LAPKIATRSQ VNGQRGRMDF FWTILKPDDA IH FESNGNF IAPEYAYKIV KKGDSTIMKS GVEYGHCNTK CQTPVGAINS SMPFHNIHPL TIGECPKYVK SNKLVLATGL RNS PLRESR GLFGAIAGFI EGGWQGMVDG WYGYHFSNEQ GSGYAADKES TQKAIDGVTN MVNSIIDKMN TQFEAVGMEF NNLE RRIEN LNKKMEDGFI DVWTYNAELL VLMLNERTLD FHDSNVKNLY DKVRLQLRDN AKELGNGCFE FYHKCDNECM ESVRN GTYD YPQYSEEARL KREEISGVGS GYIPEAPRDG QAYVRKDGEW VLLSTFLGSG LNDIFEAQKI EWHEGHHHHH H

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

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 15 / 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

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 54035
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

+
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