[English] 日本語
Yorodumi
- EMDB-26605: H1 Solomon Islands 2006 hemagglutinin in complex with Ab109 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-26605
TitleH1 Solomon Islands 2006 hemagglutinin in complex with Ab109
Map dataH1 Solomon Islands 2006 in complex with ab109
Sample
  • Complex: hemagglutinin H1 Solomon Islands/03/2006 in complex with ab109 Fab
    • Complex: Hemagglutinin
      • Protein or peptide: Hemagglutinin
    • Complex: ab109 Fab heavy chain, ab 109 Fab light chain
      • Protein or peptide: ab109 Fab heavy chain
      • Protein or peptide: ab109 Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsinfluenza / antibody / vaccine / 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
Biological speciesInfluenza A virus (A/Solomon Islands/3/2006(H1N1)) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.36 Å
AuthorsWindsor IW / Caradonna TM / Schmidt AG
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI146779 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01AI089618 United States
CitationJournal: Cell Rep / Year: 2022
Title: An epitope-enriched immunogen expands responses to a conserved viral site.
Authors: Timothy M Caradonna / Larance Ronsard / Ashraf S Yousif / Ian W Windsor / Rachel Hecht / Thalia Bracamonte-Moreno / Anne A Roffler / Max J Maron / Daniel P Maurer / Jared Feldman / Elisa ...Authors: Timothy M Caradonna / Larance Ronsard / Ashraf S Yousif / Ian W Windsor / Rachel Hecht / Thalia Bracamonte-Moreno / Anne A Roffler / Max J Maron / Daniel P Maurer / Jared Feldman / Elisa Marchiori / Ralston M Barnes / Daniel Rohrer / Nils Lonberg / Thomas H Oguin / Gregory D Sempowski / Thomas B Kepler / Masayuki Kuraoka / Daniel Lingwood / Aaron G Schmidt /
Abstract: Pathogens evade host humoral responses by accumulating mutations in surface antigens. While variable, there are conserved regions that cannot mutate without compromising fitness. Antibodies targeting ...Pathogens evade host humoral responses by accumulating mutations in surface antigens. While variable, there are conserved regions that cannot mutate without compromising fitness. Antibodies targeting these conserved epitopes are often broadly protective but remain minor components of the repertoire. Rational immunogen design leverages a structural understanding of viral antigens to modulate humoral responses to favor these responses. Here, we report an epitope-enriched immunogen presenting a higher copy number of the influenza hemagglutinin (HA) receptor-binding site (RBS) epitope relative to other B cell epitopes. Immunization in a partially humanized murine model imprinted with an H1 influenza shows H1-specific serum and >99% H1-specific B cells being RBS-directed. Single B cell analyses show a genetically restricted response that structural analysis defines as RBS-directed antibodies engaging the RBS with germline-encoded contacts. These data show how epitope enrichment expands B cell responses toward conserved epitopes and advances immunogen design approaches for next-generation viral vaccines.
History
DepositionApr 7, 2022-
Header (metadata) releaseNov 23, 2022-
Map releaseNov 23, 2022-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_26605.png

Downloads & links

-
Map

FileDownload / File: emd_26605.map.gz / Format: CCP4 / Size: 137.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationH1 Solomon Islands 2006 in complex with ab109
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 330 pix.
= 272.25 Å		0.83 Å/pix.
x 330 pix.
= 272.25 Å		0.83 Å/pix.
x 330 pix.
= 272.25 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.014
Minimum - Maximum-0.03275566 - 0.06430363
Average (Standard dev.)-0.00001172824 (±0.0024825619)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions330330330
Spacing330330330
CellA=B=C: 272.25 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : hemagglutinin H1 Solomon Islands/03/2006 in complex with ab109 Fab

EntireName: hemagglutinin H1 Solomon Islands/03/2006 in complex with ab109 Fab
Components
  • Complex: hemagglutinin H1 Solomon Islands/03/2006 in complex with ab109 Fab
    • Complex: Hemagglutinin
      • Protein or peptide: Hemagglutinin
    • Complex: ab109 Fab heavy chain, ab 109 Fab light chain
      • Protein or peptide: ab109 Fab heavy chain
      • Protein or peptide: ab109 Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: hemagglutinin H1 Solomon Islands/03/2006 in complex with ab109 Fab

SupramoleculeName: hemagglutinin H1 Solomon Islands/03/2006 in complex with ab109 Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

-
Supramolecule #2: Hemagglutinin

SupramoleculeName: Hemagglutinin / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Influenza A virus (A/Solomon Islands/3/2006(H1N1))

-
Supramolecule #3: ab109 Fab heavy chain, ab 109 Fab light chain

SupramoleculeName: ab109 Fab heavy chain, ab 109 Fab light chain / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Mus musculus (house mouse)

-
Macromolecule #1: Hemagglutinin

MacromoleculeName: Hemagglutinin / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus (A/Solomon Islands/3/2006(H1N1))
Strain: A/Solomon Islands/3/2006(H1N1)
Molecular weightTheoretical: 58.608316 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: ADPGYLLEDT ICIGYHANNS TDTVDTVLEK NVTVTHSVNL LEDSHNGKLC LLKGIAPLQL GNCSVAGWIL GNPECELLIS RESWSYIVE KPNPENGTCY PGHFADYEEL REQLSSVSSF ERFEIFPKES SWPNHTTTGV SASCSHNGES SFYKNLLWLT G KNGLYPNL ...String:
ADPGYLLEDT ICIGYHANNS TDTVDTVLEK NVTVTHSVNL LEDSHNGKLC LLKGIAPLQL GNCSVAGWIL GNPECELLIS RESWSYIVE KPNPENGTCY PGHFADYEEL REQLSSVSSF ERFEIFPKES SWPNHTTTGV SASCSHNGES SFYKNLLWLT G KNGLYPNL SKSYANNKEK EVLVLWGVHH PPNIGDQRAL YHTENAYVSV VSSHYSRKFT PEIAKRPKVR DQEGRINYYW TL LEPGDTI IFEANGNLIA PRYAFALSRG FGSGIINSNA PMDECDAKCQ TPQGAINSSL PFQNVHPVTI GECPKYVRSA KLR MVTGLR NIPSIQSRGL FGAIAGFIEG GWTGMVDGWY GYHHQNEQGS GYAADQKSTQ NAINGITNKV NSVIEKMNTQ FTAV GKEFN KLERRMENLN KKVDDGFIDI WTYNAELLVL LENERTLDFH DSNVKNLYEK VKSQLKNNAK EIGNGCFEFY HKCND ECME SVKNGTYDYP KYSEESKLNR EKIDGVRSGS GGALEVLFQ

UniProtKB: Hemagglutinin

-
Macromolecule #2: ab109 Fab heavy chain

MacromoleculeName: ab109 Fab heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.267232 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLVQSGAE VKKPGASVKV SCKASGYTFT GYYIHWVRQA PGQGLEWMGW INPNTGGTVY AQTFQARVTM TRDTSISTAY MELIRLRSD DTAVYYCARE RGTGAPDAFN IWGQGTLVTV SGASTKGPSV FPLAPSGTAA LGCLVKDYFP EPVTVSWNSG A LTSGVHTF ...String:
QVQLVQSGAE VKKPGASVKV SCKASGYTFT GYYIHWVRQA PGQGLEWMGW INPNTGGTVY AQTFQARVTM TRDTSISTAY MELIRLRSD DTAVYYCARE RGTGAPDAFN IWGQGTLVTV SGASTKGPSV FPLAPSGTAA LGCLVKDYFP EPVTVSWNSG A LTSGVHTF PAVLQSSGLY SLSSVVTVPS SSLGTQTYIC NVNHKPSNTK VDKKVEPKSC

-
Macromolecule #3: ab109 Fab light chain

MacromoleculeName: ab109 Fab light chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.806414 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIVMTQSPAS LAVSLGQRAT ISCRASKSVS TSGYSYIHWY QQKPGQPPKL LIYLATNLES GVPARFSGSG SGTDFTLNIH PVEEEDAAT YYCQHSRDTP YTFGGGTKLE IKRTVAAPSV FIFPPSDEQL KSGTASVVCL LNNFYPREAK VQWKVDNALQ S GNSQESVT ...String:
DIVMTQSPAS LAVSLGQRAT ISCRASKSVS TSGYSYIHWY QQKPGQPPKL LIYLATNLES GVPARFSGSG SGTDFTLNIH PVEEEDAAT YYCQHSRDTP YTFGGGTKLE IKRTVAAPSV FIFPPSDEQL KSGTASVVCL LNNFYPREAK VQWKVDNALQ S GNSQESVT EQDSKDSTYS LSSTLTLSKA DYEKHKVYAC EVTHQGLSSP VTKSFNRGEC

-
Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 6 / 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: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.07 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

+
Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.36 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.2) / Number images used: 67533
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
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