[English] 日本語
Yorodumi
- EMDB-61788: Structure of HBsAg in complex with FabHBC and FabGC1102 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-61788
TitleStructure of HBsAg in complex with FabHBC and FabGC1102
Map data
Sample
  • Complex: HBV surface antigen dimer in complex with FabHBC and FabGC1102
    • Protein or peptide: heavy chain of HBC
    • Protein or peptide: light chain of HBC
    • Protein or peptide: heavy chain of GC1102
    • Protein or peptide: light chain of GC1102
    • Protein or peptide: Large envelope protein
KeywordsHBV / HBsAg / Antibody / Fab / Viral protein-immune system complex / VIRAL PROTEIN / IMMUNE SYSTEM-VIRAL PROTEIN complex
Function / homologyLarge envelope protein S / Major surface antigen from hepadnavirus / caveolin-mediated endocytosis of virus by host cell / fusion of virus membrane with host endosome membrane / virion attachment to host cell / virion membrane / membrane / Large envelope protein
Function and homology information
Biological speciesHBV genotype D3 (virus) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.09 Å
AuthorsChen L / He X / Tao W
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Cell Discov / Year: 2025
Title: Structural polymorphism of the antigenic loop in HBV surface antigen dictates binding of diverse neutralizing antibodies.
Authors: Xiao He / Weiyu Tao / Yunlu Kang / Jiaxuan Xu / Xiaoyu Liu / Lei Chen /
Abstract: The Hepatitis B Virus (HBV) poses a significant health threat, causing millions of deaths each year. Hepatitis B surface antigen (HBsAg), the sole membrane protein on the HBV viral envelope, plays ...The Hepatitis B Virus (HBV) poses a significant health threat, causing millions of deaths each year. Hepatitis B surface antigen (HBsAg), the sole membrane protein on the HBV viral envelope, plays crucial roles in viral attachment to host cells and serves as the target for neutralizing antibodies (NAbs). Despite its functional and therapeutic significance, the mechanisms by which NAbs recognize HBsAg remain elusive. Here, we found that HBsAg proteins exist in distinct subtypes and are recognized by different groups of antibodies. Cryo-electron microscopy (Cryo-EM) structures of HBsAg dimers in complex with NAb Fab fragments reveal that the antigenic loop (AGL) of these distinct HBsAg types share a common structural core comprised of four β-strands. However, their surface structures exhibit unexpected polymorphism due to distinct disulfide bond linkages within the AGL region. This structural polymorphism determines the recognition of HBsAg by different groups of NAbs.
History
DepositionOct 1, 2024-
Header (metadata) releaseJul 2, 2025-
Map releaseJul 2, 2025-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_61788.png

Downloads & links

-
Map

FileDownload / File: emd_61788.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 240 pix.
= 256.08 Å		1.07 Å/pix.
x 240 pix.
= 256.08 Å		1.07 Å/pix.
x 240 pix.
= 256.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.067 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.05
Minimum - Maximum-6.2766986 - 8.555045
Average (Standard dev.)0.003224958 (±0.1684793)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 256.08002 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_61788_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: unsharpen

Fileemd_61788_additional_1.map
Annotationunsharpen
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_61788_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_61788_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : HBV surface antigen dimer in complex with FabHBC and FabGC1102

EntireName: HBV surface antigen dimer in complex with FabHBC and FabGC1102
Components
  • Complex: HBV surface antigen dimer in complex with FabHBC and FabGC1102
    • Protein or peptide: heavy chain of HBC
    • Protein or peptide: light chain of HBC
    • Protein or peptide: heavy chain of GC1102
    • Protein or peptide: light chain of GC1102
    • Protein or peptide: Large envelope protein

-
Supramolecule #1: HBV surface antigen dimer in complex with FabHBC and FabGC1102

SupramoleculeName: HBV surface antigen dimer in complex with FabHBC and FabGC1102
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: HBV genotype D3 (virus)

-
Macromolecule #1: heavy chain of HBC

MacromoleculeName: heavy chain of HBC / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.025744 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ELQLVESGGG WVQPGGSQRL SCAASGRIFR SFYMSWVRQA PGKGLEWVAT INQDGSEKLY VDSVKGRFTI SRDNAKNSLF LQMNNLRVE DTAVYYCAAW SGNSGGMDVW GQGTTVSVSS ASTKGPSVFP LAPSSKSTSG GTAALGCLVK DYFPEPVTVS W NSGALTSG ...String:
ELQLVESGGG WVQPGGSQRL SCAASGRIFR SFYMSWVRQA PGKGLEWVAT INQDGSEKLY VDSVKGRFTI SRDNAKNSLF LQMNNLRVE DTAVYYCAAW SGNSGGMDVW GQGTTVSVSS ASTKGPSVFP LAPSSKSTSG GTAALGCLVK DYFPEPVTVS W NSGALTSG VHTFPAVLQS SGLYSLSSVV TVPSSSLGTQ TYICNVNHKP SNTKVDKRV

-
Macromolecule #2: light chain of HBC

MacromoleculeName: light chain of HBC / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.101656 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SYELTQPPSV SVSPGQTVSI PCSGDKLGNK NVCWFQHKPG QSPVLVIYEV KYRPSGIPER FSGSNSGNTA TLTISGTQAM DEAAYFCQT WDSTTVVFGG GTRLTVLRTV AAPSVFIFPP SDEQLKSGTA SVVCLLNNFY PREAKVQWKV DNALQSGNSQ E SVTEQDSK ...String:
SYELTQPPSV SVSPGQTVSI PCSGDKLGNK NVCWFQHKPG QSPVLVIYEV KYRPSGIPER FSGSNSGNTA TLTISGTQAM DEAAYFCQT WDSTTVVFGG GTRLTVLRTV AAPSVFIFPP SDEQLKSGTA SVVCLLNNFY PREAKVQWKV DNALQSGNSQ E SVTEQDSK DSTYSLSSTL TLSKADYEKH KVYACEVTHQ GLSSPVTKSF NRGEC

-
Macromolecule #3: heavy chain of GC1102

MacromoleculeName: heavy chain of GC1102 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.464459 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVQLVESGGG CVKPGGSLRL SCSASGFSLT KYKMTWVRQA PGKGLEWVSS ISSTSRDIDY ADSVKGRFTI SRDNAKNSLF LQMSSLRVD DTAVYYCTRD GWLWGWDVRS NYYYNALDVW GQGTCVTVSS ASTKGPSVFP LAPSSKSTSG GTAALGCLVK D YFCECPVT ...String:
EVQLVESGGG CVKPGGSLRL SCSASGFSLT KYKMTWVRQA PGKGLEWVSS ISSTSRDIDY ADSVKGRFTI SRDNAKNSLF LQMSSLRVD DTAVYYCTRD GWLWGWDVRS NYYYNALDVW GQGTCVTVSS ASTKGPSVFP LAPSSKSTSG GTAALGCLVK D YFCECPVT VSWNSGALTS GVHTFPAVLQ SSGLYSLSSV VTVPSSSLGT QTYICNVNHK PSNTKVDKRV

-
Macromolecule #4: light chain of GC1102

MacromoleculeName: light chain of GC1102 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.399137 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIVVTQSPSS LSASVGDRVT ITCRASQGIY NSIAWYQQKC GKAPKLLLYS TSTLLSGVPS RFSGSGSGTD YTLTITNLQC EDFATYYCQ QYFVTPETFG QGTKLEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTCQDS ...String:
DIVVTQSPSS LSASVGDRVT ITCRASQGIY NSIAWYQQKC GKAPKLLLYS TSTLLSGVPS RFSGSGSGTD YTLTITNLQC EDFATYYCQ QYFVTPETFG QGTKLEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTCQDS KDCTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC

-
Macromolecule #5: Large envelope protein

MacromoleculeName: Large envelope protein / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: HBV genotype D3 (virus)
Molecular weightTheoretical: 25.430086 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MENITSGFLG PLLVLQAGFF LLTRILTIPQ SLDSWWTSLN FLGGTTVCLG QNSQSPTSNH SPTSCPPTCP GYRWMCLRRF IIFLFILLL CLIFLLVLLD YQGMLPVCPL IPGSSTTSTG PCRTCMTTAQ GTSMYPSCCC TKPSDGNCTC IPIPSSWAFG K FLWEWASA ...String:
MENITSGFLG PLLVLQAGFF LLTRILTIPQ SLDSWWTSLN FLGGTTVCLG QNSQSPTSNH SPTSCPPTCP GYRWMCLRRF IIFLFILLL CLIFLLVLLD YQGMLPVCPL IPGSSTTSTG PCRTCMTTAQ GTSMYPSCCC TKPSDGNCTC IPIPSSWAFG K FLWEWASA RFSWLSLLVP FVQWFVGLSP TVWLSVIWMM WYWGPSLYSI LSPFLPLLPI FFCLWVYI

UniProtKB: Large envelope protein

-
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 BIOQUANTUM (6k 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 / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.7000000000000001 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: 3.09 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 178344
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Details: SGD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Details: SGD
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