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- EMDB-61004: Structure of HBsAg in complex with Fab H006 -

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Basic information

Entry
Database: EMDB / ID: EMD-61004
TitleStructure of HBsAg in complex with Fab H006
Map datasharpened map
Sample
  • Complex: HBV surface antigen dimer
    • Protein or peptide: Large envelope protein
    • Protein or peptide: heavy chain of antibody H006 Fab
    • Protein or peptide: light chain of antibody H006 Fab
KeywordsHBV / HBsAg / VIRAL PROTEIN / Antibody / Fab / VIRAL PROTEIN-IMMUNE SYSTEM 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: 3.13 Å
AuthorsChen L / He X
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31821091 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
DepositionJul 31, 2024-
Header (metadata) releaseJul 2, 2025-
Map releaseJul 2, 2025-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_61004.png

Downloads & links

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Map

FileDownload / File: emd_61004.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 256 pix.
= 273.152 Å		1.07 Å/pix.
x 256 pix.
= 273.152 Å		1.07 Å/pix.
x 256 pix.
= 273.152 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.067 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.2
Minimum - Maximum-8.575499000000001 - 12.856334
Average (Standard dev.)0.0009083736 (±0.13911417)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 273.152 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_61004_msk_1.map
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Additional map: main map

Fileemd_61004_additional_1.map
Annotationmain map
Projections & Slices
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Half map: #2

Fileemd_61004_half_map_1.map
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Half map: #1

Fileemd_61004_half_map_2.map
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Sample components

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Entire : HBV surface antigen dimer

EntireName: HBV surface antigen dimer
Components
  • Complex: HBV surface antigen dimer
    • Protein or peptide: Large envelope protein
    • Protein or peptide: heavy chain of antibody H006 Fab
    • Protein or peptide: light chain of antibody H006 Fab

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Supramolecule #1: HBV surface antigen dimer

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

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Macromolecule #1: Large envelope protein

MacromoleculeName: Large envelope protein / type: protein_or_peptide / ID: 1 / 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

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Macromolecule #2: heavy chain of antibody H006 Fab

MacromoleculeName: heavy chain of antibody H006 Fab / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.645727 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QMRLVESGGG CVRPGGSLRL SCAGSGFRFT GYGIHWVRQA PGKGLEWLAY ISNDGSKKYH TDSVKGRFTV SRDNAKNTAY LQMNSLRVE ETAVYFCAKD GYLSAARGYG MDVWGQGICV TVSPSASTKG PSVFPLAPSS KSTSGGTAAL GCLVKDYFCE C PVTVSWNS ...String:
QMRLVESGGG CVRPGGSLRL SCAGSGFRFT GYGIHWVRQA PGKGLEWLAY ISNDGSKKYH TDSVKGRFTV SRDNAKNTAY LQMNSLRVE ETAVYFCAKD GYLSAARGYG MDVWGQGICV TVSPSASTKG PSVFPLAPSS KSTSGGTAAL GCLVKDYFCE C PVTVSWNS GALTSGVHTF PAVLQSSGLY SLSSVVTVPS SSLGTQTYIC NVNHKPSNTK VDKRV

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Macromolecule #3: light chain of antibody H006 Fab

MacromoleculeName: light chain of antibody H006 Fab / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.109621 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SYVLTQPPSV SVAPGQTATI TCGGNNIGGK SVHWFQQKCG QAPLLIISDD NDRPSGIPER VSGSNSGNTA TLTISRVECG DEADYYCQV WDTTSDQLVF GGGTMLTVLR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTCQD ...String:
SYVLTQPPSV SVAPGQTATI TCGGNNIGGK SVHWFQQKCG QAPLLIISDD NDRPSGIPER VSGSNSGNTA TLTISRVECG DEADYYCQV WDTTSDQLVF GGGTMLTVLR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTCQD SKDCTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC

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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: 7.41
VitrificationCryogen name: ETHANE

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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: 1.8 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.13 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 820246
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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