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- EMDB-63960: HBsAg in complex with HBC34 Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-63960
TitleHBsAg in complex with HBC34 Fab
Map dataThis is a composite map
Sample
  • Complex: Structure of the Hepatitis B virus envelope protein in complex with HBC34 Fab
    • Protein or peptide: Middle S protein
    • Protein or peptide: HBC34 Fab Heavy Chain
    • Protein or peptide: HBC34 Fab Light Chain
KeywordsHBV / HBsAg / Fab / Antigenic loop / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homologyLarge envelope protein S / Major surface antigen from hepadnavirus / membrane fusion involved in viral entry into host cell / symbiont entry into host cell / virion attachment to host cell / virion membrane / membrane / Middle S protein
Function and homology information
Biological speciesHepatitis B virus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.25 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
DepositionMar 27, 2025-
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_63960.png

Downloads & links

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Map

FileDownload / File: emd_63960.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a composite map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 320 pix.
= 266.88 Å		0.83 Å/pix.
x 320 pix.
= 266.88 Å		0.83 Å/pix.
x 320 pix.
= 266.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.834 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.74
Minimum - Maximum-0.69139683 - 3.6559503
Average (Standard dev.)0.009897491 (±0.05121362)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 266.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_63960_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_63960_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_63960_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Structure of the Hepatitis B virus envelope protein in complex wi...

EntireName: Structure of the Hepatitis B virus envelope protein in complex with HBC34 Fab
Components
  • Complex: Structure of the Hepatitis B virus envelope protein in complex with HBC34 Fab
    • Protein or peptide: Middle S protein
    • Protein or peptide: HBC34 Fab Heavy Chain
    • Protein or peptide: HBC34 Fab Light Chain

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Supramolecule #1: Structure of the Hepatitis B virus envelope protein in complex wi...

SupramoleculeName: Structure of the Hepatitis B virus envelope protein in complex with HBC34 Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Hepatitis B virus

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Macromolecule #1: Middle S protein

MacromoleculeName: Middle S protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Hepatitis B virus
Molecular weightTheoretical: 31.153318 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MQWNSTTFHQ TLQDPRVRGL YFPAGGSSSG AVNPVPTTAS PLSSIFSRIG DPALNMENIT SGFLGPLLVL QAGFFLLTRI LTIPQSLDS WWTSLNFLGG TTVCLGQNSQ SPTSNHSPTS CPPTCPGYRW MALRRFIIFL FILLLALIFL LVLLDYQGML P VCPLIPGS ...String:
MQWNSTTFHQ TLQDPRVRGL YFPAGGSSSG AVNPVPTTAS PLSSIFSRIG DPALNMENIT SGFLGPLLVL QAGFFLLTRI LTIPQSLDS WWTSLNFLGG TTVCLGQNSQ SPTSNHSPTS CPPTCPGYRW MALRRFIIFL FILLLALIFL LVLLDYQGML P VCPLIPGS STTSTGPCRT CMTTAQGTSM YPSCCCTKPS DGNCTCIPIP SSWAFGKFLW EWASARFSWL SLLVPFVQWF VG LSPTVWL SVIWMMWYWG PSLYSILSPF LPLLPIFFAL WVYI

UniProtKB: Middle S protein

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Macromolecule #2: HBC34 Fab Heavy Chain

MacromoleculeName: HBC34 Fab Heavy Chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.412146 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GSELQLVESG GGWVQPGGSQ RLSCAASGRI FRSFYMSWVR QAPGKGLEWV ATINQDGSEK LYVDSVKGRF TISRDNAKNS LFLQMNNLR VEDTAVYYCA AWSGNSGGMD VWGQGTTVSV SSLEASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA ...String:
GSELQLVESG GGWVQPGGSQ RLSCAASGRI FRSFYMSWVR QAPGKGLEWV ATINQDGSEK LYVDSVKGRF TISRDNAKNS LFLQMNNLR VEDTAVYYCA AWSGNSGGMD VWGQGTTVSV SSLEASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYICNV NHKPSNTKVD KRV

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Macromolecule #3: HBC34 Fab Light Chain

MacromoleculeName: HBC34 Fab Light Chain / type: protein_or_peptide / ID: 3 / 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

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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: 3.25 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 206975
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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