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- EMDB-64014: HBsAg in complex with H020 Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-64014
TitleHBsAg in complex with H020 Fab
Map data
Sample
  • Complex: Structure of the Hepatitis B virus envelope protein in complex with H020 Fab
    • Complex: envelope protein
      • Protein or peptide: Middle S protein
    • Complex: H020 Fab
      • Protein or peptide: H020 Fab Heavy Chain
      • Protein or peptide: H020 Fab Light Chain
KeywordsHBV / HBsAg / Fab / Antigentic 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: 2.86 Å
AuthorsChen L / Tao W / He X
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31821091 China
CitationJournal: J Mol Biol / Year: 2025
Title: The Symmetric Structure of the Antigenic Loop in Type B HBV Surface Antigen.
Authors: Weiyu Tao / Xiao He / Lei Chen /
Abstract: Hepatitis B virus (HBV) is an enveloped virus with HBV surface antigen (HBsAg) as the only protein on its viral membrane. The extracellular antigenic loop (AGL) of HBsAg plays a crucial role in viral ...Hepatitis B virus (HBV) is an enveloped virus with HBV surface antigen (HBsAg) as the only protein on its viral membrane. The extracellular antigenic loop (AGL) of HBsAg plays a crucial role in viral attachment to host cells, serves as the primary target for neutralizing antibodies (NAbs), and is subject to escape mutations. Previous studies have shown that the AGL exhibits two different structures (Type A and Type B) dictated by distinct disulfide bond linkage. However, due to the flexibility of some regions in previous structure, the complete model of AGL and its symmetry remain elusive. Here, we present the cryo-EM structure of AGL in complex with the Fab fragment of the NAb H020. The complete structure of AGL reveals its two-fold symmetry and it can bind two Fab fragments simultaneously. Further analysis elucidates the underlying mechanism of pan-serotype neutralizing capability of H020 and how escape mutations hinder its binding.
History
DepositionApr 3, 2025-
Header (metadata) releaseOct 29, 2025-
Map releaseOct 29, 2025-
UpdateOct 29, 2025-
Current statusOct 29, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_64014.png

Downloads & links

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Map

FileDownload / File: emd_64014.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 320 pix.
= 266.56 Å		0.83 Å/pix.
x 320 pix.
= 266.56 Å		0.83 Å/pix.
x 320 pix.
= 266.56 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.833 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.459
Minimum - Maximum-3.331358 - 6.165633
Average (Standard dev.)0.017496858 (±0.08613874)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 266.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_64014_msk_1.map
Projections & Slices
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Additional map: #1

Fileemd_64014_additional_1.map
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Half map: #2

Fileemd_64014_half_map_1.map
Projections & Slices
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Histogram

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Half map: #1

Fileemd_64014_half_map_2.map
Projections & Slices
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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 H020 Fab
Components
  • Complex: Structure of the Hepatitis B virus envelope protein in complex with H020 Fab
    • Complex: envelope protein
      • Protein or peptide: Middle S protein
    • Complex: H020 Fab
      • Protein or peptide: H020 Fab Heavy Chain
      • Protein or peptide: H020 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 H020 Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: envelope protein

SupramoleculeName: envelope protein / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Hepatitis B virus

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Supramolecule #3: H020 Fab

SupramoleculeName: H020 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Homo sapiens (human)

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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: H020 Fab Heavy Chain

MacromoleculeName: H020 Fab Heavy Chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.662443 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLQESGPG LVRPSETLSL TCTVSGGSIS NDYWSWIRQP PGKGLEWIGQ IHSKGDTNYN PSLKSRVTIS VDTSKNQLSL KVRSVTAAD TAVYYCARHL YRYGYRNYFD YWGQGNLVTV SSAASTKGPS VFPLAPSSKS TSGGTAALGC LVKDYFPEPV T VSWNSGAL ...String:
QVQLQESGPG LVRPSETLSL TCTVSGGSIS NDYWSWIRQP PGKGLEWIGQ IHSKGDTNYN PSLKSRVTIS VDTSKNQLSL KVRSVTAAD TAVYYCARHL YRYGYRNYFD YWGQGNLVTV SSAASTKGPS VFPLAPSSKS TSGGTAALGC LVKDYFPEPV T VSWNSGAL TSGVHTFPAV LQSSGLYSLS SVVTVPSSSL GTQTYICNVN HKPSNTKVDK RV

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Macromolecule #3: H020 Fab Light Chain

MacromoleculeName: H020 Fab Light Chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.178699 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIQMTQSPSS VSASVGDRVT IACRASQGIS SGLAWYQQKP GKAPKLLIHA ASSLQSGVPS RFSGSESGTE FTLTISSLQP EDFATYYCQ QANSFPLTFG GGTKVEFKPR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String:
DIQMTQSPSS VSASVGDRVT IACRASQGIS SGLAWYQQKP GKAPKLLIHA ASSLQSGVPS RFSGSESGTE FTLTISSLQP EDFATYYCQ QANSFPLTFG GGTKVEFKPR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS 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: 8
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: 52.0 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: 2.86 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 195817
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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