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- EMDB-62957: HBcAg in complex with Fab mAb40 -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-62957
TitleHBcAg in complex with Fab mAb40
Map data
Sample
  • Complex: HBcAg in complex with Fab mAb40
    • Protein or peptide: Capsid protein
    • Protein or peptide: Heavy chain of Fab mAb40
    • Protein or peptide: Light chain of Fab mAb40
KeywordsAntigen-antibody complex / VIRAL PROTEIN/IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


microtubule-dependent intracellular transport of viral material towards nucleus / T=4 icosahedral viral capsid / viral penetration into host nucleus / host cell / host cell cytoplasm / symbiont entry into host cell / structural molecule activity / DNA binding / RNA binding / extracellular region
Similarity search - Function
Hepatitis B virus, capsid N-terminal / Hepatitis core protein, putative zinc finger / Hepatitis core antigen / Viral capsid core domain supefamily, Hepatitis B virus / Hepatitis core antigen
Similarity search - Domain/homology
Biological speciesHepatitis B virus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.44 Å
AuthorsChen SL
Funding support China, 3 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)82322034 China
National Natural Science Foundation of China (NSFC)82172047 China
National Natural Science Foundation of China (NSFC)82270480 China
CitationJournal: To Be Published
Title: PD-1 Blockade Unleashes Local Anti-Hepatitis B Virus Humoral Immunity Targeting Recurrent Hepatocellular Carcinoma
Authors: Kuang M / Chen SL
History
DepositionJan 3, 2025-
Header (metadata) releaseJan 7, 2026-
Map releaseJan 7, 2026-
UpdateJan 7, 2026-
Current statusJan 7, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62957.png

Downloads & links

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Map

FileDownload / File: emd_62957.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 200 pix.
= 215.6 Å		1.08 Å/pix.
x 200 pix.
= 215.6 Å		1.08 Å/pix.
x 200 pix.
= 215.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.078 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-2.229776 - 3.0898302
Average (Standard dev.)0.0007248348 (±0.05120541)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 215.59999 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_62957_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_62957_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 : HBcAg in complex with Fab mAb40

EntireName: HBcAg in complex with Fab mAb40
Components
  • Complex: HBcAg in complex with Fab mAb40
    • Protein or peptide: Capsid protein
    • Protein or peptide: Heavy chain of Fab mAb40
    • Protein or peptide: Light chain of Fab mAb40

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Supramolecule #1: HBcAg in complex with Fab mAb40

SupramoleculeName: HBcAg in complex with Fab mAb40 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Hepatitis B virus

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Macromolecule #1: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Hepatitis B virus
Molecular weightTheoretical: 21.146217 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MDIDPYKEFG ATVELLSFLP SDFFPSVRDL LDTASALYRE ALESPEHCSP HHTALRQAIL CWGELMTLAT WVGVNLEDPA SRDLVVSYV NTNMGLKFRQ LLWFHISCLT FGRETVIEYL VSFGVWIRTP PAYRPPNAPI LSTLPETTVV RRRGRSPRRR T PSPRRRRS QSPRRRRSQS RESQC

UniProtKB: Capsid protein

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Macromolecule #2: Heavy chain of Fab mAb40

MacromoleculeName: Heavy chain of Fab mAb40 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 52.175016 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGWSCIILFL VATATGVHSQ LLLLQSGGGL VKPGGHMRLS CEGSGFTFGD YYMNWVRQAP GKGLEWIASM SPRETATYYA DVVRGRFII SRDNAQQSTY LQMNFLRGDD SAVYYCARGV NSRSSNYVYG FEVWGQGTTV TVSSAKTTAP SVYPLAPVCG D TTGSSVTL ...String:
MGWSCIILFL VATATGVHSQ LLLLQSGGGL VKPGGHMRLS CEGSGFTFGD YYMNWVRQAP GKGLEWIASM SPRETATYYA DVVRGRFII SRDNAQQSTY LQMNFLRGDD SAVYYCARGV NSRSSNYVYG FEVWGQGTTV TVSSAKTTAP SVYPLAPVCG D TTGSSVTL GCLVKGYFPE PVTLTWNSGS LSSGVHTFPA VLQSDLYTLS SSVTVTSSTW PSQSITCNVA HPASSTKVDK KI EPRGPTI KPCPPCKCPA PNLLGGPSVF IFPPKIKDVL MISLSPIVTC VVVDVSEDDP DVQISWFVNN VEVHTAQTQT HRE DYNSTL RVVSALPIQH QDWMSGKEFK CKVNNKDLPA PIERTISKPK GSVRAPQVYV LPPPEEEMTK KQVTLTCMVT DFMP EDIYV EWTNNGKTEL NYKNTEPVLD SDGSYFMYSK LRVEKKNWVE RNSYSCSVVH EGLHNHHTTK SFSRTPGK

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Macromolecule #3: Light chain of Fab mAb40

MacromoleculeName: Light chain of Fab mAb40 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.848732 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGWSCIILFL VATATGVHSE VVLTQSPGTL SLFPGDRATL SCRASRTIDN TYLAWYQQKP GQAPRLLIYG ASSRATGVPD RFSGGGSGT DFTLTIRRLE PEDYAVYYCQ QYASPPYTFG RGTQLEIKRA DAAPTVSIFP PSSEQLTSGG ASVVCFLNNF Y PKDINVKW ...String:
MGWSCIILFL VATATGVHSE VVLTQSPGTL SLFPGDRATL SCRASRTIDN TYLAWYQQKP GQAPRLLIYG ASSRATGVPD RFSGGGSGT DFTLTIRRLE PEDYAVYYCQ QYASPPYTFG RGTQLEIKRA DAAPTVSIFP PSSEQLTSGG ASVVCFLNNF Y PKDINVKW KIDGSERQNG VLNSWTDQDS KDSTYSMSST LTLTKDEYER HNSYTCEATH KTSTSPIVKS FNRNEC

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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: FEI FALCON IV (4k 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: 2.4 µm / Nominal defocus min: 1.4000000000000001 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: EMDB MAP
EMDB ID:

42822

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.44 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 249011
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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