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- EMDB-13733: HBc-P5T in complex with X-100 -

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Basic information

Entry
Database: EMDB / ID: EMD-13733
TitleHBc-P5T in complex with X-100
Map data
Sample
  • Complex: HBc-P5T-TX100
    • Protein or peptide: Capsid protein
  • Ligand: FRAGMENT OF TRITON X-100
KeywordsHBc-P5T (low secretion phenotype) in complex with Triton X-100 / VIRAL PROTEIN
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
Similarity search - Function
Hepatitis core antigen / Viral capsid core domain supefamily, Hepatitis B virus / Hepatitis core antigen
Similarity search - Domain/homology
Biological speciesHepatitis B virus ayw/France/Tiollais/1979 / Hepatitis B virus genotype D subtype ayw (isolate France/Tiollais/1979)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsMakbul C / Boettcher B
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG)Bo1150/17-1. Germany
CitationJournal: Viruses / Year: 2021
Title: Binding of a Pocket Factor to Hepatitis B Virus Capsids Changes the Rotamer Conformation of Phenylalanine 97.
Authors: Cihan Makbul / Christian Kraft / Matthias Grießmann / Tim Rasmussen / Kilian Katzenberger / Melina Lappe / Paul Pfarr / Cato Stoffer / Mara Stöhr / Anna-Maria Wandinger / Bettina Böttcher /
Abstract: (1) Background: During maturation of the Hepatitis B virus, a viral polymerase inside the capsid transcribes a pre-genomic RNA into a partly double stranded DNA-genome. This is followed by ...(1) Background: During maturation of the Hepatitis B virus, a viral polymerase inside the capsid transcribes a pre-genomic RNA into a partly double stranded DNA-genome. This is followed by envelopment with surface proteins inserted into a membrane. Envelopment is hypothetically regulated by a structural signal that reports the maturation state of the genome. NMR data suggest that such a signal can be mimicked by the binding of the detergent Triton X 100 to hydrophobic pockets in the capsid spikes. (2) Methods: We have used electron cryo-microscopy and image processing to elucidate the structural changes that are concomitant with the binding of Triton X 100. (3) Results: Our maps show that Triton X 100 binds with its hydrophobic head group inside the pocket. The hydrophilic tail delineates the outside of the spike and is coordinated via Lys-96. The binding of Triton X 100 changes the rotamer conformation of Phe-97 in helix 4, which enables a π-stacking interaction with Trp-62 in helix 3. Similar changes occur in mutants with low secretion phenotypes (P5T and L60V) and in a mutant with a pre-mature secretion phenotype (F97L). (4) Conclusion: Binding of Triton X 100 is unlikely to mimic structural maturation because mutants with different secretion phenotypes show similar structural responses.
History
DepositionOct 12, 2021-
Header (metadata) releaseDec 8, 2021-
Map releaseDec 8, 2021-
UpdateJul 17, 2024-
Current statusJul 17, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.026
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.026
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7pzm
  • Surface level: 0.026
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7pzm
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13733.png

Downloads & links

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Map

FileDownload / File: emd_13733.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 400 pix.
= 425.4 Å		1.06 Å/pix.
x 400 pix.
= 425.4 Å		1.06 Å/pix.
x 400 pix.
= 425.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0635 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.026 / Movie #1: 0.026
Minimum - Maximum-0.14433275 - 0.22842757
Average (Standard dev.)0.0006006262 (±0.014388461)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 425.40002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.06351.06351.0635
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z425.400425.400425.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.1440.2280.001

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Supplemental data

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Half map: #1

Fileemd_13733_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_13733_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 : HBc-P5T-TX100

EntireName: HBc-P5T-TX100
Components
  • Complex: HBc-P5T-TX100
    • Protein or peptide: Capsid protein
  • Ligand: FRAGMENT OF TRITON X-100

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Supramolecule #1: HBc-P5T-TX100

SupramoleculeName: HBc-P5T-TX100 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Hepatitis B virus ayw/France/Tiollais/1979

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Macromolecule #1: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Hepatitis B virus genotype D subtype ayw (isolate France/Tiollais/1979)
Strain: isolate France/Tiollais/1979
Molecular weightTheoretical: 21.150205 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MDIDTYKEFG 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: FRAGMENT OF TRITON X-100

MacromoleculeName: FRAGMENT OF TRITON X-100 / type: ligand / ID: 2 / Number of copies: 4 / Formula: TRT
Molecular weightTheoretical: 352.508 Da
Chemical component information

ChemComp-TRT:
FRAGMENT OF TRITON X-100 / detergent*YM

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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: 7.5
GridModel: Quantifoil R1.2/1.3 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.029 kPa
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 166890
Startup modelType of model: EMDB MAP
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 130610
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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