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- EMDB-6745: Cryo-EM structure of complex of HBsAg and Fab fragment of therape... -

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Basic information

Entry
Database: EMDB / ID: EMD-6745
TitleCryo-EM structure of complex of HBsAg and Fab fragment of therapeutic mAb-E6F6.
Map dataCryo-EM structure of HBsAg-E6F6-Fab complex
Sample
  • Complex: Complex of HBsAg with Fab fragment of therapeutic mAb-E6F6
    • Complex: HBsAg
    • Complex: E6F6-Fab
Biological speciesDrosophila (fruit flies)
Methodsingle particle reconstruction / cryo EM / Resolution: 12.0 Å
AuthorsMo X / Yuan AY
CitationJournal: To be published
Title: Structural insight into mechanism of antibody-mediated immunotherapy for persistent hepatitis B virus infection
Authors: Mo X / Yuan YA
History
DepositionMay 26, 2017-
Header (metadata) releaseJul 12, 2017-
Map releaseJul 12, 2017-
UpdateJul 12, 2017-
Current statusJul 12, 2017Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.65
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 1.65
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6745.png

Downloads & links

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Map

FileDownload / File: emd_6745.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of HBsAg-E6F6-Fab complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.81 Å/pix.
x 240 pix.
= 434.4 Å		1.81 Å/pix.
x 240 pix.
= 434.4 Å		1.81 Å/pix.
x 240 pix.
= 434.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.81 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.65 / Movie #1: 1.65
Minimum - Maximum-6.388028 - 7.948674
Average (Standard dev.)0.02168282 (±0.52592945)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-120-120-120
Dimensions240240240
Spacing240240240
CellA=B=C: 434.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.811.811.81
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z434.400434.400434.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-120-120-120
NC/NR/NS240240240
D min/max/mean-6.3887.9490.022

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Supplemental data

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Sample components

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Entire : Complex of HBsAg with Fab fragment of therapeutic mAb-E6F6

EntireName: Complex of HBsAg with Fab fragment of therapeutic mAb-E6F6
Components
  • Complex: Complex of HBsAg with Fab fragment of therapeutic mAb-E6F6
    • Complex: HBsAg
    • Complex: E6F6-Fab

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Supramolecule #1: Complex of HBsAg with Fab fragment of therapeutic mAb-E6F6

SupramoleculeName: Complex of HBsAg with Fab fragment of therapeutic mAb-E6F6
type: complex / ID: 1 / Parent: 0
Details: Surface protein of Hepatitis B virus and fab fragment generated by proteolytic cleavage of therapeutic mAb-E6F6.
Source (natural)Organism: Drosophila (fruit flies)
Recombinant expressionOrganism: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
Recombinant strain: DH5a / Recombinant plasmid: pET-Duet
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
Molecular weightExperimental: 3.24 MDa

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Supramolecule #2: HBsAg

SupramoleculeName: HBsAg / type: complex / ID: 2 / Parent: 1 / Details: Surface protein of Hepatitis B virus.

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Supramolecule #3: E6F6-Fab

SupramoleculeName: E6F6-Fab / type: complex / ID: 3 / Parent: 1
Details: Fab fragment generated by proteolytic cleavage of therapeutic mAb-E6F6.

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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

Concentration0.5 mg/mL
BufferpH: 6.5
Component:
ConcentrationFormulaName
500.0 mMNaClsodium chloride
20.0 mMTrisTris

Details: 20mM Tris (pH 6.5), 500mM NaCl
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 400 / Support film - Material: FORMVAR / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 101.325 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 5 seconds before pluning.
DetailsThis sample was monodisperse.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 70.0 K / Max: 70.0 K
DetailsPreliminary grid screening was performed manually.
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Number grids imaged: 12 / Number real images: 500 / Average exposure time: 1.0 sec. / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 3.0 µm / Calibrated defocus min: 1.0 µm / Calibrated magnification: 47000 / Illumination mode: OTHER / Imaging mode: DARK FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 47000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 56000
CTF correctionSoftware - Name: EMAN2 (ver. 2.1)
Final reconstructionNumber classes used: 72 / Applied symmetry - Point group: O (octahedral) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 12.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: EMAN2 (ver. 2.1) / Number images used: 29400
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationNumber classes: 80 / Avg.num./class: 300 / Software - Name: EMAN2 (ver. 2.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: RECIPROCAL / Protocol: AB INITIO MODEL / Overall B value: 300

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