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- EMDB-6809: The CryoEM map of HPV58 VLP in complex with the Fab fragment of a... -

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Basic information

Entry
Database: EMDB / ID: 6809
TitleThe CryoEM map of HPV58 VLP in complex with the Fab fragment of antibody A12A3
SampleHuman papillomavirus
SourceHuman papillomavirus / virus
Map data
Methodsingle particle reconstruction, at 9.5 Å resolution
AuthorsLi SW / Li ZH
CitationMBio, 2017, 8

MBio, 2017, 8 Yorodumi Papers
Crystal Structures of Two Immune Complexes Identify Determinants for Viral Infectivity and Type-Specific Neutralization of Human Papillomavirus.
Zhihai Li / Daning Wang / Ying Gu / Shuo Song / Maozhou He / Jingjie Shi / Xinlin Liu / Shuangping Wei / Jinjin Li / Hai Yu / Qingbing Zheng / Xiaodong Yan / Timothy S Baker / Jun Zhang / Jason S McLellan / Shaowei Li / Ningshao Xia

DateDeposition: Aug 10, 2017 / Header (metadata) release: Oct 25, 2017 / Map release: Oct 25, 2017 / Last update: Oct 25, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 2
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


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Supplemental images

Downloads & links

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Map

Fileemd_6809.map.gz (map file in CCP4 format, 296353 KB)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
420 pix
2.22 Å/pix.
= 931.56 Å
420 pix
2.22 Å/pix.
= 931.56 Å
420 pix
2.22 Å/pix.
= 931.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 2.218 Å
Density
Contour Level:2 (by author), 2 (movie #1):
Minimum - Maximum-7.2638855 - 11.711547
Average (Standard dev.)-3.7027E-10 (1)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions420420420
Origin555
Limit424424424
Spacing420420420
CellA=B=C: 931.56 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.2182.2182.218
M x/y/z420420420
origin x/y/z0.0000.0000.000
length x/y/z931.560931.560931.560
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS555
NC/NR/NS420420420
D min/max/mean-7.26411.712-0.000

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Supplemental data

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Sample components

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Entire Human papillomavirus

EntireName: Human papillomavirus
Details: VLP generated by recombinantly expressed; Fab Fragment generated by proteolytic cleavage of IgG antibody;
Number of components: 1

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Component #1: virus, Human papillomavirus

VirusName: Human papillomavirus / Class: VIRUS-LIKE PARTICLE
Details: VLP generated by recombinantly expressed; Fab Fragment generated by proteolytic cleavage of IgG antibody;
Empty: Yes / Enveloped: No / Isolate: OTHER
SpeciesSpecies: Human papillomavirus / virus
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionpH: 6.5
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 25 e/Å2 / Illumination mode: SPOT SCAN
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON I (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 3600
3D reconstructionResolution: 9.5 Å / Resolution method: FSC 0.143 CUT-OFF

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  • Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
  • Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
  • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

External links: The 2017 Nobel Prize in Chemistry - Press Release

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