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- EMDB-9611: Anthrax Toxin Receptor 1-bound the Seneca Valley Virus in neutral... -

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Basic information

Entry
Database: EMDB / ID: 9611
TitleAnthrax Toxin Receptor 1-bound the Seneca Valley Virus in neutral conditions
Map data
SampleSeneca valley virusSenecavirus:
virus / VP1 / VP3 / vp2 / VP4 / Anthrax toxin receptor 1 / (ligand) x 2
Function / homologyAnthrax toxin receptor, extracellular / von Willebrand factor A-like domain superfamily / Anthrax toxin receptor, C-terminal / Uptake and function of anthrax toxins / VWFA domain profile. / Anthrax receptor extracellular domain / Anthrax receptor C-terminus region / von Willebrand factor type A domain / von Willebrand factor, type A / Anthrax toxin receptor ...Anthrax toxin receptor, extracellular / von Willebrand factor A-like domain superfamily / Anthrax toxin receptor, C-terminal / Uptake and function of anthrax toxins / VWFA domain profile. / Anthrax receptor extracellular domain / Anthrax receptor C-terminus region / von Willebrand factor type A domain / von Willebrand factor, type A / Anthrax toxin receptor / negative regulation of extracellular matrix assembly / reproductive process / filopodium membrane / toxin transport / blood vessel development / positive regulation of metallopeptidase activity / lamellipodium membrane / substrate adhesion-dependent cell spreading / actin cytoskeleton reorganization / collagen binding / transmembrane signaling receptor activity / actin filament binding / endosome membrane / external side of plasma membrane / cell surface / integral component of membrane / plasma membrane / metal ion binding / Anthrax toxin receptor 1
Function and homology information
SourceSeneca valley virus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / 3.38 Å resolution
AuthorsLou ZY / Cao L
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Seneca Valley virus attachment and uncoating mediated by its receptor anthrax toxin receptor 1.
Authors: Lin Cao / Ran Zhang / Tingting Liu / Zixian Sun / Mingxu Hu / Yuna Sun / Lingpeng Cheng / Yu Guo / Sheng Fu / Junjie Hu / Xiangmin Li / Chengqi Yu / Hanyang Wang / Huanchun Chen / Xueming Li / Elizabeth E Fry / David I Stuart / Ping Qian / Zhiyong Lou / Zihe Rao
Validation ReportPDB-ID: 6adr

SummaryFull reportAbout validation report
DateDeposition: Aug 2, 2018 / Header (metadata) release: Jan 30, 2019 / Map release: Feb 6, 2019 / Last update: Feb 6, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6adr
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_9611.map.gz (map file in CCP4 format, 665501 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
550 pix
1.1 Å/pix.
= 605. Å
550 pix
1.1 Å/pix.
= 605. Å
550 pix
1.1 Å/pix.
= 605. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density
Contour Level:0.02 (by author), 0.02 (movie #1):
Minimum - Maximum-0.063087806 - 0.11678787
Average (Standard dev.)0.0011857471 (0.0063620913)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions550550550
Origin0.00.00.0
Limit549.0549.0549.0
Spacing550550550
CellA=B=C: 605.0 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z550550550
origin x/y/z0.0000.0000.000
length x/y/z605.000605.000605.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-6-10-25
NX/NY/NZ564636
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS550550550
D min/max/mean-0.0630.1170.001

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Supplemental data

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Sample components

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Entire Seneca valley virus

EntireName: Seneca valley virus / Number of components: 8

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Component #1: virus, Seneca valley virus

VirusName: Seneca valley virusSenecavirus / Class: VIRION / Empty: Yes / Enveloped: No / Isolate: STRAIN
SpeciesSpecies: Seneca valley virus

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Component #2: protein, VP1

ProteinName: VP1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 28.494023 kDa
SourceSpecies: Seneca valley virus

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Component #3: protein, VP3

ProteinName: VP3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.393938 kDa
SourceSpecies: Seneca valley virus

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Component #4: protein, vp2

ProteinName: vp2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.843289 kDa
SourceSpecies: Seneca valley virus

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Component #5: protein, VP4

ProteinName: VP4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.393875 kDa
SourceSpecies: Seneca valley virus

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Component #6: protein, Anthrax toxin receptor 1

ProteinName: Anthrax toxin receptor 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.31602 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli BL21 (bacteria)

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Component #7: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Component #8: ligand, water

LigandName: water / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 1.801505 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 6
VitrificationCryogen name: OTHER

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 1.63 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON II (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 15460
3D reconstructionResolution: 3.38 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Refinement protocol: rigid body
Output model

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