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- EMDB-9796: AAV5 in complex with AAVR -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-9796
TitleAAV5 in complex with AAVR
Map data
SampleAdeno-associated virus - 5
  • capsid protein VP1
  • PKD1
  • Capsid proteinCapsid
  • Dyslexia-associated protein KIAA0319-like protein
Function / homology
Function and homology information


viral capsid / cytoplasmic vesicle / Golgi membrane / structural molecule activity / integral component of membrane / plasma membrane
Capsid/spike protein, ssDNA virus / Parvovirus coat protein VP2 / MANSC domain profile. / Polycystic kidney disease (PKD) domain profile. / PKD domain / Parvovirus coat protein VP2 / Parvovirus coat protein VP1, N-terminal / Immunoglobulin-like fold / MANSC domain / Parvovirus coat protein VP1 ...Capsid/spike protein, ssDNA virus / Parvovirus coat protein VP2 / MANSC domain profile. / Polycystic kidney disease (PKD) domain profile. / PKD domain / Parvovirus coat protein VP2 / Parvovirus coat protein VP1, N-terminal / Immunoglobulin-like fold / MANSC domain / Parvovirus coat protein VP1 / PKD/Chitinase domain / Dyslexia-associated protein KIAA0319-like protein / PKD domain superfamily / Parvovirus coat protein VP1/VP2
Dyslexia-associated protein KIAA0319-like protein / Capsid protein
Biological speciesAdeno-associated virus - 5 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.18 Å
AuthorsLou Z / Zhang R
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China China
CitationJournal: To Be Published
Title: Divergent engagements between adeno-associated viruses with their cellular receptor AAVR
Authors: Lou Z / Zhang R
Validation ReportPDB-ID: 6jcs

SummaryFull reportAbout validation report
History
DepositionJan 30, 2019-
Header (metadata) releaseAug 7, 2019-
Map releaseAug 14, 2019-
UpdateAug 14, 2019-
Current statusAug 14, 2019Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6jcs
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6jcs
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_9796.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 380 pix.
= 353.4 Å
0.93 Å/pix.
x 380 pix.
= 353.4 Å
0.93 Å/pix.
x 380 pix.
= 353.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.12124219 - 0.24112643
Average (Standard dev.)0.004192867 (±0.017954214)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-189-189-189
Dimensions380380380
Spacing380380380
CellA=B=C: 353.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.930.930.93
M x/y/z380380380
origin x/y/z0.0000.0000.000
length x/y/z353.400353.400353.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-189-189-189
NC/NR/NS380380380
D min/max/mean-0.1210.2410.004

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Supplemental data

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Sample components

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Entire Adeno-associated virus - 5

EntireName: Adeno-associated virus - 5 / Number of components: 5

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Component #1: protein, Adeno-associated virus - 5

ProteinName: Adeno-associated virus - 5 / Recombinant expression: No

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Component #2: protein, capsid protein VP1

ProteinName: capsid protein VP1 / Recombinant expression: No
SourceSpecies: Adeno-associated virus - 5

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Component #3: cellular-component, PKD1

Cellular-componentName: PKD1 / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #4: protein, Capsid protein

ProteinName: Capsid proteinCapsid / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 58.213078 kDa
SourceSpecies: Adeno-associated virus - 5

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Component #5: protein, Dyslexia-associated protein KIAA0319-like protein

ProteinName: Dyslexia-associated protein KIAA0319-like protein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.911322 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Experimental details

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Sample preparation

SpecimenSpecimen state: 2D array / Method: cryo EM
Sample solutionpH: 8
VitrificationCryogen name: ETHANE

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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: 36 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: 12590
3D reconstructionResolution: 3.18 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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