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- EMDB-9795: AAV1 in neutral condition at 3.07 Ang -

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Basic information

Entry
Database: EMDB / ID: EMD-9795
TitleAAV1 in neutral condition at 3.07 Ang
Map data
Sample
  • Virus: Adeno-associated virus - 1
    • Protein or peptide: Capsid proteinCapsid
Keywordsadeno-associated virus / AAV1 / VIRUS
Function / homologyPhospholipase A2-like domain / Phospholipase A2-like domain / Parvovirus coat protein VP2 / Parvovirus coat protein VP1/VP2 / Parvovirus coat protein VP2 / Capsid/spike protein, ssDNA virus / T=1 icosahedral viral capsid / structural molecule activity / Capsid protein
Function and homology information
Biological speciesAdeno-associated virus - 1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.07 Å
AuthorsLou Z / Zhang R
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China China
CitationJournal: Nat Commun / Year: 2019
Title: Divergent engagements between adeno-associated viruses with their cellular receptor AAVR.
Authors: Ran Zhang / Guangxue Xu / Lin Cao / Zixian Sun / Yong He / Mengtian Cui / Yuna Sun / Shentao Li / Huapeng Li / Lan Qin / Mingxu Hu / Zhengjia Yuan / Zipei Rao / Wei Ding / Zihe Rao / Zhiyong Lou /
Abstract: Adeno-associated virus (AAV) receptor (AAVR) is an essential receptor for the entry of multiple AAV serotypes with divergent rules; however, the mechanism remains unclear. Here, we determine the ...Adeno-associated virus (AAV) receptor (AAVR) is an essential receptor for the entry of multiple AAV serotypes with divergent rules; however, the mechanism remains unclear. Here, we determine the structures of the AAV1-AAVR and AAV5-AAVR complexes, revealing the molecular details by which PKD1 recognizes AAV5 and PKD2 is solely engaged with AAV1. PKD2 lies on the plateau region of the AAV1 capsid. However, the AAV5-AAVR interface is strikingly different, in which PKD1 is bound at the opposite side of the spike of the AAV5 capsid than the PKD2-interacting region of AAV1. Residues in strands F/G and the CD loop of PKD1 interact directly with AAV5, whereas residues in strands B/C/E and the BC loop of PKD2 make contact with AAV1. These findings further the understanding of the distinct mechanisms by which AAVR recognizes various AAV serotypes and provide an example of a single receptor engaging multiple viral serotypes with divergent rules.
History
DepositionJan 30, 2019-
Header (metadata) releaseOct 23, 2019-
Map releaseOct 23, 2019-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
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  • Surface view colored by radius
  • Surface level: 0.05
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  • Surface view with fitted model
  • Atomic models: PDB-6jcr
  • Surface level: 0.05
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6jcr
  • Imaged by Jmol
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

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Map

FileDownload / File: emd_9795.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.93 Å
Density
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.112543255 - 0.21353179
Average (Standard dev.)0.0033591904 (±0.016540088)
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-0.1130.2140.003

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Supplemental data

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Sample components

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Entire : Adeno-associated virus - 1

EntireName: Adeno-associated virus - 1
Components
  • Virus: Adeno-associated virus - 1
    • Protein or peptide: Capsid proteinCapsid

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Supramolecule #1: Adeno-associated virus - 1

SupramoleculeName: Adeno-associated virus - 1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 85106 / Sci species name: Adeno-associated virus - 1 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Adeno-associated virus - 1
Molecular weightTheoretical: 58.228344 KDa
SequenceString: DGVGNASGNW HCDSTWLGDR VITTSTRTWA LPTYNNHLYK QISSASTGAS NDNHYFGYST PWGYFDFNRF HCHFSPRDWQ RLINNNWGF RPKRLNFKLF NIQVKEVTTN DGVTTIANNL TSTVQVFSDS EYQLPYVLGS AHQGCLPPFP ADVFMIPQYG Y LTLNNGSQ ...String:
DGVGNASGNW HCDSTWLGDR VITTSTRTWA LPTYNNHLYK QISSASTGAS NDNHYFGYST PWGYFDFNRF HCHFSPRDWQ RLINNNWGF RPKRLNFKLF NIQVKEVTTN DGVTTIANNL TSTVQVFSDS EYQLPYVLGS AHQGCLPPFP ADVFMIPQYG Y LTLNNGSQ AVGRSSFYCL EYFPSQMLRT GNNFTFSYTF EEVPFHSSYA HSQSLDRLMN PLIDQYLYYL NRTQNQSGSA QN KDLLFSR GSPAGMSVQP KNWLPGPCYR QQRVSKTKTD NNNSNFTWTG ASKYNLNGRE SIINPGTAMA SHKDDEDKFF PMS GVMIFG KESAGASNTA LDNVMITDEE EIKATNPVAT ERFGTVAVNF QSSSTDPATG DVHAMGALPG MVWQDRDVYL QGPI WAKIP HTDGHFHPSP LMGGFGLKNP PPQILIKNTP VPANPPAEFS ATKFASFITQ YSTGQVSVEI EWELQKENSK RWNPE VQYT SNYAKSANVD FTVDNNGLYT EPRPIGTRYL TRPL

UniProtKB: Capsid protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation state2D array

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 1.6 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 2642

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