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- PDB-6jcs: AAV5 in complex with AAVR -

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Basic information

Entry
Database: PDB / ID: 6jcs
TitleAAV5 in complex with AAVR
Components
  • Capsid proteinCapsid
  • Dyslexia-associated protein KIAA0319-like protein
KeywordsVIRUS / adeno-associated virus / AAV5 / receptor / AAVR
Function / homology
Function and homology information


T=1 icosahedral viral capsid / neuron migration / cytoplasmic vesicle / Golgi membrane / nucleolus / structural molecule activity / Golgi apparatus / membrane / plasma membrane
Similarity search - Function
Dyslexia-associated protein KIAA0319-like / MANSC domain / MANSC domain profile. / Empty Capsid Viral Protein 2 / Parvovirus coat protein VP1/VP2 / PKD domain / Polycystic kidney disease (PKD) domain profile. / PKD domain / PKD domain superfamily / PKD/Chitinase domain ...Dyslexia-associated protein KIAA0319-like / MANSC domain / MANSC domain profile. / Empty Capsid Viral Protein 2 / Parvovirus coat protein VP1/VP2 / PKD domain / Polycystic kidney disease (PKD) domain profile. / PKD domain / PKD domain superfamily / PKD/Chitinase domain / Repeats in polycystic kidney disease 1 (PKD1) and other proteins / Phospholipase 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 / Beta Complex / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Dyslexia-associated protein KIAA0319-like protein / Capsid protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Adeno-associated virus - 5
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.18 Å
AuthorsLou, Z. / Zhang, R.
Funding support China, 1items
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, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 6, 2019Group: Data collection / Other / Category: cell / Item: _cell.Z_PDB
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

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  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Capsid protein
R: Dyslexia-associated protein KIAA0319-like protein


Theoretical massNumber of molelcules
Total (without water)69,1242
Polymers69,1242
Non-polymers00
Water0
1
A: Capsid protein
R: Dyslexia-associated protein KIAA0319-like protein
x 60


Theoretical massNumber of molelcules
Total (without water)4,147,464120
Polymers4,147,464120
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Capsid protein
R: Dyslexia-associated protein KIAA0319-like protein
x 5


  • icosahedral pentamer
  • 346 kDa, 10 polymers
Theoretical massNumber of molelcules
Total (without water)345,62210
Polymers345,62210
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Capsid protein
R: Dyslexia-associated protein KIAA0319-like protein
x 6


  • icosahedral 23 hexamer
  • 415 kDa, 12 polymers
Theoretical massNumber of molelcules
Total (without water)414,74612
Polymers414,74612
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein Capsid protein / Capsid


Mass: 58213.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Adeno-associated virus - 5 / References: UniProt: Q9YIJ1
#2: Protein Dyslexia-associated protein KIAA0319-like protein / Adeno-associated virus receptor / AAVR


Mass: 10911.322 Da / Num. of mol.: 1 / Fragment: PKD1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIAA0319L, AAVR, KIAA1837, PP791 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IZA0

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: 2D ARRAY / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Adeno-associated virus - 5COMPLEXall0MULTIPLE SOURCES
2capsid protein VP1COMPLEX#11NATURAL
3PKD1Polycystin 1ORGANELLE OR CELLULAR COMPONENT#21RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Adeno-associated virus - 582300
23Homo sapiens (human)9606
Source (recombinant)Organism: Escherichia coli (E. coli)
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Homo sapiens
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 36 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.11.1_2575: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.18 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 12590 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.015026
ELECTRON MICROSCOPYf_angle_d1.0086863
ELECTRON MICROSCOPYf_dihedral_angle_d6.1362942
ELECTRON MICROSCOPYf_chiral_restr0.061722
ELECTRON MICROSCOPYf_plane_restr0.008909

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