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- EMDB-22988: Adeno-associated virus serotype 5 in complex with the cellular re... -

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Basic information

Entry
Database: EMDB / ID: EMD-22988
TitleAdeno-associated virus serotype 5 in complex with the cellular receptor AAVR at 2.5 Angstroms resolution, AAV5 AAVR
Map dataAdeno-associated virus serotype 5 bound to its cellular receptor AAVR, cryo-em sharpened map at 2.5 Angstroms resolution.
Sample
  • Virus: Adeno-associated virus - 5
    • Protein or peptide: Dyslexia-associated protein KIAA0319-like protein
    • Protein or peptide: Capsid protein
KeywordsAAV5 / AAV / AAV-5 / AAVR / Adeno Associated Virus / PKD domain / VIRUS LIKE PARTICLE / parvovirus / virus / gene therapy / Receptor / Adeno-associated virus receptor / PKD1 / PKD
Function / homology
Function and homology information


proacrosomal vesicle fusion / response to auditory stimulus / flagellated sperm motility / T=1 icosahedral viral capsid / receptor-mediated endocytosis of virus by host cell / trans-Golgi network / neuron migration / cytoplasmic vesicle / Golgi membrane / nucleolus ...proacrosomal vesicle fusion / response to auditory stimulus / flagellated sperm motility / T=1 icosahedral viral capsid / receptor-mediated endocytosis of virus by host cell / trans-Golgi network / neuron migration / cytoplasmic vesicle / Golgi membrane / nucleolus / structural molecule activity / Golgi apparatus / membrane / plasma membrane
Similarity search - Function
Dyslexia-associated protein KIAA0319-like / : / Dyslexia-associated protein KIAA0319 N-terminal domain / KIAA0319 C-terminal domain / MANSC domain / MANSC domain profile. / K319L-like, PKD domain / Polycystic kidney disease (PKD) domain profile. / PKD domain / PKD domain superfamily ...Dyslexia-associated protein KIAA0319-like / : / Dyslexia-associated protein KIAA0319 N-terminal domain / KIAA0319 C-terminal domain / MANSC domain / MANSC domain profile. / K319L-like, 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 / Immunoglobulin-like fold
Similarity search - Domain/homology
Dyslexia-associated protein KIAA0319-like protein / Capsid protein
Similarity search - Component
Biological speciesHomo sapiens (human) / Adeno-associated virus - 5
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsSilveria M / Chapman MS
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM122564 United States
CitationJournal: Viruses / Year: 2020
Title: The Structure of an AAV5-AAVR Complex at 2.5 angstrom Resolution: Implications for Cellular Entry and Immune Neutralization of AAV Gene Therapy Vectors.
Authors: Silveria MA / Large EE / Zane GM / White TA / Chapman MS
History
DepositionNov 12, 2020-
Header (metadata) releaseDec 16, 2020-
Map releaseDec 16, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 36
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 36
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7kpn
  • Surface level: 36
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7kpn
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22988.png

Downloads & links

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Map

FileDownload / File: emd_22988.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAdeno-associated virus serotype 5 bound to its cellular receptor AAVR, cryo-em sharpened map at 2.5 Angstroms resolution.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
0.67 Å/pix.
x 512 pix.
= 340.558 Å		0.67 Å/pix.
x 512 pix.
= 340.558 Å		0.67 Å/pix.
x 512 pix.
= 340.558 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.66515 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 36.0 / Movie #1: 36
Minimum - Maximum-100.954629999999995 - 175.991060000000004
Average (Standard dev.)-0.000000041663426 (±10.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-255-255-255
Dimensions512512512
Spacing512512512
CellA=B=C: 340.558 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.665152343750.665152343750.66515234375
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z340.558340.558340.558
α/β/γ90.00090.00090.000
start NX/NY/NZ-255-255-255
NX/NY/NZ512512512
MAP C/R/S213
start NC/NR/NS-255-255-255
NC/NR/NS512512512
D min/max/mean-100.955175.991-0.000

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Supplemental data

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Mask #1

Fileemd_22988_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Adeno-associated virus serotype 5 bound to its cellular...

Fileemd_22988_additional_1.map
AnnotationAdeno-associated virus serotype 5 bound to its cellular receptor AAVR, cryo-em unsharpened map at 2.5 Angstroms resolution.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Adeno-associated virus serotype 5 bound to its cellular...

Fileemd_22988_half_map_1.map
AnnotationAdeno-associated virus serotype 5 bound to its cellular receptor AAVR, cryo-em half map 2 of 2 for a map at 2.5 Angstroms resolution.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Adeno-associated virus serotype 5 bound to its cellular...

Fileemd_22988_half_map_2.map
AnnotationAdeno-associated virus serotype 5 bound to its cellular receptor AAVR, cryo-em half map 1 of 2 for a map at 2.5 Angstroms resolution.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Adeno-associated virus - 5

EntireName: Adeno-associated virus - 5
Components
  • Virus: Adeno-associated virus - 5
    • Protein or peptide: Dyslexia-associated protein KIAA0319-like protein
    • Protein or peptide: Capsid protein

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Supramolecule #1: Adeno-associated virus - 5

SupramoleculeName: Adeno-associated virus - 5 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Expressed using SF9 cells with a pfastbac LIC vector. Purified with cesium chloride ultracentrifugation.
NCBI-ID: 82300 / Sci species name: Adeno-associated virus - 5 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 3.746 MDa
Virus shellShell ID: 1 / Name: VP3 / Diameter: 250.0 Å / T number (triangulation number): 1

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Macromolecule #1: Dyslexia-associated protein KIAA0319-like protein

MacromoleculeName: Dyslexia-associated protein KIAA0319-like protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.182744 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MASHHHHHHV SAGESVQITL PKNEVQLNAY VLQEPPKGET YTYDWQLITH PRDYSGEMEG KHSQILKLSK LTPGLYEFKV IVEGQNAHG EGYVNVTVKP EPRKNRPPIA IVSPQFQEIS LPTTSTVIDG SQSTDDDKIV QYHWEELKGP LREEKISEDT A ILKLSKLV ...String:
MASHHHHHHV SAGESVQITL PKNEVQLNAY VLQEPPKGET YTYDWQLITH PRDYSGEMEG KHSQILKLSK LTPGLYEFKV IVEGQNAHG EGYVNVTVKP EPRKNRPPIA IVSPQFQEIS LPTTSTVIDG SQSTDDDKIV QYHWEELKGP LREEKISEDT A ILKLSKLV PGNYTFSLTV VDSDGATNST TANLTVNKAV D

UniProtKB: Dyslexia-associated protein KIAA0319-like protein

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Macromolecule #2: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Adeno-associated virus - 5
Molecular weightTheoretical: 80.366211 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: SFVDHPPDWL EEVGEGLREF LGLEAGPPKP KPNQQHQDQA RGLVLPGYNY LGPGNGLDRG EPVNRADEVA REHDISYNEQ LEAGDNPYL KYNHADAEFQ EKLADDTSFG GNLGKAVFQA KKRVLEPFGL VEEGAKTAPT GKRIDDHFPK RKKARTEEDS K PSTSSDAE ...String:
SFVDHPPDWL EEVGEGLREF LGLEAGPPKP KPNQQHQDQA RGLVLPGYNY LGPGNGLDRG EPVNRADEVA REHDISYNEQ LEAGDNPYL KYNHADAEFQ EKLADDTSFG GNLGKAVFQA KKRVLEPFGL VEEGAKTAPT GKRIDDHFPK RKKARTEEDS K PSTSSDAE AGPSGSQQLQ IPAQPASSLG ADTMSAGGGG PLGDNNQGAD GVGNASGDWH CDSTWMGDRV VTKSTRTWVL PS YNNHQYR EIKSGSVDGS NANAYFGYST PWGYFDFNRF HSHWSPRDWQ RLINNYWGFR PRSLRVKIFN IQVKEVTVQD STT TIANNL TSTVQVFTDD DYQLPYVVGN GTEGCLPAFP PQVFTLPQYG YATLNRDNTE NPTERSSFFC LEYFPSKMLR TGNN FEFTY NFEEVPFHSS FAPSQNLFKL ANPLVDQYLY RFVSTNNTGG VQFNKNLAGR YANTYKNWFP GPMGRTQGWN LGSGV NRAS VSAFATTNRM ELEGASYQVP PQPNGMTNNL QGSNTYALEN TMIFNSQPAN PGTTATYLEG NMLITSESET QPVNRV AYN VGGQMATNNQ SSTTAPATGT YNLQEIVPGS VWMERDVYLQ GPIWAKIPET GAHFHPSPAM GGFGLKHPPP MMLIKNT PV PGNITSFSDV PVSSFITQYS TGQVTVEMEW ELKKENSKRW NPEIQYTNNY NDPQFVDFAP DSTGEYRTTR PIGTRYLT R PL

UniProtKB: Capsid protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.75 mg/mL
BufferpH: 7.4
Component:
ConcentrationNameFormula
50.0 mMHEPES
25.0 mMMagnesium chlorideMgCl2
25.0 mMSodium chlorideNaCl
GridModel: PELCO Ultrathin Carbon with Lacey Carbon / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV
Details: Two 2uL aliquots applied to grid (manual blotting between), prior to automated 3 second blot before plunging..
DetailsMonodisperse

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 93.0 K / Max: 93.0 K
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 11520 pixel / Digitization - Dimensions - Height: 8184 pixel / Number grids imaged: 1 / Number real images: 734 / Average electron dose: 32.9 e/Å2 / Details: Pixel size was 0.664 angstrom.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: -2.7 µm / Nominal defocus min: -0.7000000000000001 µm / Nominal magnification: 64000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 168275
Details: LoG Picker was used for initial automated particle selection. Templates were then generated by 2D classification, followed by particle template selection in Relion 3.0.
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 159673
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final 3D classificationSoftware - Name: RELION (ver. 3.0)
Details: Multiple rounds of 2D classification and 3D classification were used to remove outliers, resulting in 159,673 particles after deduplication.

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Atomic model buiding 1

Initial modelPDB ID:

3ntt


Chain - Source name: PDB / Chain - Initial model type: experimental model
DetailsStand-alone RSRef was used for refinement of magnification, resolution, envelope correction and atomic B-factors. This was alternated with RSRef-embedded CNS was used for molecular dynamics optimization (1st round) and stereochemically-restrained all-atom least-squares optimization.
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: Least-squares residual
Output model

PDB-7kpn:
Adeno-associated virus serotype 5 in complex with the cellular receptor AAVR at 2.5 Angstroms resolution, AAV5 AAVR

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