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- PDB-9umb: Structure of Modified adeno-associated viral vector, AAV5-BCD -

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Basic information

Entry
Database: PDB / ID: 9umb
TitleStructure of Modified adeno-associated viral vector, AAV5-BCD
ComponentsCapsid protein
KeywordsVIRUS / adeno-associated virus / AAV5
Function / homologyPhospholipase A2-like domain / Phospholipase A2-like domain / Parvovirus coat protein VP2 / Parvovirus coat protein VP1/VP2 / Parvovirus coat protein VP1/VP2 / Capsid/spike protein, ssDNA virus / T=1 icosahedral viral capsid / structural molecule activity / Capsid protein
Function and homology information
Biological speciesadeno-associated virus 5
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.55 Å
AuthorsZhang, H. / Burtseva, A.D. / Strelkova, A.N. / Perepelkina, M.P. / Iurlova, E.V. / Gershovich, P.M. / Prokof'ev, A.V. / Kolesnichenko, A.S. / Gulnova, A.R. / Nurtdinov, R.F. ...Zhang, H. / Burtseva, A.D. / Strelkova, A.N. / Perepelkina, M.P. / Iurlova, E.V. / Gershovich, P.M. / Prokof'ev, A.V. / Kolesnichenko, A.S. / Gulnova, A.R. / Nurtdinov, R.F. / Vasilev, A.A. / Yakovlev, P.A. / Popov, V.O. / Boyko, K.M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of Modified adeno-associated viral vector, AAV5-BCD
Authors: Zhang, H. / Burtseva, A. / Boyko, K.
History
DepositionApr 21, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 30, 2025Provider: repository / Type: Initial release
Revision 1.0Apr 30, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 30, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 30, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 30, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 30, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Capsid protein
B: Capsid protein
C: Capsid protein
D: Capsid protein
E: Capsid protein
F: Capsid protein
G: Capsid protein
H: Capsid protein
I: Capsid protein
J: Capsid protein
K: Capsid protein
L: Capsid protein
M: Capsid protein
N: Capsid protein
O: Capsid protein
P: Capsid protein
Q: Capsid protein
R: Capsid protein
S: Capsid protein
T: Capsid protein
U: Capsid protein
V: Capsid protein
W: Capsid protein
X: Capsid protein
Y: Capsid protein
Z: Capsid protein
a: Capsid protein
b: Capsid protein
c: Capsid protein
d: Capsid protein
e: Capsid protein
f: Capsid protein
g: Capsid protein
h: Capsid protein
i: Capsid protein
j: Capsid protein
k: Capsid protein
l: Capsid protein
m: Capsid protein
n: Capsid protein
o: Capsid protein
p: Capsid protein
q: Capsid protein
r: Capsid protein
s: Capsid protein
t: Capsid protein
u: Capsid protein
v: Capsid protein
w: Capsid protein
x: Capsid protein
y: Capsid protein
z: Capsid protein
1: Capsid protein
2: Capsid protein
3: Capsid protein
4: Capsid protein
5: Capsid protein
6: Capsid protein
7: Capsid protein
8: Capsid protein


Theoretical massNumber of molelcules
Total (without water)4,828,04360
Polymers4,828,04360
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein ...
Capsid protein


Mass: 80467.391 Da / Num. of mol.: 60
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) adeno-associated virus 5 / Gene: cap, VP1 / Production host: Homo sapiens (human) / References: UniProt: Q9YIJ1
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: adeno-associated virus 5 / Type: VIRUS / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: adeno-associated virus 5
Source (recombinant)Organism: Homo sapiens (human)
Details of virusEmpty: YES / Enveloped: NO / Isolate: SEROTYPE / Type: VIRUS-LIKE PARTICLE
Buffer solutionpH: 8.2
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: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Calibrated defocus min: 1000 nm / Calibrated defocus max: 2000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: REFMAC / Version: 5.8.0430 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.55 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 285362 / Symmetry type: POINT
RefinementResolution: 2.55→2.55 Å / Cor.coef. Fo:Fc: 0.58 / SU B: 8.713 / SU ML: 0.172 / ESU R: 0.3
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.39877 --
obs0.39877 3716324 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 24.215 Å2
Refinement stepCycle: 1 / Total: 246600
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0090.012254280
ELECTRON MICROSCOPYr_bond_other_d00.016223920
ELECTRON MICROSCOPYr_angle_refined_deg2.2661.798347460
ELECTRON MICROSCOPYr_angle_other_deg0.8141.737514920
ELECTRON MICROSCOPYr_dihedral_angle_1_deg6.158530900
ELECTRON MICROSCOPYr_dihedral_angle_2_deg24.93851440
ELECTRON MICROSCOPYr_dihedral_angle_3_deg24.5911037200
ELECTRON MICROSCOPYr_dihedral_angle_4_deg
ELECTRON MICROSCOPYr_chiral_restr0.1080.236060
ELECTRON MICROSCOPYr_gen_planes_refined0.0080.02311700
ELECTRON MICROSCOPYr_gen_planes_other0.0010.0265460
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it2.9262.238123780
ELECTRON MICROSCOPYr_mcbond_other2.9262.238123780
ELECTRON MICROSCOPYr_mcangle_it5.0984.057154620
ELECTRON MICROSCOPYr_mcangle_other5.0984.057154621
ELECTRON MICROSCOPYr_scbond_it4.252.558130500
ELECTRON MICROSCOPYr_scbond_other4.252.558130501
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other7.2524.495192841
ELECTRON MICROSCOPYr_long_range_B_refined11.67626.94934203
ELECTRON MICROSCOPYr_long_range_B_other11.67626.94934204
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork3.716 275340 -
obs--100 %

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