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- PDB-6e9d: Sub-2 Angstrom Ewald Curvature-Corrected Single-Particle Cryo-EM ... -

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Database: PDB / ID: 6e9d
TitleSub-2 Angstrom Ewald Curvature-Corrected Single-Particle Cryo-EM Reconstruction of AAV-2 L336C
ComponentsCapsid protein VP1
KeywordsVIRUS LIKE PARTICLE / AAV-2 L336C / Gene therapy / Ewald sphere curvature correction / Per particle CTF
Function / homologyParvovirus coat protein VP1, N-terminal / Parvovirus coat protein VP2 / Capsid/spike protein, ssDNA virus / Parvovirus coat protein VP1/VP2 / Parvovirus coat protein VP2 / Parvovirus coat protein VP1 / T=1 icosahedral viral capsid / permeabilization of host organelle membrane involved in viral entry into host cell / viral entry via permeabilization of inner membrane / host cell nucleolus ...Parvovirus coat protein VP1, N-terminal / Parvovirus coat protein VP2 / Capsid/spike protein, ssDNA virus / Parvovirus coat protein VP1/VP2 / Parvovirus coat protein VP2 / Parvovirus coat protein VP1 / T=1 icosahedral viral capsid / permeabilization of host organelle membrane involved in viral entry into host cell / viral entry via permeabilization of inner membrane / host cell nucleolus / clathrin-dependent endocytosis of virus by host cell / virion attachment to host cell / structural molecule activity / Capsid protein VP1
Function and homology information
Specimen sourceHuman adenovirus 2
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 1.86 Å resolution
AuthorsTan, Y.Z. / Aiyer, S. / Mietzsch, M. / Hull, J.A. / McKenna, R. / Baker, T.S. / Agbandje-McKenna, M. / Lyumkis, D.
CitationJournal: Nat Commun / Year: 2018
Title: Sub-2 Å Ewald curvature corrected structure of an AAV2 capsid variant.
Authors: Yong Zi Tan / Sriram Aiyer / Mario Mietzsch / Joshua A Hull / Robert McKenna / Joshua Grieger / R Jude Samulski / Timothy S Baker / Mavis Agbandje-McKenna / Dmitry Lyumkis
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 31, 2018 / Release: Aug 15, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Aug 15, 2018Structure modelrepositoryInitial release
1.1Sep 19, 2018Structure modelData collection / Database referencescitation / citation_author_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

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Deposited unit
A: Capsid protein VP1
B: Capsid protein VP1
C: Capsid protein VP1
D: Capsid protein VP1
E: Capsid protein VP1
F: Capsid protein VP1
G: Capsid protein VP1
H: Capsid protein VP1
I: Capsid protein VP1
J: Capsid protein VP1
K: Capsid protein VP1
L: Capsid protein VP1
M: Capsid protein VP1
N: Capsid protein VP1
O: Capsid protein VP1
P: Capsid protein VP1
Q: Capsid protein VP1
R: Capsid protein VP1
S: Capsid protein VP1
T: Capsid protein VP1
U: Capsid protein VP1
V: Capsid protein VP1
W: Capsid protein VP1
X: Capsid protein VP1
Y: Capsid protein VP1
Z: Capsid protein VP1
1: Capsid protein VP1
2: Capsid protein VP1
3: Capsid protein VP1
4: Capsid protein VP1
5: Capsid protein VP1
6: Capsid protein VP1
a: Capsid protein VP1
b: Capsid protein VP1
c: Capsid protein VP1
d: Capsid protein VP1
e: Capsid protein VP1
f: Capsid protein VP1
g: Capsid protein VP1
h: Capsid protein VP1
i: Capsid protein VP1
j: Capsid protein VP1
k: Capsid protein VP1
l: Capsid protein VP1
m: Capsid protein VP1
n: Capsid protein VP1
o: Capsid protein VP1
p: Capsid protein VP1
q: Capsid protein VP1
r: Capsid protein VP1
s: Capsid protein VP1
t: Capsid protein VP1
u: Capsid protein VP1
v: Capsid protein VP1
w: Capsid protein VP1
x: Capsid protein VP1
y: Capsid protein VP1
z: Capsid protein VP1
7: Capsid protein VP1
8: Capsid protein VP1

Theoretical massNumber of molelcules
Total (without water)4,921,28060

  • idetical with deposited unit
  • defined by author
  • Evidence: none
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)935590
ΔGint (kcal/M)-3762
Surface area (Å2)792190


#1: Protein/peptide ...
Capsid protein VP1 /

Mass: 82021.336 Da / Num. of mol.: 60 / Mutation: L336C / Source: (gene. exp.) Human adenovirus 2 / Gene: VP1 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P03135
#2: Water ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 11820 / Formula: H2O / Water

Experimental details


EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

Sample preparation

ComponentName: Adeno-associated virus - 2 / Type: VIRUS / Entity ID: 1 / Source: RECOMBINANT
Molecular weightValue: 3.9 MDa / Experimental value: NO
Source (natural)Organism: Adeno-associated virus - 2
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm) / Plasmid: pFastBac1-HM / Strain: Sf9
Details of virusEmpty: YES / Enveloped: NO / Virus isolate: STRAIN / Virus type: VIRUS-LIKE PARTICLE
Natural hostOrganism: Homo sapiens
Virus shellName: Icosahedral capsidCapsid / Diameter: 250 nm / Triangulation number (T number): 1
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer ID
1150 mMsodium chlorideNaCl1
22 mMmagnesium chlorideMgCl21
350 mMHEPESC8H18N2O4S1
SpecimenConc.: 1.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 / Grid type: Quantifoil, UltrAuFoil, R1.2/1.3
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Humidity: 80 % / Chamber temperature: 277 kelvins
Details: Double blotting was used to increase particle concentration. Sample was added to a plasma-cleaned (Gatan Solarus) grid and blotted away using Whatman grade 4 filter paper after 20 second wait time.

Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS / Details: Beam tilt in 8 directions +/- 5 mrad
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 37000 / Nominal defocus max: 2000 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / C2 aperture diameter: 70 microns / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 3.5 sec. / Electron dose: 22.5 e/Å2 / Details: Stage shift mode for data collection / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of grids imaged: 1 / Number of real images: 1317
Image scansSampling size: 5 microns / Width: 3838 / Height: 3710 / Movie frames/image: 70 / Used frames/image: 5-19


EM software
1Gautomatch0.56particle selection
2Leginonimage acquisition
4RELION2.1CTF correction
7Coot0.8.9.1model fitting
9PHENIX1.13model refinement
10cryoSPARC0.65initial Euler assignment
11FREALIGN9.11final Euler assignment
13FREALIGN9.113D reconstruction
Image processingDetails: super-resolution mode
CTF correctionDetails: CTF estimation per particle - Gctf, CTF estimation per micrograph - CTFFIND4
Particle selectionDetails: Template-based picking by generating template from a 2-D classification of an initial subset of data.
Number of particles selected: 78194
SymmetryPoint symmetry: I
3D reconstructionResolution: 1.86 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 30515 / Algorithm: FOURIER SPACE / Details: Frequency limited refinement / Symmetry type: POINT
Atomic model buildingOverall b value: 61.9 / Ref protocol: RIGID BODY FIT / Ref space: REAL / Target criteria: Correlation coefficient, EM ringer score
Atomic model buildingPDB-ID: 1LP3

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