[English] 日本語
Yorodumi
- PDB-6e9d: Sub-2 Angstrom Ewald Curvature-Corrected Single-Particle Cryo-EM ... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
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

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-9012
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-9012
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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
Polyers4,921,28060
Non-polymers00
Water212,93711820
1


  • 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

-
Components

#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

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
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

-
Processing

EM software
IDNameVersionCategory
1Gautomatch0.56particle selection
2Leginonimage acquisition
4RELION2.1CTF correction
7Coot0.8.9.1model fitting
9PHENIX1.13model refinement
10cryoSPARC0.65initial Euler assignment
11FREALIGN9.11final Euler assignment
12FREALIGN9.11classification
13FREALIGN9.113D reconstruction
Image processingDetails: super-resolution mode
CTF correctionDetails: CTF estimation per particle - Gctf, CTF estimation per micrograph - CTFFIND4
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
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

+
About Yorodumi

-
News

-
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.: Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator

External links: EMDB at PDBe / Contact to PDBj

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more