Home
About
Browse
Covid-19
Organism Classification
Alphafold Collection
Virus Classification
Indian Data
Documentation
Contact
Search Type
PDB Id
Uniprot Id
Source Organism
Host Organism
Protein Name
Method
Summary
Structure Feature
Experiment
Ligands & Environment
3JCA
?
?
Download file
FASTA
PDB
MMCIF
Binary MMCIF
XML
Structure Factors
Full Validation Report
Validation File (XML)
Validation File (CIF)
FASTA Zipped(.gz)
PDB Zipped(.gz)
MMCIF Zipped(.gz)
Binary MMCIF Zipped(.gz)
Structure Factors Zipped(.gz)
Validation File Zipped (.xml.gz)
Validation File Zipped (.cif.gz)
ELECTRON MICROSCOPY
Sample
Mouse Mammary Tumor Virus intasome complex
Specimen Preperation
Sample Aggregation State
PARTICLE
Vitrification Instrument
HOMEMADE PLUNGER
Cryogen Name
ETHANE
Sample Vitrification Details
Sample containing MMTV intasomes in SEC buffer (to which the detergent NP-40 was added to a final concentration of 0.05%) was applied onto a freshly plasma-treated (6s, Gatan Solarus plasma cleaner) holey carbon C-flat grid (CF-1.2/1.3-4C, Protochips, Inc.), allowing the sample to adsorb for 30 seconds and then plunge-freezing in liquid ethane using a manual cryo-plunger in an ambient environment of 4 degrees C.
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
30307
Reported Resolution (Å)
4.8
Resolution Method
FSC 0.143 CUT-OFF
Other Details
Local FSC values range from 4-5 A. (Single particle details: IN-NTD and IN-CCD domains of flanking INs 5-8 were computationally removed using Relion after assignment of Euler angles to full octameric particles and masking out of flanking regions.) (Single particle - Applied symmetry: C2)
Refinement Type
Symmetry Type
POINT
Map-Model Fitting and Refinement
ID
1
Refinement Space
REAL
Refinement Protocol
OTHER
Refinement Target
FSC, Rosetta energy
Overall B Value
300
Fitting Procedure
?
Details
REFINEMENT PROTOCOL--real-space refinement DETAILS--Initial components solved by X-ray were rigid-body docked. Linker regions were built de novo from the EM density. The full model was refined using real-space methods in Rosetta.
Data Acquisition
Detector Type
GATAN K2 (4k x 4k)
Electron Dose (electrons/Å
2
)
40
Imaging Experiment
Date of Experiment
2015-04-15
Temprature (Kelvin)
Microscope Model
FEI TITAN KRIOS
Minimum Defocus (nm)
1000
Maximum Defocus (nm)
4000
Minimum Tilt Angle (degrees)
?
Maximum Tilt Angle (degrees)
?
Nominal CS
2.7
Imaging Mode
BRIGHT FIELD
Specimen Holder Model
FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification
22500
Calibrated Magnification
38167
Source
FIELD EMISSION GUN
Acceleration Voltage (kV)
300
Imaging Details
?
Imaging Experiment
Task
Software Package
Version
MODEL FITTING
Rosetta
?
RECONSTRUCTION
FREALIGN
?
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
.
each particle
Feedback
Feedback Form
Name
Email
Institute
Feedback
Submit
