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PDB Id
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Protein Name
Method
Summary
Structure Feature
Experiment
Ligands & Environment
9DCH
pdb_00009dch
10.2210/pdb9dch/pdb
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FASTA
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Structure Factors
Full Validation Report
Validation File (XML)
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Binary MMCIF Zipped(.gz)
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Validation File Zipped (.xml.gz)
Validation File Zipped (.cif.gz)
ELECTRON MICROSCOPY
Sample
Single-stranded RNA-mediated dimer of Polycomb Repressive Complex 2
Specimen Preperation
Sample Aggregation State
PARTICLE
Vitrification Instrument
LEICA EM GP
Cryogen Name
ETHANE
Sample Vitrification Details
2-3s of single side blotting
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
120658
Reported Resolution (Å)
3.4
Resolution Method
FSC 0.143 CUT-OFF
Other Details
?
Refinement Type
Symmetry Type
POINT
Map-Model Fitting and Refinement
ID
1
Refinement Space
?
Refinement Protocol
?
Refinement Target
?
Overall B Value
?
Fitting Procedure
?
Details
Individual PRC2 protomers were built using cryo-EM maps from the multibody refinement. The coordinates of G-quadruplex RNA-bound PRC2 six-subunit complex (PDB: 8FYH) provided a starting model from which all the coordinates were adjusted and rebuilt in the new map using COOT. The model of each PRC2 promoter was subjected to global refinement and minimization in real space using PHENIX. These were then subjected to manual inspection and adjustment in COOT, followed by refinement again in PHENIX. TERRAmut RNA model was generated using a 10-nucleotide single-stranded fragment (UGAGUGUGAG) using AlphaFold3 and then docked into our map for the position we designated as the RNA density.
Data Acquisition
Detector Type
FEI FALCON IV (4k x 4k)
Electron Dose (electrons/Å
2
)
50
Imaging Experiment
Date of Experiment
?
Temprature (Kelvin)
Microscope Model
FEI TITAN KRIOS
Minimum Defocus (nm)
500
Maximum Defocus (nm)
1900
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
?
Calibrated Magnification
130000
Source
FIELD EMISSION GUN
Acceleration Voltage (kV)
300
Imaging Details
?
Imaging Experiment
Task
Software Package
Version
PARTICLE SELECTION
RELION
5
IMAGE ACQUISITION
EPU
?
CTF CORRECTION
RELION
5
MODEL FITTING
Coot
?
INITIAL EULER ASSIGNMENT
RELION
5
FINAL EULER ASSIGNMENT
RELION
5
CLASSIFICATION
RELION
5
RECONSTRUCTION
RELION
5
MODEL REFINEMENT
PHENIX
?
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION
CTFind
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