+
Open data
-
Basic information
Entry | Database: PDB / ID: 8ihm | ||||||
---|---|---|---|---|---|---|---|
Title | Eaf3 CHD domain bound to the nucleosome | ||||||
![]() |
| ||||||
![]() | TRANSCRIPTION / HDAC | ||||||
Function / homology | ![]() Rpd3S complex / NuA4 histone acetyltransferase complex / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin remodeling / protein heterodimerization activity / DNA repair / regulation of DNA-templated transcription / DNA binding / nucleus Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.58 Å | ||||||
![]() | Zhang, Y. / Gang, C. | ||||||
Funding support | 1items
| ||||||
![]() | ![]() Title: Structural basis for nucleosome binding and catalysis by the yeast Rpd3S/HDAC holoenzyme. Authors: Yueyue Zhang / Mengxue Xu / Po Wang / Jiahui Zhou / Guangxian Wang / Shuailong Han / Gang Cai / Xuejuan Wang / ![]() | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 316.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 236.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 42.1 KB | Display | |
Data in CIF | ![]() | 65.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 35449MC ![]() 8ihnC ![]() 8ihtC M: map data used to model this data C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
|
---|---|
1 |
|
-
Components
-Protein , 5 types, 9 molecules AEBFCGDHN
#1: Protein | Mass: 15331.982 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 11263.231 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Protein | Mass: 13978.241 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #4: Protein | Mass: 13524.752 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #8: Protein | | Mass: 13858.936 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
---|
-DNA chain , 2 types, 2 molecules IJ
#5: DNA chain | Mass: 50291.000 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|---|
#6: DNA chain | Mass: 51256.629 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Protein/peptide , 1 types, 1 molecules M
#7: Protein/peptide | Mass: 2206.506 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-
Sample preparation
Component | Name: Eaf3 CHD domain bound to the nucleosome / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES |
---|---|
Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.6 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-
Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2800 nm / Nominal defocus min: 1800 nm |
Image recording | Electron dose: 53 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-
Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
3D reconstruction | Resolution: 3.58 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 107252 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
|