+
Open data
-
Basic information
Entry | Database: PDB / ID: 7yfj | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of human WTAP | ||||||
![]() | Pre-mRNA-splicing regulator WTAP | ||||||
![]() | PROTEIN BINDING / WTAP-VIRMA / m6A writer | ||||||
Function / homology | ![]() RNA N6-methyladenosine methyltransferase complex / : / regulation of alternative mRNA splicing, via spliceosome / Processing of Capped Intron-Containing Pre-mRNA / RNA splicing / mRNA processing / nuclear membrane / nuclear speck / cell cycle / nucleoplasm ...RNA N6-methyladenosine methyltransferase complex / : / regulation of alternative mRNA splicing, via spliceosome / Processing of Capped Intron-Containing Pre-mRNA / RNA splicing / mRNA processing / nuclear membrane / nuclear speck / cell cycle / nucleoplasm / identical protein binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yan, X.H. / Guan, Z.Y. / Tang, C. / Yin, P. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: AI-empowered integrative structural characterization of mA methyltransferase complex. Authors: Xuhui Yan / Kai Pei / Zeyuan Guan / Feiqing Liu / Junjun Yan / Xiaohuan Jin / Qiang Wang / Mengjun Hou / Chun Tang / Ping Yin / ![]() | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 98.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 75.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 463.4 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 464.6 KB | Display | |
Data in XML | ![]() | 10 KB | Display | |
Data in CIF | ![]() | 13 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7yg4C C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 14389.101 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-EDO / | #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.32 Å3/Da / Density % sol: 62.97 % |
---|---|
Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop Details: MES, magnesium nitrate, sodium bromide, PEG6000, glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 31, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 2.397→48.9 Å / Num. obs: 16547 / % possible obs: 99.5 % / Redundancy: 20 % / Biso Wilson estimate: 55.6 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.031 / Rrim(I) all: 0.103 / Net I/σ(I): 19.8 |
Reflection shell | Resolution: 2.397→2.49 Å / Redundancy: 20.7 % / Rmerge(I) obs: 0.978 / Mean I/σ(I) obs: 4.6 / Num. unique obs: 1679 / CC1/2: 0.978 / Rpim(I) all: 0.3 / % possible all: 99.6 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| |||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 81.56 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→45.64 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 24.8693 Å / Origin y: 31.4866 Å / Origin z: 14.2729 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: ALL |