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- PDB-7axx: Structure of WDR5:CS-VIP8 crystal after illumination at 405 nm an... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7axx | |||||||||||||||
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Title | Structure of WDR5:CS-VIP8 crystal after illumination at 405 nm and room temperature | |||||||||||||||
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![]() | TRANSFERASE / WDR5 / cyclic strained visible-light photoswitches / MLL1 complex disruption / inhibition of hematopoiesis | |||||||||||||||
Function / homology | ![]() MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / Cardiogenesis / regulation of tubulin deacetylation / histone methyltransferase complex / Formation of WDR5-containing histone-modifying complexes ...MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / Cardiogenesis / regulation of tubulin deacetylation / histone methyltransferase complex / Formation of WDR5-containing histone-modifying complexes / regulation of cell division / regulation of embryonic development / MLL1 complex / histone acetyltransferase complex / positive regulation of gluconeogenesis / methylated histone binding / transcription initiation-coupled chromatin remodeling / skeletal system development / gluconeogenesis / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / mitotic spindle / PKMTs methylate histone lysines / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Neddylation / HATs acetylate histones / histone binding / regulation of cell cycle / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus Similarity search - Function | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Werel, L. / Essen, L.-O. | |||||||||||||||
![]() | ![]() Title: Bistable Photoswitch Allows in Vivo Control of Hematopoiesis. Authors: Albert, L. / Nagpal, J. / Steinchen, W. / Zhang, L. / Werel, L. / Djokovic, N. / Ruzic, D. / Hoffarth, M. / Xu, J. / Kaspareit, J. / Abendroth, F. / Royant, A. / Bange, G. / Nikolic, K. / ...Authors: Albert, L. / Nagpal, J. / Steinchen, W. / Zhang, L. / Werel, L. / Djokovic, N. / Ruzic, D. / Hoffarth, M. / Xu, J. / Kaspareit, J. / Abendroth, F. / Royant, A. / Bange, G. / Nikolic, K. / Ryu, S. / Dou, Y. / Essen, L.O. / Vazquez, O. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 141.1 KB | Display | ![]() |
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PDB format | ![]() | 108.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7axpC ![]() 7axqC ![]() 7axsC ![]() 7axuC ![]() 6iamS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 36635.438 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: WDR5, component of MLL1 methyltransferase complex, chromatin regulator Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein/peptide | ( Mass: 943.966 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: cyclic peptide, cyclic strained visible-light photoswitch, WDR5-binder, disrupts MLL1 complex via MLL1-WDR5 inhibition Source: (synth.) ![]() |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.83 Å3/Da / Density % sol: 32.82 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 10% (w/v) PEG20000, 20% (v/v) PEG550 MME, 0.02 M sodium formate, 0.02 M ammonium acetate, 0.02 M trisodium citrate, 0.02 M sodium potassium L-tartrate, 0.02 M sodium oxamate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 19, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→44.01 Å / Num. obs: 25827 / % possible obs: 96.07 % / Redundancy: 5.9 % / Biso Wilson estimate: 21.32 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.08507 / Rpim(I) all: 0.03712 / Rrim(I) all: 0.09312 / Net I/σ(I): 11.32 |
Reflection shell | Resolution: 1.79→1.859 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.6186 / Mean I/σ(I) obs: 1.44 / Num. unique obs: 6956 / CC1/2: 0.615 / Rpim(I) all: 0.4115 / Rrim(I) all: 0.7499 / % possible all: 66.56 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6IAM Resolution: 1.79→44.01 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.948 / SU B: 6.703 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.136 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.346 Å2
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Refinement step | Cycle: LAST / Resolution: 1.79→44.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.795→1.841 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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