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Yorodumi- PDB-7axq: Structure of the cryo-trapped WDR5:CS-VIP8 cocrystal after illumi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7axq | ||||||||||||
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Title | Structure of the cryo-trapped WDR5:CS-VIP8 cocrystal after illumination at 405 nm and 180 K | ||||||||||||
Components |
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Keywords | TRANSFERASE / WDR5 / cyclic strained visible-light photoswitches / MLL1 complex disruption / inhibition of hematopoiesis | ||||||||||||
Function / homology | Function and homology information MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / : / Cardiogenesis / histone methyltransferase complex / regulation of tubulin deacetylation ...MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / : / Cardiogenesis / histone methyltransferase complex / regulation of tubulin deacetylation / Formation of WDR5-containing histone-modifying complexes / regulation of cell division / MLL1 complex / regulation of embryonic development / histone acetyltransferase complex / positive regulation of gluconeogenesis / transcription initiation-coupled chromatin remodeling / methylated histone binding / 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 | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.562 Å | ||||||||||||
Authors | Werel, L. / Essen, L.-O. | ||||||||||||
Citation | Journal: Acs Cent.Sci. / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7axq.cif.gz | 85 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7axq.ent.gz | 61.2 KB | Display | PDB format |
PDBx/mmJSON format | 7axq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ax/7axq ftp://data.pdbj.org/pub/pdb/validation_reports/ax/7axq | HTTPS FTP |
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-Related structure data
Related structure data | 7axpC 7axsC 7axuC 7axxC 6iamS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Homo sapiens (human) / Gene: WDR5, BIG3 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P61964 |
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#2: Protein/peptide | Mass: 915.999 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,cyclic peptide, cyclic strained visible-light photoswitch, WDR5-binder, ...Details: cyclic peptide, cyclic strained visible-light photoswitch, WDR5-binder, disrupts MLL1 complex via MLL1-WDR5 inhibition,cyclic peptide, cyclic strained visible-light photoswitch, WDR5-binder, disrupts MLL1 complex via MLL1-WDR5 inhibition,cyclic peptide, cyclic strained visible-light photoswitch, WDR5-binder, disrupts MLL1 complex via MLL1-WDR5 inhibition Source: (synth.) Homo sapiens (human) |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.35 % |
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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: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
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: 1.56→44.59 Å / Num. obs: 42057 / % possible obs: 97.56 % / Redundancy: 6.4 % / Biso Wilson estimate: 20.92 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.0902 / Net I/σ(I): 10.78 |
Reflection shell | Resolution: 1.562→1.618 Å / Rmerge(I) obs: 1.096 / Mean I/σ(I) obs: 1.34 / Num. unique obs: 3264 / CC1/2: 0.552 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6IAM Resolution: 1.562→44.547 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.59 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 95.06 Å2 / Biso mean: 23.1909 Å2 / Biso min: 10.71 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.562→44.547 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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