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Yorodumi- PDB-6iam: Modulating Protein-Protein Interactions with Visible Light Peptid... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6iam | |||||||||
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Title | Modulating Protein-Protein Interactions with Visible Light Peptide Backbone Switches | |||||||||
Components |
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Keywords | TRANSFERASE / histone modification / trimethylation at 'Lys-4' / epigenetic transcriptional activation / NSL complex / osteoblasts differentiation / leukemia | |||||||||
Function / homology | Function and homology information PML body organization / 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 ...PML body organization / 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 / ubiquitin-like protein ligase binding / regulation of embryonic development / MLL1 complex / protein sumoylation / transcription factor binding / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / 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 / protein tag activity / 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 / identical protein binding / nucleus Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.51 Å | |||||||||
Authors | Werel, L. / Essen, L.-O. | |||||||||
Citation | Journal: Chembiochem / Year: 2019 Title: Modulating Protein-Protein Interactions with Visible-Light-Responsive Peptide Backbone Photoswitches. Authors: Albert, L. / Penalver, A. / Djokovic, N. / Werel, L. / Hoffarth, M. / Ruzic, D. / Xu, J. / Essen, L.O. / Nikolic, K. / Dou, Y. / Vazquez, O. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6iam.cif.gz | 202.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6iam.ent.gz | 159.6 KB | Display | PDB format |
PDBx/mmJSON format | 6iam.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ia/6iam ftp://data.pdbj.org/pub/pdb/validation_reports/ia/6iam | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 33690.238 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: First 28 amino acids were removed / Source: (gene. exp.) Homo sapiens (human) / Gene: WDR5, BIG3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61964 |
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-Protein/peptide , 2 types, 2 molecules BC
#2: Protein/peptide | Mass: 1461.716 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
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#3: Protein/peptide | Mass: 444.501 Da / Num. of mol.: 1 / Fragment: UNP residues 5-8 Source method: isolated from a genetically manipulated source Details: Residual peptide from SUMO-tag, that was cleaved before crystalliisation Source: (gene. exp.) Homo sapiens (human) / Gene: SUMO1P1, SUMO5, UBL2, UBL6 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G2XKQ0 |
-Non-polymers , 3 types, 428 molecules
#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.83 Å3/Da / Density % sol: 32.83 % / Description: fine needles |
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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 / Ambient temp details: Oxford Cryosystems 700 series / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å |
Detector | Type: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Sep 26, 2018 / Details: MD3-UP Microdiffractometer |
Radiation | Monochromator: U20.2 undulator (14.2 keV) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 1.51→37.49 Å / Num. obs: 42377 / % possible obs: 99.3 % / Redundancy: 4 % / Biso Wilson estimate: 11.27 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.0899 / Rpim(I) all: 0.0506 / Rrim(I) all: 0.104 / Χ2: 0.999 / Net I/σ(I): 9.04 |
Reflection shell | Resolution: 1.51→1.564 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.713 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4073 / CC1/2: 0.617 / Rpim(I) all: 0.414 / Rrim(I) all: 0.827 / Χ2: 0.874 / % possible all: 96.22 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.51→37.49 Å / Cross valid method: THROUGHOUT
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Displacement parameters | Biso max: 118.72 Å2 / Biso mean: 18.2115 Å2 / Biso min: 5.41 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.51→37.49 Å
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