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Yorodumi- PDB-5lug: Crystal structure of human Spindlin-2B protein in complex with AR... -
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-Basic information
Entry | Database: PDB / ID: 5lug | ||||||
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Title | Crystal structure of human Spindlin-2B protein in complex with ART(M3L)QTA(2MR)KS peptide | ||||||
Components |
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Keywords | CELL CYCLE / SPINDLIN-2B (protein): PEPTIDE BINDING PROTEIN / SPINDLIN MEMBER 2B / SPIN2B / TUDOR DOMAIN | ||||||
Function / homology | Function and homology information gamete generation / cell cycle / Chromatin modifying enzymes / methylated histone binding / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / epigenetic regulation of gene expression / Assembly of the ORC complex at the origin of replication / DNA methylation ...gamete generation / cell cycle / Chromatin modifying enzymes / methylated histone binding / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / epigenetic regulation of gene expression / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / HDMs demethylate histones / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / gene expression / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / regulation of cell cycle / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / regulation of DNA-templated transcription / apoptotic process / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å | ||||||
Authors | Srikannathasan, V. / Gileadi, C. / Talon, R. / Shrestha, L. / Kopec, J. / Szykowska, A. / Burgess-Brown, N. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. ...Srikannathasan, V. / Gileadi, C. / Talon, R. / Shrestha, L. / Kopec, J. / Szykowska, A. / Burgess-Brown, N. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / von Delft, F. / Oppermann, U. / Huber, K. | ||||||
Citation | Journal: To be published Title: Crystal structure of human Spindlin-2B protein in complex with ART(M3L)QTA(2MR)KS peptide Authors: Srikannathasan, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lug.cif.gz | 373.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lug.ent.gz | 316.9 KB | Display | PDB format |
PDBx/mmJSON format | 5lug.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lu/5lug ftp://data.pdbj.org/pub/pdb/validation_reports/lu/5lug | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 25506.025 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: ART(M3L)QTA(2MR)KS peptide / Source: (gene. exp.) Homo sapiens (human) / Gene: SPIN-2, hCG_1642309 / Plasmid: pNIC-CTHF Details (production host): C -terminal, TEV cleavable hexahistidine tag Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): R3-Rosetta / References: UniProt: A0A024R9Y9, UniProt: Q9BPZ2*PLUS #2: Protein/peptide | Mass: 1219.457 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: ART(M3L)QTA(2MR)KS - co crystallised and no density for KS and 2MR show dual conformation. Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli #1/H766 (bacteria) / References: UniProt: P68431*PLUS #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-2MR / | #5: 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: 2.52 Å3/Da / Density % sol: 51.11 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 25% PEG3350, 0.1M Bis-Tris pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å |
Detector | Type: DECTRIS PILATUS3 R CdTe 300K / Detector: PIXEL / Date: Apr 16, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→20 Å / Num. obs: 107508 / % possible obs: 99.4 % / Redundancy: 3.8 % / Biso Wilson estimate: 23.9 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.071 / Rrim(I) all: 0.145 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.532 / Mean I/σ(I) obs: 2.9 / Num. unique all: 15448 / CC1/2: 0.88 / Rpim(I) all: 0.32 / Rrim(I) all: 0.623 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Resolution: 1.7→19.902 Å / SU ML: 0.18 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 29.32 Details: initial refinement carried on REFMAC then later and final refinement done by PHENIX refinement; Protein residues do not have density: ESSESPPTEREPG Some residues side chain are removed due ...Details: initial refinement carried on REFMAC then later and final refinement done by PHENIX refinement; Protein residues do not have density: ESSESPPTEREPG Some residues side chain are removed due to lack of density.Some residues have dual conformation.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 111.32 Å2 / Biso mean: 23.8694 Å2 / Biso min: 10.2 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.7→19.902 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30
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Refinement TLS params. | Method: refined / Origin x: 25.7106 Å / Origin y: 4.9808 Å / Origin z: -17.6784 Å
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Refinement TLS group |
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