+Open data
-Basic information
Entry | Database: PDB / ID: 3mp6 | |||||||||
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Title | Complex Structure of Sgf29 and dimethylated H3K4 | |||||||||
Components |
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Keywords | HISTONE BINDING PROTEIN / Histone / Tudor Domain / H3K4me2 / SAGA | |||||||||
Function / homology | Function and homology information ADA complex / SAGA complex localization to transcription regulatory region / SLIK (SAGA-like) complex / SAGA complex / detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity ...ADA complex / SAGA complex localization to transcription regulatory region / SLIK (SAGA-like) complex / SAGA complex / detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / Chromatin modifying enzymes / epigenetic regulation of gene expression / methylated histone binding / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / ATP-binding cassette (ABC) transporter complex / Assembly of the ORC complex at the origin of replication / cell chemotaxis / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / 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 / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / protein localization / HDMs demethylate histones / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / gene expression / RUNX1 regulates transcription of genes involved in differentiation of HSCs / outer membrane-bounded periplasmic space / chromatin organization / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / periplasmic space / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / DNA damage response / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus Similarity search - Function | |||||||||
Biological species | Escherichia coli K-12 (bacteria) unidentified (others) Saccharomyces cerevisiae S288c (yeast) synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å | |||||||||
Authors | Li, J. / Wu, M. / Ruan, J. / Zang, J. | |||||||||
Citation | Journal: Embo J. / Year: 2011 Title: Sgf29 binds histone H3K4me2/3 and is required for SAGA complex recruitment and histone H3 acetylation Authors: Bian, C. / Xu, C. / Ruan, J. / Lee, K.K. / Burke, T.L. / Tempel, W. / Barsyte, D. / Li, J. / Wu, M. / Zhou, B.O. / Fleharty, B.E. / Paulson, A. / Allali-Hassani, A. / Zhou, J.Q. / Mer, G. / ...Authors: Bian, C. / Xu, C. / Ruan, J. / Lee, K.K. / Burke, T.L. / Tempel, W. / Barsyte, D. / Li, J. / Wu, M. / Zhou, B.O. / Fleharty, B.E. / Paulson, A. / Allali-Hassani, A. / Zhou, J.Q. / Mer, G. / Grant, P.A. / Workman, J.L. / Zang, J. / Min, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mp6.cif.gz | 133.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mp6.ent.gz | 99.4 KB | Display | PDB format |
PDBx/mmJSON format | 3mp6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mp/3mp6 ftp://data.pdbj.org/pub/pdb/validation_reports/mp/3mp6 | HTTPS FTP |
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-Related structure data
Related structure data | 3lx7C 3me9C 3meaC 3metC 3meuC 3mevC 3mewC 3mp1C 3mp8C 1hsjS 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: 57521.965 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: chimera of Maltose-binding periplasmic protein, SAGA-associated factor 29 Source: (gene. exp.) Escherichia coli K-12 (bacteria), (gene. exp.) unidentified (others), (gene. exp.) Saccharomyces cerevisiae S288c (yeast) Strain: K12, S288c / Gene: malE, SGF29 / Plasmid: pET23b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0AEX9, UniProt: P25554 |
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#2: Protein/peptide | Mass: 503.616 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) synthetic construct (others) / References: UniProt: P68431*PLUS |
#3: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.11 % / Mosaicity: 0.312 ° |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 25% PEG3350, 0.1M sodium acetate, pH 4.5, vapor diffusion, hanging drop, temperature 281K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Nov 15, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.48→50 Å / Num. all: 86450 / Num. obs: 86450 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.5 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.072 / Rsym value: 0.06 / Χ2: 0.976 / Net I/σ(I): 25.7 |
Reflection shell | Resolution: 1.48→1.51 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.447 / Mean I/σ(I) obs: 3.4 / Num. unique all: 4216 / Rsym value: 0.4 / Χ2: 0.728 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HSJ Resolution: 1.48→31.17 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.945 / Occupancy max: 1 / Occupancy min: 0 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 43.17 Å2 / Biso mean: 15.248 Å2 / Biso min: 2.72 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.48→31.17 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.478→1.516 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 20
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