+Open data
-Basic information
Entry | Database: PDB / ID: 4gq3 | ||||||
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Title | Human menin with bound inhibitor MI-2 | ||||||
Components | Menin | ||||||
Keywords | TRANSCRIPTION/TRANSCRIPTION inhibitor / Tumor Suppressor / Nucleus / TRANSCRIPTION-TRANSCRIPTION inhibitor complex | ||||||
Function / homology | Function and homology information Y-form DNA binding / negative regulation of telomerase activity / negative regulation of cyclin-dependent protein serine/threonine kinase activity / negative regulation of JNK cascade / MLL1/2 complex / T-helper 2 cell differentiation / osteoblast development / histone methyltransferase complex / Formation of WDR5-containing histone-modifying complexes / positive regulation of transforming growth factor beta receptor signaling pathway ...Y-form DNA binding / negative regulation of telomerase activity / negative regulation of cyclin-dependent protein serine/threonine kinase activity / negative regulation of JNK cascade / MLL1/2 complex / T-helper 2 cell differentiation / osteoblast development / histone methyltransferase complex / Formation of WDR5-containing histone-modifying complexes / positive regulation of transforming growth factor beta receptor signaling pathway / MLL1 complex / R-SMAD binding / cleavage furrow / negative regulation of cell cycle / RHO GTPases activate IQGAPs / negative regulation of osteoblast differentiation / four-way junction DNA binding / response to UV / transcription initiation-coupled chromatin remodeling / transcription repressor complex / negative regulation of protein phosphorylation / Deactivation of the beta-catenin transactivating complex / Post-translational protein phosphorylation / response to gamma radiation / phosphoprotein binding / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Formation of the beta-catenin:TCF transactivating complex / negative regulation of DNA-binding transcription factor activity / nuclear matrix / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / MAPK cascade / protein-macromolecule adaptor activity / double-stranded DNA binding / chromosome, telomeric region / transcription cis-regulatory region binding / endoplasmic reticulum lumen / negative regulation of cell population proliferation / DNA repair / negative regulation of DNA-templated transcription / DNA damage response / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å | ||||||
Authors | Shi, A. / Murai, M.J. / He, S. / Lund, G.L. / Hartley, T. / Purohit, T. / Reddy, G. / Chruszcz, M. / Grembecka, J. / Cierpicki, T. | ||||||
Citation | Journal: Blood / Year: 2012 Title: Structural insights into inhibition of the bivalent menin-MLL interaction by small molecules in leukemia. Authors: Shi, A. / Murai, M.J. / He, S. / Lund, G. / Hartley, T. / Purohit, T. / Reddy, G. / Chruszcz, M. / Grembecka, J. / Cierpicki, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4gq3.cif.gz | 118.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4gq3.ent.gz | 88.4 KB | Display | PDB format |
PDBx/mmJSON format | 4gq3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gq/4gq3 ftp://data.pdbj.org/pub/pdb/validation_reports/gq/4gq3 | HTTPS FTP |
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-Related structure data
Related structure data | 4gpqC 4gq4C 4gq6C 3re2S 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 54570.223 Da / Num. of mol.: 1 / Mutation: A541t Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MEN1, SCG2 / Production host: Escherichia coli (E. coli) / References: UniProt: O00255 |
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-Non-polymers , 5 types, 382 molecules
#2: Chemical | ChemComp-0RO / | ||||
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#3: Chemical | ChemComp-PEG / | ||||
#4: Chemical | ChemComp-UNX / #5: Chemical | ChemComp-SO4 / #6: Water | ChemComp-HOH / | |
-Details
Sequence details | THE CRYSTALLIZ |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.72 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2 M ammonium acetate, 0.1 M HEPES pH 7.5 and 25% w/v PEG 3,350. This solution was mixed 1:1 with 2.5mg/mL protein in 50mM Tris-HCl (pH 8.0), 50mM NaCl, and 1mM TCEP. Prior to data ...Details: 0.2 M ammonium acetate, 0.1 M HEPES pH 7.5 and 25% w/v PEG 3,350. This solution was mixed 1:1 with 2.5mg/mL protein in 50mM Tris-HCl (pH 8.0), 50mM NaCl, and 1mM TCEP. Prior to data collection, crystals were transferred into a cryo-solution containing 20% PEG550 MME and flash-frozen in liquid nitrogen, 200 mM 0RO, VAPOR DIFFUSION, SITTING DROP, temperature 283K |
-Data collection
Diffraction |
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Diffraction source |
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Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD | ||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength | Relative weight: 1 | ||||||||||||
Reflection | Resolution: 1.56→39.41 Å / Num. obs: 60554 / % possible obs: 86.4 % / Redundancy: 3.8 % / Rsym value: 0.06 / Net I/σ(I): 25.5 | ||||||||||||
Reflection shell | Resolution: 1.56→1.59 Å / Mean I/σ(I) obs: 3.5 / Rsym value: 0.686 / % possible all: 92.1 |
-Processing
Software | Name: REFMAC / Version: 5.6.0119 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3RE2 Resolution: 1.56→39.41 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.534 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.294 Å2
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Refinement step | Cycle: LAST / Resolution: 1.56→39.41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.56→1.601 Å / Total num. of bins used: 20
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