+Open data
-Basic information
Entry | Database: PDB / ID: 4crv | ||||||
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Title | Complex of human CNOT9 and CNOT1 including two tryptophans | ||||||
Components |
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Keywords | GENE REGULATION / TNRC6 BINDING / MIRISC / MRNA SILENCING / MRNA DEADENYLATION / ARGONAUTE / TRANSCRIPTION | ||||||
Function / homology | Function and homology information positive regulation of cytoplasmic mRNA processing body assembly / CCR4-NOT core complex / armadillo repeat domain binding / CCR4-NOT complex / regulation of stem cell population maintenance / negative regulation of retinoic acid receptor signaling pathway / positive regulation of mRNA catabolic process / nuclear-transcribed mRNA poly(A) tail shortening / negative regulation of intracellular estrogen receptor signaling pathway / sex differentiation ...positive regulation of cytoplasmic mRNA processing body assembly / CCR4-NOT core complex / armadillo repeat domain binding / CCR4-NOT complex / regulation of stem cell population maintenance / negative regulation of retinoic acid receptor signaling pathway / positive regulation of mRNA catabolic process / nuclear-transcribed mRNA poly(A) tail shortening / negative regulation of intracellular estrogen receptor signaling pathway / sex differentiation / trophectodermal cell differentiation / miRNA-mediated post-transcriptional gene silencing / Deadenylation of mRNA / nuclear retinoic acid receptor binding / M-decay: degradation of maternal mRNAs by maternally stored factors / regulatory ncRNA-mediated gene silencing / peroxisomal membrane / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / positive regulation of epidermal growth factor receptor signaling pathway / epidermal growth factor receptor binding / nuclear receptor coactivator activity / nuclear estrogen receptor binding / P-body / kinase binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / cytokine-mediated signaling pathway / positive regulation of peptidyl-serine phosphorylation / negative regulation of translation / molecular adaptor activity / protein domain specific binding / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / protein-containing complex / extracellular space / RNA binding / membrane / nucleus / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Boland, A. / Chen, Y. / Izaurralde, E. / Weichenrieder, O. | ||||||
Citation | Journal: Mol.Cell / Year: 2014 Title: A Ddx6-Cnot1 Complex and W-Binding Pockets in Cnot9 Reveal Direct Links between Mirna Target Recognition and Silencing Authors: Chen, Y. / Boland, A. / Kuzuoglu-Ozturk, D. / Bawankar, P. / Loh, B. / Chang, C.T. / Weichenrieder, O. / Izaurralde, E. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4crv.cif.gz | 219.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4crv.ent.gz | 175.8 KB | Display | PDB format |
PDBx/mmJSON format | 4crv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cr/4crv ftp://data.pdbj.org/pub/pdb/validation_reports/cr/4crv | HTTPS FTP |
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-Related structure data
Related structure data | 4cruSC 4crwC S: Starting model for refinement C: citing same article (ref.) |
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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: 29174.605 Da / Num. of mol.: 1 / Fragment: CNOT1 CN9BD DOMAIN, DUF3819, RESIDUES 1356-1607 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PETMCN(PNYC) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: A5YKK6 |
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#2: Protein | Mass: 31072.189 Da / Num. of mol.: 1 / Fragment: CNOT9 ARM DOMAIN, RESIDUES 19-285 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PETMCN(PNEA) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: Q92600 |
#3: Chemical | ChemComp-TRP / |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
Sequence details | THE SIX N-TERMINAL RESIDUES REMAIN FROM THE EXPRESSION TAG OF CHAIN A. THE SIX N-TERMINAL RESIDUES ...THE SIX N-TERMINAL RESIDUES REMAIN FROM THE EXPRESSION |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 61 % / Description: NONE |
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Crystal grow | pH: 6 Details: 0.1M MES (PH=6.0), 11% PEG6000, 0.05M MG-CHLORIDE, 0.04M L-TRYPTOPHAN |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 19, 2013 / Details: DYNAMICALLY BENDABLE MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→61.1 Å / Num. obs: 45149 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Biso Wilson estimate: 43 Å2 / Rsym value: 0.06 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 2.05→2.1 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.79 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4CRU Resolution: 2.05→61.138 Å / SU ML: 0.25 / σ(F): 1.36 / Phase error: 27.12 / Stereochemistry target values: ML Details: TLS PARAMETERS WERE REFINED. SIDE CHAINS OF THE FOLLOWING RESIDUES WERE TRUNCATED AT CB ATOMS. CHAIN A, RESIDUES 1353, 1399, 1478, 1586, 1587. CHAIN B, RESIDUES 15, 17, 169. THE FOLLOWING ...Details: TLS PARAMETERS WERE REFINED. SIDE CHAINS OF THE FOLLOWING RESIDUES WERE TRUNCATED AT CB ATOMS. CHAIN A, RESIDUES 1353, 1399, 1478, 1586, 1587. CHAIN B, RESIDUES 15, 17, 169. THE FOLLOWING RESIDUES ARE DISORDERED. CHAIN A, RESIDUES 1350 TO 1352, 1588 TO 1602, 1604 TO 1607. CHAIN B, RESIDUES 13, 14.
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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 mean: 64.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→61.138 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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