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- PDB-5fu6: NOT module of the human CCR4-NOT complex (Crystallization mutant) -
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Open data
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Basic information
Entry | Database: PDB / ID: 5fu6 | ||||||
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Title | NOT module of the human CCR4-NOT complex (Crystallization mutant) | ||||||
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![]() | GENE REGULATION / DEADENYLATION / MRNA DECAY / CCR4-NOT / TRANSCRIPTION / TRANSLATIONAL REPRESSION | ||||||
Function / homology | ![]() 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 / trophectodermal cell 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 / 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 / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / peroxisomal membrane / 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 / transcription corepressor binding / nuclear estrogen receptor binding / transcription coregulator activity / P-body / regulation of translation / positive regulation of cold-induced thermogenesis / molecular adaptor activity / negative regulation of translation / protein domain specific binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / RNA binding / extracellular space / nucleoplasm / membrane / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Raisch, T. / Bhandari, D. / Sabath, K. / Helms, S. / Valkov, E. / Weichenrieder, O. / Izaurralde, E. | ||||||
![]() | ![]() Title: Distinct Modes of Recruitment of the Ccr4-not Complex by Drosophila and Vertebrate Nanos Authors: Raisch, T. / Bhandari, D. / Sabath, K. / Helms, S. / Valkov, E. / Weichenrieder, O. / Izaurralde, E. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. THE SHEET STRUCTURES OF CHAINS B, C, E, F ARE ... SHEET DETERMINATION METHOD: AUTHOR PROVIDED. THE SHEET STRUCTURES OF CHAINS B, C, E, F ARE BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED EACH FOR CHAINS B, C, E, F. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 713.2 KB | Display | ![]() |
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PDB format | ![]() | 595.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 474.3 KB | Display | ![]() |
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Full document | ![]() | 495.4 KB | Display | |
Data in XML | ![]() | 56 KB | Display | |
Data in CIF | ![]() | 76.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5fu7C ![]() 4c0dS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 61620.102 Da / Num. of mol.: 2 Fragment: NOT1 SUPERFAMILY HOMOLOGY DOMAIN, RESIDUES 1833-2361 Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 22945.076 Da / Num. of mol.: 2 Fragment: NOT ANCHOR REGION AND NOT-BOX DOMAIN, RESIDUES 350-540 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Protein | Mass: 18267.590 Da / Num. of mol.: 2 Fragment: NOT ANCHOR REGION AND NOT-BOX DOMAIN, RESIDUES 607-748 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Sequence details | CHAIN A, D. THE SIX N-TERMINAL RESIDUES REMAIN FROM THE EXPRESSION TAG. CHAIN B, E. THE SIX N- ...CHAIN A, D. THE SIX N-TERMINAL RESIDUES REMAIN FROM THE EXPRESSION | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.5 % / Description: NONE |
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Crystal grow | pH: 5.5 Details: 0.2 M SODIUM ACETATE, 0.1 M SODIUM CITRATE PH 5.5, 10 % PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 8, 2015 / Details: DYNAMICALLY BENDABLE MIRROR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99982 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. obs: 43109 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 3.26 % / Biso Wilson estimate: 81.37 Å2 / Rsym value: 0.08 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 2.9→2.98 Å / Redundancy: 3.27 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.63 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4C0D Resolution: 2.9→48.24 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.9284 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.349 Details: THE FOLLOWING RESIDUES ARE DISORDERED. CHAIN A, 1833 TO 1841, 2005 TO 2009. CHAIN D, 1833 TO 1841, 2004 TO 2007. SIDE-CHAINS OF THE FOLLOWING RESIDUES WERE TRUNCATED AT CB ATOMS. CHAIN B, ...Details: THE FOLLOWING RESIDUES ARE DISORDERED. CHAIN A, 1833 TO 1841, 2005 TO 2009. CHAIN D, 1833 TO 1841, 2004 TO 2007. SIDE-CHAINS OF THE FOLLOWING RESIDUES WERE TRUNCATED AT CB ATOMS. CHAIN B, RESIDUE 489. CHAIN D, RESIDUE 2008. CHAIN E, RESIDUE 531.
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Displacement parameters | Biso mean: 83.94 Å2
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Refine analyze | Luzzati coordinate error obs: 0.346 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→48.24 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→2.98 Å / Total num. of bins used: 20
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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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