+Open data
-Basic information
Entry | Database: PDB / ID: 4gmj | ||||||
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Title | Structure of human NOT1 MIF4G domain co-crystallized with CAF1 | ||||||
Components | (CCR4-NOT transcription complex subunit ...) x 2 | ||||||
Keywords | RNA BINDING PROTEIN / CCR4-NOT / mRNA DECAY / DEADENYLASE / TRANSCRIPTION | ||||||
Function / homology | Function and homology information regulation of tyrosine phosphorylation of STAT protein / positive regulation of cytoplasmic mRNA processing body assembly / poly(A)-specific ribonuclease / poly(A)-specific ribonuclease activity / CCR4-NOT core complex / armadillo repeat domain binding / CCR4-NOT complex / miRNA-mediated gene silencing by mRNA destabilization / RNA exonuclease activity / regulation of stem cell population maintenance ...regulation of tyrosine phosphorylation of STAT protein / positive regulation of cytoplasmic mRNA processing body assembly / poly(A)-specific ribonuclease / poly(A)-specific ribonuclease activity / CCR4-NOT core complex / armadillo repeat domain binding / CCR4-NOT complex / miRNA-mediated gene silencing by mRNA destabilization / RNA exonuclease activity / 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 / deadenylation-dependent decapping of nuclear-transcribed mRNA / 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 / P-body assembly / 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 / intracellular non-membrane-bounded organelle / negative regulation of type I interferon-mediated signaling pathway / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / positive regulation of viral genome replication / nuclear estrogen receptor binding / P-body / transcription corepressor activity / regulation of translation / 3'-5'-RNA exonuclease activity / DNA-binding transcription factor binding / defense response to virus / molecular adaptor activity / nuclear body / negative regulation of translation / nuclear speck / protein domain specific binding / negative regulation of cell population proliferation / negative regulation of gene expression / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / RNA binding / extracellular space / membrane / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Petit, P. / Weichenrieder, O. / Wohlbold, L. / Izaurralde, E. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2012 Title: The structural basis for the interaction between the CAF1 nuclease and the NOT1 scaffold of the human CCR4-NOT deadenylase complex Authors: Petit, A.P. / Wohlbold, L. / Bawankar, P. / Huntzinger, E. / Schmidt, S. / Izaurralde, E. / Weichenrieder, O. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR DETERMINED |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4gmj.cif.gz | 556.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4gmj.ent.gz | 463.8 KB | Display | PDB format |
PDBx/mmJSON format | 4gmj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4gmj_validation.pdf.gz | 483.1 KB | Display | wwPDB validaton report |
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Full document | 4gmj_full_validation.pdf.gz | 492.4 KB | Display | |
Data in XML | 4gmj_validation.xml.gz | 51.4 KB | Display | |
Data in CIF | 4gmj_validation.cif.gz | 70.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gm/4gmj ftp://data.pdbj.org/pub/pdb/validation_reports/gm/4gmj | HTTPS FTP |
-Related structure data
Related structure data | 4gmlC 2d5rS 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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2 |
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3 |
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Unit cell |
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-Components
-CCR4-NOT transcription complex subunit ... , 2 types, 6 molecules ACEBDF
#1: Protein | Mass: 26628.979 Da / Num. of mol.: 3 / Fragment: NOT1 MIF4G domain, UNP RESIDUES 1093-1317 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AD-005, CDC39, CNOT1, KIAA1007, NOT1 / Plasmid: pNEA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 Codon Plus / References: UniProt: A5YKK6 #2: Protein | Mass: 32776.035 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CAF1, CNOT7 / Plasmid: pNEA / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta II / References: UniProt: Q9UIV1 |
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-Non-polymers , 4 types, 225 molecules
#3: Chemical | ChemComp-MG / #4: Chemical | #5: Chemical | #6: 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: 3.28 Å3/Da / Density % sol: 62.55 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.2 Details: 0.1M Tris-HCl, 16% PEG8000, 0.2M MgCl2, 0.2M AMSO4, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: May 14, 2012 |
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: 2.7→82.21 Å / Num. obs: 63214 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 44.7 Å2 / Rmerge(I) obs: 0.112 / Rsym value: 0.096 / Net I/σ(I): 11 |
Reflection shell | Resolution: 2.7→2.85 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.676 / Mean I/σ(I) obs: 2.5 / Num. unique all: 9227 / Rsym value: 0.577 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2D5R Resolution: 2.7→76.7 Å / SU ML: 0.39 / σ(F): 1.34 / Phase error: 26.47 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 26.698 Å2 / ksol: 0.323 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.7→76.7 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23
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