+Open data
-Basic information
Entry | Database: PDB / ID: 8jj6 | ||||||
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Title | Structure of the NELF-BCE complex | ||||||
Components |
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Keywords | TRANSCRIPTION / transcription elongation factor / negative transcription elongation factor(NELF) | ||||||
Function / homology | Function and homology information NELF complex / NTRK3 as a dependence receptor / negative regulation of stem cell differentiation / Abortive elongation of HIV-1 transcript in the absence of Tat / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / negative regulation of transcription elongation by RNA polymerase II / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / HIV elongation arrest and recovery ...NELF complex / NTRK3 as a dependence receptor / negative regulation of stem cell differentiation / Abortive elongation of HIV-1 transcript in the absence of Tat / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / negative regulation of transcription elongation by RNA polymerase II / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / stem cell differentiation / TP53 Regulates Transcription of DNA Repair Genes / cell population proliferation / negative regulation of DNA-templated transcription / RNA binding / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.72 Å | ||||||
Authors | Wang, Z. / Cao, Y. / Qin, Y. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: The crystal structure of the human NELF-B, NELF-C, and NELF-E trimeric complex Authors: Wang, Z. / Cao, Y. / Qin, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8jj6.cif.gz | 299.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8jj6.ent.gz | 240 KB | Display | PDB format |
PDBx/mmJSON format | 8jj6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jj/8jj6 ftp://data.pdbj.org/pub/pdb/validation_reports/jj/8jj6 | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-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: 63842.949 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NELFB / Production host: Escherichia coli (E. coli) / References: UniProt: Q8WX92 #2: Protein | Mass: 16886.957 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NELFCD / Production host: Escherichia coli (E. coli) / References: UniProt: H0UI80 #3: Protein | Mass: 5712.895 Da / Num. of mol.: 2 / Mutation: L8M, N20M, L30M Source method: isolated from a genetically manipulated source Details: In order to gain the selenomethionine-labeled crystals, amino acid mutated: L8M, N20M, L30M Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) #4: 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: 2.83 Å3/Da / Density % sol: 56.58 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1M BICINE pH 8.5 and 20% v/v Polyethylene glycol 300 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Apr 28, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. obs: 53240 / % possible obs: 100 % / Redundancy: 29.2 % / Biso Wilson estimate: 41.53 Å2 / Rmerge(I) obs: 0.287 / Net I/σ(I): 14.75 |
Reflection shell | Resolution: 2.7→2.75 Å / Rmerge(I) obs: 1.647 / Num. unique obs: 2629 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.72→37.51 Å / SU ML: 0.3335 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.7981 / Stereochemistry target values: GeoStd + Monomer Library
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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: 43.5 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.72→37.51 Å
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Refine LS restraints |
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LS refinement shell |
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