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- PDB-4ajy: von Hippel-Lindau protein-ElonginB-ElonginC complex, bound to Hif... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ajy | ||||||
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Title | von Hippel-Lindau protein-ElonginB-ElonginC complex, bound to Hif1- alpha peptide | ||||||
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Function / homology | ![]() epithelial cell differentiation involved in mammary gland alveolus development / neural fold elevation formation / iris morphogenesis / positive regulation of chemokine-mediated signaling pathway / hypoxia-inducible factor-1alpha signaling pathway / elastin metabolic process / glandular epithelial cell maturation / regulation of transforming growth factor beta2 production / connective tissue replacement involved in inflammatory response wound healing / cardiac ventricle morphogenesis ...epithelial cell differentiation involved in mammary gland alveolus development / neural fold elevation formation / iris morphogenesis / positive regulation of chemokine-mediated signaling pathway / hypoxia-inducible factor-1alpha signaling pathway / elastin metabolic process / glandular epithelial cell maturation / regulation of transforming growth factor beta2 production / connective tissue replacement involved in inflammatory response wound healing / cardiac ventricle morphogenesis / negative regulation of mesenchymal cell apoptotic process / hemoglobin biosynthetic process / positive regulation of hormone biosynthetic process / mesenchymal cell apoptotic process / positive regulation of mitophagy / Cellular response to hypoxia / retina vasculature development in camera-type eye / intestinal epithelial cell maturation / negative regulation of growth / regulation of protein neddylation / collagen metabolic process / PTK6 Expression / intracellular oxygen homeostasis / regulation of cellular response to hypoxia / negative regulation of bone mineralization / B-1 B cell homeostasis / vascular endothelial growth factor production / lactate metabolic process / RHOBTB3 ATPase cycle / negative regulation of receptor signaling pathway via JAK-STAT / transcription elongation factor activity / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / transcription regulator activator activity / dopaminergic neuron differentiation / target-directed miRNA degradation / elongin complex / STAT3 nuclear events downstream of ALK signaling / VCB complex / positive regulation of cytokine production involved in inflammatory response / negative regulation of thymocyte apoptotic process / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Van Molle, I. / Thomann, A. / Buckley, D.L. / So, E.C. / Lang, S. / Crews, C.M. / Ciulli, A. | ||||||
![]() | ![]() Title: Dissecting Fragment-Based Lead Discovery at the Von Hippel-Lindau Protein:Hypoxia Inducible Factor 1Alpha Protein-Protein Interface. Authors: Van Molle, I. / Thomann, A. / Buckley, D.L. / So, E.C. / Lang, S. / Crews, C.M. / Ciulli, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 91.8 KB | Display | ![]() |
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PDB format | ![]() | 68.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3ztcC ![]() 3ztdC ![]() 4awjC ![]() 1lm8S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE ... , 2 types, 2 molecules BC
#1: Protein | Mass: 13147.781 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 10974.616 Da / Num. of mol.: 1 / Fragment: 17-112 Source method: isolated from a genetically manipulated source Details: EXTRA MET AT N-TERMINUS DUE TO CLONING / Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
-Protein/peptide / Protein , 2 types, 2 molecules HV
#3: Protein/peptide | Mass: 2260.457 Da / Num. of mol.: 1 / Fragment: RESIDUES 559-577 / Mutation: YES / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
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#4: Protein | Mass: 18840.438 Da / Num. of mol.: 1 / Fragment: RESIDUES 54-213 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
-Non-polymers , 2 types, 243 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-GOL / ![]() |
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#6: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.36 % / Description: NONE |
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Crystal grow![]() | Details: 0.1 M K PHOSPHATE PH 6.6 0.2 M (NH4)2SO4 20% PEG MME 5000 5 MM DTT |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 22, 2011 / Details: KIRKPATRICK-BAEZ PAIR OF BI-MORPH MIRRORS |
Radiation | Monochromator: CHANNEL CUT CRYOGENICALLY COOLED MONOCHROMATOR CRYSTAL Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.73→45 Å / Num. obs: 46307 / % possible obs: 99.7 % / Observed criterion σ(I): 3 / Redundancy: 7.4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 22.19 |
Reflection shell | Resolution: 1.73→1.84 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 3.09 / % possible all: 98.8 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1LM8 Resolution: 1.73→42.5 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.097 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY
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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: 24.567 Å2
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Refinement step | Cycle: LAST / Resolution: 1.73→42.5 Å
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Refine LS restraints |
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