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Yorodumi- PDB-1lqb: Crystal structure of a hydroxylated HIF-1 alpha peptide bound to ... -
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-Basic information
Entry | Database: PDB / ID: 1lqb | ||||||
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Title | Crystal structure of a hydroxylated HIF-1 alpha peptide bound to the pVHL/elongin-C/elongin-B complex | ||||||
Components |
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Keywords | GENE REGULATION / protein-peptide complex / tumor suppressor / cancer / proteosomal degradation / ubiquitin / prolyl hydroxylation | ||||||
Function / homology | Function and homology information 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 / glandular epithelial cell maturation / elastin metabolic process / 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 / glandular epithelial cell maturation / elastin metabolic process / 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 / PTK6 promotes HIF1A stabilization / digestive tract morphogenesis / positive regulation of hormone biosynthetic process / mesenchymal cell apoptotic process / retina vasculature development in camera-type eye / Cellular response to hypoxia / intestinal epithelial cell maturation / positive regulation of mitophagy / negative regulation of growth / regulation of protein neddylation / collagen metabolic process / PTK6 Expression / regulation of cellular response to hypoxia / negative regulation of bone mineralization / intracellular oxygen homeostasis / B-1 B cell homeostasis / vascular endothelial growth factor production / RHOBTB3 ATPase cycle / negative regulation of receptor signaling pathway via JAK-STAT / transcription regulator activator activity / E-box binding / transcription elongation factor activity / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / target-directed miRNA degradation / dopaminergic neuron differentiation / lactate metabolic process / elongin complex / VCB complex / STAT3 nuclear events downstream of ALK signaling / positive regulation of cytokine production involved in inflammatory response / negative regulation of thymocyte apoptotic process / motile cilium / positive regulation of vascular endothelial growth factor receptor signaling pathway / negative regulation of TOR signaling / positive regulation of signaling receptor activity / insulin secretion involved in cellular response to glucose stimulus / Replication of the SARS-CoV-1 genome / response to iron ion / response to muscle activity / neural crest cell migration / Cul5-RING ubiquitin ligase complex / Regulation of gene expression by Hypoxia-inducible Factor / regulation of glycolytic process / embryonic hemopoiesis / Cul2-RING ubiquitin ligase complex / embryonic placenta development / intracellular non-membrane-bounded organelle / DNA-binding transcription repressor activity / DNA-binding transcription activator activity / regulation of aerobic respiration / muscle cell cellular homeostasis / positive regulation of neuroblast proliferation / SUMOylation of ubiquitinylation proteins / positive regulation of epithelial cell migration / axonal transport of mitochondrion / bone mineralization / heart looping / outflow tract morphogenesis / negative regulation of transcription elongation by RNA polymerase II / intracellular glucose homeostasis / positive regulation of insulin secretion involved in cellular response to glucose stimulus / 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 / cellular response to interleukin-1 / ubiquitin-like ligase-substrate adaptor activity / positive regulation of vascular endothelial growth factor production / neuroblast proliferation / negative regulation of reactive oxygen species metabolic process / TOR signaling / positive regulation of blood vessel endothelial cell migration / Tat-mediated elongation of the HIV-1 transcript / epithelial to mesenchymal transition / Formation of HIV-1 elongation complex containing HIV-1 Tat / cis-regulatory region sequence-specific DNA binding / chondrocyte differentiation / Formation of HIV elongation complex in the absence of HIV Tat / negative regulation of signal transduction / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / positive regulation of chemokine production / negative regulation of miRNA transcription / axon cytoplasm / negative regulation of TORC1 signaling / RNA Polymerase II Pre-transcription Events / positive regulation of endothelial cell proliferation / lactation Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Hon, W.C. / Wilson, M.I. / Harlos, K. / Claridge, T.D. / Schofield, C.J. / Pugh, C.W. / Maxwell, P.H. / Ratcliffe, P.J. / Stuart, D.I. / Jones, E.Y. | ||||||
Citation | Journal: Nature / Year: 2002 Title: Structural basis for the recognition of hydroxyproline in HIF-1 alpha by pVHL. Authors: Hon, W.C. / Wilson, M.I. / Harlos, K. / Claridge, T.D. / Schofield, C.J. / Pugh, C.W. / Maxwell, P.H. / Ratcliffe, P.J. / Stuart, D.I. / Jones, E.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lqb.cif.gz | 87.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lqb.ent.gz | 65.6 KB | Display | PDB format |
PDBx/mmJSON format | 1lqb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1lqb_validation.pdf.gz | 462.8 KB | Display | wwPDB validaton report |
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Full document | 1lqb_full_validation.pdf.gz | 470.3 KB | Display | |
Data in XML | 1lqb_validation.xml.gz | 16.5 KB | Display | |
Data in CIF | 1lqb_validation.cif.gz | 22.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lq/1lqb ftp://data.pdbj.org/pub/pdb/validation_reports/lq/1lqb | HTTPS FTP |
-Related structure data
Related structure data | 1vcbS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
-Protein , 3 types, 3 molecules ABC
#1: Protein | Mass: 13147.781 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q15370 |
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#2: Protein | Mass: 10843.420 Da / Num. of mol.: 1 / Fragment: residues 17-112 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q15369 |
#3: Protein | Mass: 18702.291 Da / Num. of mol.: 1 / Fragment: residues 52-213 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P40337 |
-Protein/peptide , 1 types, 1 molecules D
#4: Protein/peptide | Mass: 3979.335 Da / Num. of mol.: 1 / Fragment: residues 549-582 / Source method: obtained synthetically Details: The peptide was synthesized with a biotin tag at the N-terminus and with P564 as a 4(R)hydroxyproline. The sequence of the peptide is naturally found in homo sapiens (human). References: UniProt: Q16665 |
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-Non-polymers , 2 types, 85 molecules
#5: Chemical | ChemComp-SO4 / |
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#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.64 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: HEPES, PEG2000 monomethylester, ammonium sulfate, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 30, 2001 |
Radiation | Monochromator: Diamond [111] and Ge crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 24245 / % possible obs: 76 % / Redundancy: 18.5 % / Biso Wilson estimate: 17 Å2 / Rsym value: 0.06 / Net I/σ(I): 20 |
Reflection shell | Resolution: 2→2.07 Å / Mean I/σ(I) obs: 1 / Rsym value: 0.49 / % possible all: 30 |
Reflection | *PLUS Highest resolution: 2 Å / Lowest resolution: 30 Å / % possible obs: 76 % / Num. measured all: 448657 / Rmerge(I) obs: 0.06 |
Reflection shell | *PLUS Highest resolution: 2 Å / % possible obs: 30 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1VCB.pdb Resolution: 2→29.26 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 38.5116 Å2 / ksol: 0.341289 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36 Å2
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Refine analyze | Luzzati coordinate error free: 0.35 Å / Luzzati sigma a free: 0.29 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→29.26 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 30 Å / Rfactor obs: 0.225 / Rfactor Rfree: 0.278 / Rfactor Rwork: 0.226 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Lowest resolution: 2.07 Å / Rfactor Rfree: 0.352 / Rfactor Rwork: 0.289 |