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Structure of a HIF-1a-pVHL-ElonginB-ElonginC Complex
Biology and Chemistry Report
1LM8
  •   Structure Details   Hide

    Structure Keywords

    Keywords TRANSCRIPTION
    Text REGULATION, tumor suppressor, oxygen sensing, TRANSCRIPTION

    Polymeric Molecules

    Chain B
    Description ELONGIN B 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 13147.9 
    Source Method genetically manipulated  
    Chain C
    Description ELONGIN C 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 10843.5 
    Source Method genetically manipulated  
    Chain V
    Description Von Hippel-Lindau disease tumor suppressor 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 18558.3 
    Source Method genetically manipulated  
    Entity Name VHL 
    Chain H
    Description Hypoxia-inducible factor 1 alpha 
    Fragment Residues 556-575 
    Nonstandard Linkage no 
    Nonstandard Monomers yes 
    Polymer Type polypeptide(L) 
    Formula Weight 2427.7 
    Source Method synthetic  
    Entity Name HIF-1 alpha, ARNT interacting protein, MOP1 

     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    B ELOB_HUMAN B7WPD3     
    C ELOC_HUMAN E5RGD9     
    H HIF1A_HUMAN C0LZJ3     
    V VHL_HUMAN B2RE45     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain B
    GO ID   Ontology GO Term Definition
    6351   Transcription DNA Templated  The Cellular Synthesis of RNA On a Template of Dna. 
    6355   Regulation of Transcription DNA Templated  Any Process That Modulates the Frequency Rate or Extent of Cellular DNA Templated Transcription. 
    5634   Nucleus  A Membrane Bounded Organelle of Eukaryotic Cells in Which Chromosomes Are Housed and Replicated. in Most Cells the Nucleus Contains All of the Cell's Chromosomes Except the Organellar Chromosomes and Is the Site of RNA Synthesis and Processing. in Some Species or in Specialized Cell Types RNA Metabolism or DNA Replication May Be Absent. 
    5515   Protein Binding  Interacting Selectively and Non Covalently with Any Protein or Protein Complex (a Complex of Two or More Proteins That May Include Other Nonprotein Molecules). 


     
  •   Gene Details   Hide

    Genetic Source

    Chain V
    Common Name Human
    Scientific Name Homo sapiens  
    Genus Homo
    Host Scientific Name Escherichia coli  
    Host Genus Escherichia
    Host Vector Type Plasmid
    Host Plasmid Name pGEX-4T-3


    Chain C
    Common Name Human
    Scientific Name Homo sapiens  
    Genus Homo
    Host Scientific Name Escherichia coli  
    Host Genus Escherichia
    Host Vector Type Plasmid
    Host Plasmid Name pBB75


    Chain B
    Common Name Human
    Scientific Name Homo sapiens  
    Genus Homo
    Host Scientific Name Escherichia coli  
    Host Genus Escherichia
    Host Vector Type Plasmid
    Host Plasmid Name pGEX-4T-3


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    3 3p25.3 7428     von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase VHL    
    8 8q21.11 6921     transcription elongation factor B (SIII), polypeptide 1 (15kDa, elongin C) TCEB1    
    14 14q23.2 3091     hypoxia inducible factor 1, alpha subunit (basic helix-loop-helix transcription factor) HIF1A    
    16 16p12.3 6923     transcription elongation factor B (SIII), polypeptide 2 (18kDa, elongin B) TCEB2    

    Single Nucleotide Polymorphisms (from LS-SNP database)

    SNP ID LsSnp Link dbSNP Link Chain PDB position Amino acid changes Secondary structure Solvent Accessibility Chromosome Chromosome position Ligand
    rs148522364 LS-SNP   dbSNP   B 8 R - > Q Beta Ladder 9% (Intermediate) 16 2827109
    rs11552267 LS-SNP   dbSNP   B 23 T - > R Beta 23% (Intermediate) 16 2827064
    rs149340862 LS-SNP   dbSNP   B 35 L - > F Helix 28% (Intermediate) 16 2827029
    rs76369032 LS-SNP   dbSNP   B 45 Y - > D Beta Ladder 11% (Intermediate) 16 2826999
    rs1804323 LS-SNP   dbSNP   B 52 D - > E Coil 55% (Exposed) 16 2825540
    rs138732435 LS-SNP   dbSNP   B 54 G - > S Turn 80% (Exposed) 16 2825536
    rs146145908 LS-SNP   dbSNP   B 66 T - > A Turn 64% (Exposed) 16 2825500
    rs41496149 LS-SNP   dbSNP   C 61 N - > D Beta Ladder 48% (Exposed) 8 74859023
    rs11553730 LS-SNP   dbSNP   C 66 P - > H Coil 18% (Intermediate) 8 74859007
    rs201996089 LS-SNP   dbSNP   C 96 A - > G Coil 35% (Intermediate) 8 74858917
    rs1060663 LS-SNP   dbSNP   C 98 E - > Q 3/10 Helix 47% (Exposed) 8 74858912
    rs142376463 LS-SNP   dbSNP   H 570 D - > G Coil 88% (Exposed) 14 62207522
    rs113612866 LS-SNP   dbSNP   V 61 P - > A Coil 79% (Exposed) 3 10183712
    rs104893827 LS-SNP   dbSNP   V 63 L - > P Bend 5% (Buried) 3 10183719
    rs104893826 LS-SNP   dbSNP   V 64 R - > P Coil 29% (Intermediate) 3 10183722
    rs5030803 LS-SNP   dbSNP   V 74 V - > G Beta Ladder 0% (Buried) 3 10183752
    rs5030804 LS-SNP   dbSNP   V 78 N - > S Beta Ladder 0% (Buried) 3 10183764
    rs200885420 LS-SNP   dbSNP   V 79 R - > C Coil 28% (Intermediate) 3 10183766
    rs5030805 LS-SNP   dbSNP   V 80 S - > IN Bend 2% (Buried) 3 10183770
    rs193922608 LS-SNP   dbSNP   V 81 P - > L Bend 44% (Exposed) 3 10183773
    rs104893829 LS-SNP   dbSNP   V 81 P - > S Bend 44% (Exposed) 3 10183772
    rs5030827 LS-SNP   dbSNP   V 84 V - > L Beta Ladder 0% (Buried) 3 10183781
    rs5030828 LS-SNP   dbSNP   V 85 L - > P Beta Ladder 13% (Intermediate) 3 10183785
    rs119103277 LS-SNP   dbSNP   V 88 W - > S Beta Ladder 6% (Buried) 3 10183794
    rs5030807 LS-SNP   dbSNP   V 89 L - > HP Beta Ladder 0% (Buried) 3 10183797
    rs143985153 LS-SNP   dbSNP   V 90 N - > S Coil 11% (Intermediate) 3 10183800
    rs5030808 LS-SNP   dbSNP   V 93 G - > RS Bend 12% (Intermediate) 3 10183808
    rs5030809 LS-SNP   dbSNP   V 98 Y - > H Coil 18% (Intermediate) 3 10183823
    rs193922609 LS-SNP   dbSNP   V 107 R - > P Beta Ladder 11% (Intermediate) 3 10183851
    rs17855706 LS-SNP   dbSNP   V 110 H - > Y Beta Ladder 22% (Intermediate) 3 10183859
    rs104893824 LS-SNP   dbSNP   V 112 Y - > HN Beta Ladder 9% (Buried) 3 10183865
    rs5030811 LS-SNP   dbSNP   V 115 H - > Y Coil 0% (Buried) 3 10188200
    rs5030812 LS-SNP   dbSNP   V 115 H - > R Coil 0% (Buried) 3 10188201
    rs5030830 LS-SNP   dbSNP   V 118 L - > P Beta Ladder 0% (Buried) 3 10188210
    rs5030832 LS-SNP   dbSNP   V 121 D - > G Beta Ladder 11% (Intermediate) 3 10188219
    rs193922610 LS-SNP   dbSNP   V 124 T - > I Turn 43% (Exposed) 3 10188228
    rs104893831 LS-SNP   dbSNP   V 126 D - > NY Coil 4% (Buried) 3 10188233
    rs200131013 LS-SNP   dbSNP   V 130 V - > A Beta Ladder 1% (Buried) 3 10188246
    rs104893830 LS-SNP   dbSNP   V 130 V - > L Beta Ladder 1% (Buried) 3 10188245
    rs119103278 LS-SNP   dbSNP   V 135 L - > F Coil 24% (Intermediate) 3 10188262
    rs5030833 LS-SNP   dbSNP   V 136 F - > C Beta 6% (Buried) 3 10188264
    rs193922611 LS-SNP   dbSNP   V 153 L - > Q Coil 0% (Buried) 3 10188315
    rs121913346 LS-SNP   dbSNP   V 158 L - > Q Helix 0% (Buried) 3 10191480
    rs5030818 LS-SNP   dbSNP   V 161 R - > *G Helix 14% (Intermediate) 3 10191488
    rs28940297 LS-SNP   dbSNP   V 163 L - > P Helix 4% (Buried) 3 10191495
    rs104893825 LS-SNP   dbSNP   V 166 V - > F Helix 1% (Buried) 3 10191503
    rs5030820 LS-SNP   dbSNP   V 167 R - > GW Helix 14% (Intermediate) 3 10191506
    rs5030821 LS-SNP   dbSNP   V 167 R - > Q Helix 14% (Intermediate) 3 10191507
    rs193922613 LS-SNP   dbSNP   V 175 Y - > C 3/10 Helix 9% (Buried) 3 10191531
    rs5030822 LS-SNP   dbSNP   V 178 L - > Q Bend 5% (Buried) 3 10191540
    rs5030824 LS-SNP   dbSNP   V 188 L - > V Helix 2% (Buried) 3 10191569
    rs28940301 LS-SNP   dbSNP   V 191 H - > D Coil 59% (Exposed) 3 10191578
    rs28940300 LS-SNP   dbSNP   V 192 P - > S Coil 20% (Intermediate) 3 10191581
    rs28940298 LS-SNP   dbSNP   V 200 R - > W Helix 33% (Intermediate) 3 10191605
    rs199926195 LS-SNP   dbSNP   V 205 R - > C Helix 53% (Exposed) 3 10191620
    rs121913347 LS-SNP   dbSNP   V 208 H - > Y Coil 88% (Exposed) 3 10191629