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An Information Portal to 105097 Biological Macromolecular Structures

von Hippel-Lindau protein-ElonginB-ElonginC complex, bound to Hif1- alpha peptide
Biology and Chemistry Report
4AJY
  •   Structure Details   Hide

    Structure Keywords

    Keywords TRANSCRIPTION
    Text E3 UBIQUITIN LIGASE, TRANSCRIPTION FACTOR, HYPOXIC SIGNALING, TRANSCRIPTION

    Polymeric Molecules

    Chain B
    Description TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 2 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 13147.9 
    Source Method genetically manipulated  
    Entity Name ELONGIN 18 KDA SUBUNIT, ELONGIN-B, ELOB, RNA POLYMERASE II TRANSCRIPTION FACTOR SIII SUBUNIT B, SIII P18 
    Chain C
    Description TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 1 
    Fragment 17-112 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 10974.7 
    Source Method genetically manipulated  
    Entity Name ELONGIN 15 KDA SUBUNIT, ELONGIN-C, ELOC, RNA POLYMERASE II TRANSCRIPTION FACTOR SIII SUBUNIT C, SIII P15 
    Chain H
    Description HYPOXIA-INDUCIBLE FACTOR 1-ALPHA 
    Fragment RESIDUES 559-577 
    Mutation YES 
    Nonstandard Linkage no 
    Nonstandard Monomers yes 
    Polymer Type polypeptide(L) 
    Formula Weight 2260.5 
    Source Method synthetic  
    Entity Name HIF-1-ALPHA, HIF1-ALPHA, ARNT-INTERACTING PROTEIN, BASIC-HELIX-LOOP-HELIX-PAS PROTEIN MOP1, CLASS E BASIC HELIX-LOOP-HELIX PROTEIN 78, BHLHE78, MEMBER OF PAS PROTEIN 1, PAS DOMAIN-CONTAINING PROTEIN 8 
    Chain V
    Description VON HIPPEL-LINDAU DISEASE TUMOR SUPPRESSOR 
    Fragment RESIDUES 54-213 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 18840.6 
    Source Method genetically manipulated  
    Entity Name PROTEIN G7, PVHL, PVHL54-213 

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    GOL  GLYCEROL  C3 H8 O3   92.09  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    B ELOB_HUMAN B7WPD3     
    C ELOC_HUMAN E5RGD9     
    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. 
    6366   Transcription From RNA Polymerase Ii Promoter  The Synthesis of RNA From a DNA Template by RNA Polymerase Ii Originating At an RNA Polymerase Ii Promoter. Includes Transcription of Messenger RNA (mrna) and Certain Small Nuclear Rnas (snrnas). 
    6368   Transcription Elongation From RNA Polymerase Ii Promoter  The Extension of an RNA Molecule After Transcription Initiation and Promoter Clearance At an RNA Polymerase Ii Promoter by the Addition of Ribonucleotides Catalyzed by RNA Polymerase Ii. 
    6461   Protein Complex Assembly  The Aggregation Arrangement and Bonding Together of a Set of Components to Form a Protein Complex. 
    10467   Gene Expression  The Process in Which a Gene's Sequence Is Converted Into a Mature Gene Product or Products (proteins or Rna). This Includes the Production of an RNA Transcript As Well As Any Processing to Produce a Mature RNA Product or an MRNA (for Protein Coding Genes) and the Translation of That MRNA Into Protein. Some Protein Processing Events May Be Included When They Are Required to Form an Active Form of a Product From an Inactive Precursor Form. 
    16032   Viral Process  A Multi Organism Process in Which a Virus Is a Participant. the Other Participant Is the Host. Includes Infection of a Host Cell Replication of the Viral Genome and Assembly of Progeny Virus Particles. in Some Cases the Viral Genetic Material May Integrate Into the Host Genome and Only Subsequently Under Particular Circumstances 'complete' Its Life Cycle. 
    16567   Protein Ubiquitination  The Process in Which One or More Ubiquitin Groups Are Added to a Protein. 
    50434   Positive Regulation of Viral Transcription  Any Process That Activates or Increases the Frequency Rate or Extent of Viral Transcription. 
    61418   Regulation of Transcription From RNA Polymerase Ii Promoter in Response to Hypoxia  Any Process That Modulates the Frequency Rate or Extent of Transcription From an RNA Polymerase Ii Promoter As a Result of a Hypoxia Stimulus. 
    71456   Cellular Response to Hypoxia  Any Process That Results in a Change in State or Activity of a Cell (in Terms of Movement Secretion Enzyme Production Gene Expression Etc.) As a Result of a Stimulus Indicating Lowered Oxygen Tension. Hypoxia Defined As a Decline in O2 Levels Below Normoxic Levels of 20.8 20.95% Results in Metabolic Adaptation At Both the Cellular and Organismal Level. 
    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. 
    5654   Nucleoplasm  That Part of the Nuclear Content Other Than the Chromosomes or the Nucleolus. 
    5829   Cytosol  The Part of the Cytoplasm That Does Not Contain Organelles But Which Does Contain Other Particulate Matter Such As Protein Complexes. 
    31462   Cul2 Ring Ubiquitin Ligase Complex  A Ubiquitin Ligase Complex in Which a Cullin From the Cul2 Subfamily and a Ring Domain Protein Form the Catalytic Core; Substrate Specificity Is Conferred by an Elongin Bc Adaptor and a Socs/bc Box Protein. 
    31466   Cul5 Ring Ubiquitin Ligase Complex  A Ubiquitin Ligase Complex in Which a Cullin From the Cul5 Subfamily and a Ring Domain Protein Form the Catalytic Core; Substrate Specificity Is Conferred by an Elongin Bc Adaptor and a Socs/bc Box Protein. 
    70062   Extracellular Vesicular Exosome  A Membrane Bounded Vesicle That Is Released Into the Extracellular Region by Fusion of the Limiting Endosomal Membrane of a Multivesicular Body with the Plasma Membrane. 
    70449   Elongin Complex  A Transcription Elongation Factor Complex That Suppresses RNA Polymerase Ii Pausing and May Act by Promoting Proper Alignment of the 3' End of Nascent Transcripts with the Polymerase Catalytic Site. Consists of a Transcriptionally Active Elongin a Subunit (abut 100 Kda)and Two Smaller Elongin B (about 18 Kda) and Elongin C (about 15 Kda)subunits. 
    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). 
    31625   Ubiquitin Protein Ligase Binding  Interacting Selectively and Non Covalently with a Ubiquitin Protein Ligase Enzyme Any of the E3 Proteins. 
    Chain C
    GO ID   Ontology GO Term Definition
    6511   Ubiquitin Dependent Protein Catabolic Process  The Chemical Reactions and Pathways Resulting in the Breakdown of a Protein or Peptide by Hydrolysis of Its Peptide Bonds Initiated by the Covalent Attachment of a Ubiquitin Group or Multiple Ubiquitin Groups to the Protein. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain V
    Common Name Human
    Scientific Name Homo sapiens  
    Host Scientific Name Escherichia coli  
    Host Strain Bl21(de3)
    Host Vector Pet28a
    Host Vector Type Plasmid


    Chain C
    Common Name Human
    Scientific Name Homo sapiens  
    Host Scientific Name Escherichia coli  
    Host Strain Bl21(de3)
    Host Vector Pcdf_duet
    Host Vector Type Plasmid


    Chain B
    Common Name Human
    Scientific Name Homo sapiens  
    Host Scientific Name Escherichia coli  
    Host Strain Bl21(de3)
    Host Vector Pcdf_duet
    Host Vector Type Plasmid


    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% (Buried) 16 2827109
    rs11552267 LS-SNP   dbSNP   B 23 T - > R Beta 23% (Intermediate) 16 2827064
    rs149340862 LS-SNP   dbSNP   B 35 L - > F Helix 27% (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 61% (Exposed) 16 2825540
    rs138732435 LS-SNP   dbSNP   B 54 G - > S Turn 64% (Exposed) 16 2825536
    rs146145908 LS-SNP   dbSNP   B 66 T - > A 3/10 Helix 61% (Exposed) 16 2825500
    rs41496149 LS-SNP   dbSNP   C 61 N - > D Beta Ladder 60% (Exposed) 8 74859023
    rs11553730 LS-SNP   dbSNP   C 66 P - > H Coil 17% (Intermediate) 8 74859007
    rs201996089 LS-SNP   dbSNP   C 96 A - > G Coil 36% (Intermediate) 8 74858917
    rs1060663 LS-SNP   dbSNP   C 98 E - > Q 3/10 Helix 45% (Exposed) 8 74858912
    rs142376463 LS-SNP   dbSNP   H 570 D - > G Coil 90% (Exposed) 14 62207522
    rs113612866 LS-SNP   dbSNP   V 61 P - > A Coil 46% (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 31% (Intermediate) 3 10183722
    rs5030803 LS-SNP   dbSNP   V 74 V - > G Beta Ladder 1% (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 31% (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 43% (Exposed) 3 10183773
    rs104893829 LS-SNP   dbSNP   V 81 P - > S Bend 43% (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 15% (Intermediate) 3 10183785
    rs119103277 LS-SNP   dbSNP   V 88 W - > S Beta Ladder 5% (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 19% (Intermediate) 3 10183800
    rs5030808 LS-SNP   dbSNP   V 93 G - > RS Bend 14% (Intermediate) 3 10183808
    rs5030809 LS-SNP   dbSNP   V 98 Y - > H Coil 17% (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 27% (Intermediate) 3 10183859
    rs104893824 LS-SNP   dbSNP   V 112 Y - > HN Beta Ladder 8% (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 42% (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 23% (Intermediate) 3 10188262
    rs5030833 LS-SNP   dbSNP   V 136 F - > C Beta 8% (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 13% (Intermediate) 3 10191488
    rs28940297 LS-SNP   dbSNP   V 163 L - > P Helix 2% (Buried) 3 10191495
    rs104893825 LS-SNP   dbSNP   V 166 V - > F Helix 0% (Buried) 3 10191503
    rs5030820 LS-SNP   dbSNP   V 167 R - > GW Helix 15% (Intermediate) 3 10191506
    rs5030821 LS-SNP   dbSNP   V 167 R - > Q Helix 15% (Intermediate) 3 10191507
    rs193922613 LS-SNP   dbSNP   V 175 Y - > C 3/10 Helix 8% (Buried) 3 10191531
    rs5030822 LS-SNP   dbSNP   V 178 L - > Q Bend 2% (Buried) 3 10191540
    rs5030824 LS-SNP   dbSNP   V 188 L - > V Helix 0% (Buried) 3 10191569
    rs28940301 LS-SNP   dbSNP   V 191 H - > D Coil 56% (Exposed) 3 10191578
    rs28940300 LS-SNP   dbSNP   V 192 P - > S Coil 18% (Intermediate) 3 10191581
    rs28940298 LS-SNP   dbSNP   V 200 R - > W Helix 36% (Exposed) 3 10191605
    rs199926195 LS-SNP   dbSNP   V 205 R - > C Helix 63% (Exposed) 3 10191620