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CRYSTAL STRUCTURE OF SOCS-4 IN COMPLEX WITH ELONGIN-B AND ELONGIN-C AT 2.55A RESOLUTION
Biology and Chemistry Report
2IZV
  •   Structure Details   Hide

    Structure Keywords

    Keywords TRANSCRIPTION
    Text SIGNAL TRANSDUCTION INHIBITOR, GROWTH REGULATION, SIGNAL TRANSDUCTION, SH2 DOMAIN, TRANSCRIPTION, NUCLEAR PROTEIN, UBL CONJUGATION PATHWAY, TRANSCRIPTION REGULATION

    Polymeric Molecules

    Chain A
    Description SUPPRESSOR OF CYTOKINE SIGNALING 4 
    Fragment RESIDUES 274-437 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 21736.8 
    Source Method genetically manipulated  
    Entity Name SOCS-4 ELONGIN B, C COMPLEX, SOCS-4, SOCS-7, SUPPRESSOR OF CYTOKINE SIGNALING 7 
    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 RNA POLYMERASE II TRANSCRIPTION FACTOR SIII SUBUNIT B, SIII P18, ELONGIN B, ELOB, ELONGIN 18 KDA SUBUNIT 
    Chain C
    Description TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 1 
    Fragment RESIDUES 17-112 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 10974.7 
    Source Method genetically manipulated  
    Entity Name RNA POLYMERASE II TRANSCRIPTION FACTOR SIII SUBUNIT C, SIII P15, ELONGIN-C, ELOC, ELONGIN 15 KDA SUBUNIT 

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    CL  CHLORIDE ION  Cl   35.45  View 
    EDO  1,2-ETHANEDIOL  C2 H6 O2   62.07  View 
    NA  SODIUM ION  Na   22.99  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A SOCS4_HUMAN Q8WXH5     
    B ELOB_HUMAN B7WPD3     
    C ELOC_HUMAN E5RGD9     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A
    GO ID   Ontology GO Term Definition
    7175   Negative Regulation of Epidermal Growth Factor Activated Receptor Activity  Any Process That Stops Prevents or Reduces the Frequency Rate or Extent of Egf Activated Receptor Activity. 
    32436   Positive Regulation of Proteasomal Ubiquitin Dependent Protein Catabolic Process  Any Process That Activates or Increases the Frequency Rate or Extent of the Breakdown of a Protein or Peptide by Hydrolysis of Its Peptide Bonds Initiated by the Covalent Attachment of Ubiquitin and Mediated by the Proteasome. 
    35556   Intracellular Signal Transduction  The Process in Which a Signal Is Passed On to Downstream Components Within the Cell Which Become Activated Themselves to Further Propagate the Signal and Finally Trigger a Change in the Function or State of the Cell. 
    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 C
    Common Name Human
    Scientific Name Homo sapiens  
    Host Scientific Name Escherichia coli  
    Host Cell Line Bl21(de3) R3
    Host Vector P11


    Chain B
    Common Name Human
    Scientific Name Homo sapiens  
    Host Scientific Name Escherichia coli  
    Host Cell Line Bl21(de3) R3
    Host Vector P11


    Chain A
    Common Name Human
    Scientific Name Homo sapiens  
    Host Scientific Name Escherichia coli  
    Host Cell Line Bl21(de3) R3
    Host Vector P11


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    8 8q21.11 6921     transcription elongation factor B (SIII), polypeptide 1 (15kDa, elongin C) TCEB1    
    14 14q22.1 122809     suppressor of cytokine signaling 4 SOCS4    
    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
    rs116819699 LS-SNP   dbSNP   A 282 N - > S Helix 8% (Buried) 14 55510604
    rs202122469 LS-SNP   dbSNP   A 328 S - > N Turn 62% (Exposed) 14 55510742
    rs115105527 LS-SNP   dbSNP   A 336 E - > G Beta Ladder 14% (Intermediate) 14 55510766
    rs140153508 LS-SNP   dbSNP   A 344 F - > S Bend 16% (Intermediate) 14 55510790
    rs139444469 LS-SNP   dbSNP   A 382 I - > V Coil 33% (Intermediate) 14 55510903
    rs200297224 LS-SNP   dbSNP   A 404 D - > G Helix 79% (Exposed) 14 55510970
    rs115447566 LS-SNP   dbSNP   A 413 S - > P Helix 69% (Exposed) 14 55510996
    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 30% (Intermediate) 16 2827029
    rs76369032 LS-SNP   dbSNP   B 45 Y - > D Beta Ladder 12% (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 69% (Exposed) 16 2825536
    rs146145908 LS-SNP   dbSNP   B 66 T - > A Turn 45% (Exposed) 16 2825500
    rs41496149 LS-SNP   dbSNP   C 61 N - > D Beta Ladder 64% (Exposed) 8 74859023
    rs11553730 LS-SNP   dbSNP   C 66 P - > H Coil 19% (Intermediate) 8 74859007
    rs201996089 LS-SNP   dbSNP   C 96 A - > G Coil 44% (Exposed) 8 74858917
    rs1060663 LS-SNP   dbSNP   C 98 E - > Q Helix 48% (Exposed) 8 74858912