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CRYSTAL STRUCTURE OF SOCS-2 IN COMPLEX WITH ELONGIN-B AND ELONGIN-C AT 1.9A RESOLUTION
Biology and Chemistry Report
2C9W
  •   Structure Details   Hide

    Structure Keywords

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

    Polymeric Molecules

    Chain A
    Description SUPPRESSOR OF CYTOKINE SIGNALING 2 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 19273.4 
    Source Method genetically manipulated  
    Entity Name HUMAN SOCS2, SOCS-2, CYTOKINE-INDUCIBLE SH2 PROTEIN 2, CIS-2, STAT-INDUCED STAT INHIBITOR 2, SSI-2 
    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 HUMAN ELONGIN B, 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 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 10974.7 
    Source Method genetically manipulated  
    Entity Name HUMAN ELONGIN C, 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
    NI  NICKEL (II) ION  Ni   58.69  View 
    SO4  SULFATE ION  O4 S   96.06  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A SOCS2_HUMAN A8K3D1     
    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
    1558   Regulation of Cell Growth  Any Process That Modulates the Frequency Rate Extent or Direction of Cell Growth. 
    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. 
    46426   Negative Regulation of Jak Stat Cascade  Any Process That Stops Prevents or Reduces the Frequency Rate or Extent of the Jak Stat Signaling Pathway Activity. 
    5737   Cytoplasm  All of the Contents of a Cell Excluding the Plasma Membrane and Nucleus But Including Other Subcellular Structures. 
    5159   Insulin Like Growth Factor Receptor Binding  Interacting Selectively and Non Covalently with the Insulin Like Growth Factor Receptor. 
    8269   Jak Pathway Signal Transduction Adaptor Activity  The Binding Activity of a Molecule That Brings Together Two Molecules of the Jak Signal Transduction Pathway Permitting Them to Function in a Coordinated Way. 
    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  


    Chain B
    Common Name Human
    Scientific Name Homo sapiens  
    Host Scientific Name Escherichia coli  


    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    
    12 12q 8835     suppressor of cytokine signaling 2 SOCS2    
    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
    rs201377221 LS-SNP   dbSNP   A 47 G - > V Bend 26% (Intermediate) 12 93968498
    rs3741676 LS-SNP   dbSNP   A 52 S - > N Turn 80% (Exposed) 12 93968513
    rs148346233 LS-SNP   dbSNP   A 76 S - > L Coil 76% (Exposed) 12 93968585
    rs142112015 LS-SNP   dbSNP   A 158 T - > KR Bend 47% (Exposed) 12 93968831
    rs186564713 LS-SNP   dbSNP   A 170 T - > S Helix 10% (Intermediate) 12 93968866
    rs150871727 LS-SNP   dbSNP   A 173 K - > E Helix 65% (Exposed) 12 93968875
    rs139375613 LS-SNP   dbSNP   A 176 G - > S Bend 74% (Exposed) 12 93968884
    rs148522364 LS-SNP   dbSNP   B 8 R - > Q Beta Ladder 9% (Buried) 16 2827109
    rs11552267 LS-SNP   dbSNP   B 23 T - > R Beta 24% (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 13% (Intermediate) 16 2826999
    rs1804323 LS-SNP   dbSNP   B 52 D - > E Coil 66% (Exposed) 16 2825540
    rs138732435 LS-SNP   dbSNP   B 54 G - > S Turn 79% (Exposed) 16 2825536
    rs146145908 LS-SNP   dbSNP   B 66 T - > A Turn 54% (Exposed) 16 2825500
    rs41496149 LS-SNP   dbSNP   C 61 N - > D Beta Ladder 61% (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 42% (Exposed) 8 74858917
    rs1060663 LS-SNP   dbSNP   C 98 E - > Q Helix 46% (Exposed) 8 74858912