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(-) Description

Title :  STRUCTURE OF THE MEDIATOR MED7/MED21 (MED7/SRB7) SUBCOMPLEX
 
Authors :  S. Baumli, S. Hoeppner, P. Cramer
Date :  18 Jan 05  (Deposition) - 22 Feb 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Gene Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Baumli, S. Hoeppner, P. Cramer
A Conserved Mediator Hinge Revealed In The Structure Of The Med7. Med21 (Med7. Srb7) Heterodimer.
J. Biol. Chem. V. 280 18171 2005
PubMed-ID: 15710619  |  Reference-DOI: 10.1074/JBC.M413466200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RNA POLYMERASE II MEDIATOR COMPLEX PROTEIN MED7
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET24D
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 102-205
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: RNA POLYMERASE II TRANSCRIPTIONAL REGULATION MEDIATOR 7
 
Molecule 2 - RNA POLYMERASE II HOLOENZYME COMPONENT SRB7
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET24D
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: MED21, RNAPII COMPLEX COMPONENT SRB7, SUPPRESSOR OF RNA POLYMERASE B SRB7

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1YKH)

(-) Sites  (0, 0)

(no "Site" information available for 1YKH)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1YKH)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1YKH)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1YKH)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1YKH)

(-) Exons   (2, 2)

Asymmetric/Biological Unit (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YDR308C1YDR308C.1IV:1078446-1078024423MED21_YEAST1-1401401B:2-130 (gaps)129
2.1YOL135C1YOL135C.1XV:70044-69376669MED7_YEAST1-2222221A:111-20595

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:95
 aligned with MED7_YEAST | Q08278 from UniProtKB/Swiss-Prot  Length:222

    Alignment length:95
                                   120       130       140       150       160       170       180       190       200     
           MED7_YEAST   111 NYQYKIQELRKLLKSLLLNYLELIGVLSINPDMYERKVENIRTILVNIHHLLNEYRPHQSRESLIMLLEEQLEYKRGEIREIEQVCKQVHDKLTS 205
               SCOP domains d1ykha_ A: automated matches                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------- CATH domains
               Pfam domains Med7-1ykhA01 A:111-204                                                                        - Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------- PROSITE
               Transcript 2 Exon 2.1  PDB: A:111-205 UniProt: 1-222 [INCOMPLETE]                                            Transcript 2
                 1ykh A 111 NYQYKIQELRKLLKSLLLNYLELIGVLSINPDMYERKVENIRTILVNIHHLLNEYRPHQSRESLIMLLEEQLEYKRGEIREIEQVCKQVHDKLTS 205
                                   120       130       140       150       160       170       180       190       200     


Chain B from PDB  Type:PROTEIN  Length:114
 aligned with MED21_YEAST | P47822 from UniProtKB/Swiss-Prot  Length:140

    Alignment length:129
                                    11        21        31        41        51        61        71        81        91       101       111       121         
          MED21_YEAST     2 TDRLTQLQICLDQMTEQFCATLNYIDKNHGFERLTVNEPQMSDKHATVVPPEEFSNTIDELSTDIILKTRQINKLIDSLPGVDVSAEEQLRKIDMLQKKLVEVEDEKIEAIKKKEKLLRHVDSLIEDFV 130
               SCOP domains d1ykhb1 B:2-130 RNA polymerase I               I holoenzyme component SRB7 (MED21)                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains Med21-1ykhB01 B:2-130                                                                                                             Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhh....---------------..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:2-130 (gaps) UniProt: 1-140 [INCOMPLETE]                                                                         Transcript 1
                 1ykh B   2 TDRMTQLQICLDQMTEQFCATLNYIDKNHGFE---------------VVPPEEFSNTIDELSTDIILKTRQINKLIDSLPGVDVSAEEQLRKIDMLQKKLVEVEDEKIEAIKKKEKLMRHVDSMIEDFV 130
                                    11        21        31 |       -       |51        61        71        81        91       101       111       121         
                                                          33              49
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1YKH)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Med21] (2)
(-)
Clan: no clan defined [family: Med7] (2)

(-) Gene Ontology  (14, 22)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (MED7_YEAST | Q08278)
molecular function
    GO:0001104    RNA polymerase II transcription cofactor activity    Interacting selectively and non-covalently with an RNA polymerase II (RNAP II) regulatory transcription factor and also with the RNAP II basal transcription machinery in order to modulate transcription. Cofactors generally do not bind DNA, but rather mediate protein-protein interactions between regulatory transcription factors and the basal RNAP II transcription machinery.
    GO:0003674    molecular_function    Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
    GO:0005515    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).
biological process
    GO:0000122    negative regulation of transcription from RNA polymerase II promoter    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0006357    regulation of transcription from RNA polymerase II promoter    Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0070847    core mediator complex    A protein complex that interacts with the carboxy-terminal domain of the largest subunit of RNA polymerase II and plays an active role in transducing the signal from a transcription factor to the transcriptional machinery. The core mediator complex has a stimulatory effect on basal transcription, and contains most of the same subdomains as the larger form of mediator complex -- a head domain comprising proteins known in Saccharomyces as Srb2, -4, and -5, Med6, -8, and -11, and Rox3 proteins; a middle domain comprising Med1, -4, and -7, Nut1 and -2, Cse2, Rgr1, Soh1, and Srb7 proteins; and a tail consisting of Gal11p, Med2p, Pgd1p, and Sin4p -- but lacks the regulatory subcomplex comprising Ssn2, -3, and -8, and Srb8 proteins. Metazoan core mediator complexes have similar modular structures and include homologs of yeast Srb and Med proteins.
    GO:0016592    mediator complex    A protein complex that interacts with the carboxy-terminal domain of the largest subunit of RNA polymerase II and plays an active role in transducing the signal from a transcription factor to the transcriptional machinery. The mediator complex is required for activation of transcription of most protein-coding genes, but can also act as a transcriptional corepressor. The Saccharomyces complex contains several identifiable subcomplexes: a head domain comprising Srb2, -4, and -5, Med6, -8, and -11, and Rox3 proteins; a middle domain comprising Med1, -4, and -7, Nut1 and -2, Cse2, Rgr1, Soh1, and Srb7 proteins; a tail consisting of Gal11p, Med2p, Pgd1p, and Sin4p; and a regulatory subcomplex comprising Ssn2, -3, and -8, and Srb8 proteins. Metazoan mediator complexes have similar modular structures and include homologs of yeast Srb and Med proteins.
    GO:0005634    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.

Chain B   (MED21_YEAST | P47822)
molecular function
    GO:0001103    RNA polymerase II repressing transcription factor binding    Interacting selectively and non-covalently with an RNA polymerase II transcription repressing factor, a protein involved in negative regulation of transcription.
    GO:0001105    RNA polymerase II transcription coactivator activity    Interacting selectively and non-covalently with an RNA polymerase II (RNAP II) regulatory transcription factor and also with the RNAP II basal transcription machinery in order to increase the frequency, rate or extent of transcription. Cofactors generally do not bind DNA, but rather mediate protein-protein interactions between activating transcription factors and the basal RNAP II transcription machinery.
    GO:0001106    RNA polymerase II transcription corepressor activity    Interacting selectively and non-covalently with an RNA polymerase II repressing transcription factor and also with the RNA polymerase II basal transcription machinery in order to stop, prevent, or reduce the frequency, rate or extent of transcription. Cofactors generally do not bind DNA, but rather mediate protein-protein interactions between repressive transcription factors and the basal transcription machinery.
    GO:0005515    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).
biological process
    GO:0000122    negative regulation of transcription from RNA polymerase II promoter    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0070847    core mediator complex    A protein complex that interacts with the carboxy-terminal domain of the largest subunit of RNA polymerase II and plays an active role in transducing the signal from a transcription factor to the transcriptional machinery. The core mediator complex has a stimulatory effect on basal transcription, and contains most of the same subdomains as the larger form of mediator complex -- a head domain comprising proteins known in Saccharomyces as Srb2, -4, and -5, Med6, -8, and -11, and Rox3 proteins; a middle domain comprising Med1, -4, and -7, Nut1 and -2, Cse2, Rgr1, Soh1, and Srb7 proteins; and a tail consisting of Gal11p, Med2p, Pgd1p, and Sin4p -- but lacks the regulatory subcomplex comprising Ssn2, -3, and -8, and Srb8 proteins. Metazoan core mediator complexes have similar modular structures and include homologs of yeast Srb and Med proteins.
    GO:0016592    mediator complex    A protein complex that interacts with the carboxy-terminal domain of the largest subunit of RNA polymerase II and plays an active role in transducing the signal from a transcription factor to the transcriptional machinery. The mediator complex is required for activation of transcription of most protein-coding genes, but can also act as a transcriptional corepressor. The Saccharomyces complex contains several identifiable subcomplexes: a head domain comprising Srb2, -4, and -5, Med6, -8, and -11, and Rox3 proteins; a middle domain comprising Med1, -4, and -7, Nut1 and -2, Cse2, Rgr1, Soh1, and Srb7 proteins; a tail consisting of Gal11p, Med2p, Pgd1p, and Sin4p; and a regulatory subcomplex comprising Ssn2, -3, and -8, and Srb8 proteins. Metazoan mediator complexes have similar modular structures and include homologs of yeast Srb and Med proteins.
    GO:0005634    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.

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  1ykh
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  MED21_YEAST | P47822
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  MED7_YEAST | Q08278
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        MED21_YEAST | P47822: 1yke 5sva
        MED7_YEAST | Q08278: 1yke 3fbi 3fbn 5sva

(-) Related Entries Specified in the PDB File

1yke STRUCTURE OF THE DEDIATOR MED7/MED21 (MED7/SRB7) SUBCOMPLEX