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Title :   STRUCTURE OF THE MEDIATOR MED7/MED21 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 :   3.30

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)
Biol. Unit 3: A,B,C,D  (1x)

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)

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

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D
Biological Unit 3 (1x)	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

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

(no "Site" information available for 1YKE)

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

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

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

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

Asymmetric Unit (2, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YDR308C	1	YDR308C.1	IV:1078446-1078024	423	MED21_YEAST	1-140	140	2	B:3-133 (gaps) D:3-130 (gaps)	131 128

2.1	YOL135C	1	YOL135C.1	XV:70044-69376	669	MED7_YEAST	1-222	222	2	A:108-205 C:108-205	98 98

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:98
 aligned with MED7_YEAST | Q08278 from UniProtKB/Swiss-Prot  Length:222

    Alignment length:98
                                   117       127       137       147       157       167       177       187       197        
           MED7_YEAST   108 ESTNYQYKIQELRKLLKSLLLNYLELIGVLSINPDMYERKVENIRTILVNIHHLLNEYRPHQSRESLIMLLEEQLEYKRGEIREIEQVCKQVHDKLTS 205
               SCOP domains d1ykea1 A:108-205 RNA polymerase II mediator complex protein MED7                                  SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
               Transcript 2 Exon 2.1  PDB: A:108-205 UniProt: 1-222 [INCOMPLETE]                                               Transcript 2
                 1yke A 108 ESTNYQYKIQELRKLLKSLLLNYLELIGVLSINPDMYERKVENIRTILVNIHHLLNEYRPHQSRESLIMLLEEQLEYKRGEIREIEQVCKQVHDKLTS 205
                                   117       127       137       147       157       167       177       187       197

Chain B from PDB  Type:PROTEIN  Length:119
 aligned with MED21_YEAST | P47822 from UniProtKB/Swiss-Prot  Length:140

    Alignment length:131
                                    12        22        32        42        52        62        72        82        92       102       112       122       132 
          MED21_YEAST     3 DRLTQLQICLDQMTEQFCATLNYIDKNHGFERLTVNEPQMSDKHATVVPPEEFSNTIDELSTDIILKTRQINKLIDSLPGVDVSAEEQLRKIDMLQKKLVEVEDEKIEAIKKKEKLLRHVDSLIEDFVDGI 133
               SCOP domains d1ykeb1 B:3-133 RNA polymerase II             holoenzyme component SRB7 (MED21)                                                     SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh------------...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:3-133 (gaps) UniProt: 1-140 [INCOMPLETE]                                                                           Transcript 1
                 1yke B   3 DRLTQLQICLDQMTEQFCATLNYIDKNHGFERL------------TVVPPEEFSNTIDELSTDIILKTRQINKLIDSLPGVDVSAEEQLRKIDMLQKKLVEVEDEKIEAIKKKEKLLRHVDSLIEDFVDGI 133
                                    12        22        32  |      -     |  52        62        72        82        92       102       112       122       132 
                                                           35           48

Chain C from PDB  Type:PROTEIN  Length:98
 aligned with MED7_YEAST | Q08278 from UniProtKB/Swiss-Prot  Length:222

    Alignment length:98
                                   117       127       137       147       157       167       177       187       197        
           MED7_YEAST   108 ESTNYQYKIQELRKLLKSLLLNYLELIGVLSINPDMYERKVENIRTILVNIHHLLNEYRPHQSRESLIMLLEEQLEYKRGEIREIEQVCKQVHDKLTS 205
               SCOP domains d1ykec1 C:108-205 RNA polymerase II mediator complex protein MED7                                  SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Med7-1ykeC01 C:108-204                                                                           - Pfam domains (1)
           Pfam domains (2) Med7-1ykeC02 C:108-204                                                                           - Pfam domains (2)
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
               Transcript 2 Exon 2.1  PDB: C:108-205 UniProt: 1-222 [INCOMPLETE]                                               Transcript 2
                 1yke C 108 ESTNYQYKIQELRKLLKSLLLNYLELIGVLSINPDMYERKVENIRTILVNIHHLLNEYRPHQSRESLIMLLEEQLEYKRGEIREIEQVCKQVHDKLTS 205
                                   117       127       137       147       157       167       177       187       197

Chain D from PDB  Type:PROTEIN  Length:113
 aligned with MED21_YEAST | P47822 from UniProtKB/Swiss-Prot  Length:140

    Alignment length:128
                                    12        22        32        42        52        62        72        82        92       102       112       122        
          MED21_YEAST     3 DRLTQLQICLDQMTEQFCATLNYIDKNHGFERLTVNEPQMSDKHATVVPPEEFSNTIDELSTDIILKTRQINKLIDSLPGVDVSAEEQLRKIDMLQKKLVEVEDEKIEAIKKKEKLLRHVDSLIEDFV 130
               SCOP domains d1yked1 D:3-130 RNA polymerase                II holoenzyme component SRB7 (MED21)                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Med21-1ykeD01 D:3-130                                                                                                            Pfam domains (1)
           Pfam domains (2) Med21-1ykeD02 D:3-130                                                                                                            Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhh.......---------------......hhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: D:3-130 (gaps) UniProt: 1-140 [INCOMPLETE]                                                                        Transcript 1
                 1yke D   3 DRLTQLQICLDQMTEQFCATLNYIDKNHGFE---------------VVPPEEFSNTIDELSTDIILKTRQINKLIDSLPGVDVSAEEQLRKIDMLQKKLVEVEDEKIEAIKKKEKLLRHVDSLIEDFV 130
                                    12        22        32|        -      | 52        62        72        82        92       102       112       122        
                                                         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 '\|'

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

Asymmetric Unit(hide GO term definitions)

Chain A,C (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,D (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.

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

1ykh	THE SAME PROTEIN INCLUDING L5M/L119M AND L125M MUTATIONS

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