ISDA

Deposition Date 2014-09-29

Release Date 2015-02-04

Last Version Date 2024-05-08

Entry Detail

PDB ID:

4V1M

Keywords:

TRANSCRIPTION

Title:

Architecture of the RNA polymerase II-Mediator core transcription initiation complex

Biological Source:

Source Organism:

SYNTHETIC CONSTRUCT (Taxon ID: 32630)
SACCHAROMYCES CEREVISIAE (Taxon ID: 4932)

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

6.60 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1
Gene (Uniprot):RPO21
Chain IDs:A
Chain Length:1733
Number of Molecules:1
Biological Source:SACCHAROMYCES CEREVISIAE

UniProt ID:P04050 Pfam ID:PF04997, PF00623, PF04983, PF05000, PF04998, PF04992, PF04990, PF05001 EC:2.7.7.6

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2
Gene (Uniprot):RPB2
Chain IDs:B
Chain Length:1224
Number of Molecules:1
Biological Source:SACCHAROMYCES CEREVISIAE

UniProt ID:P08518 Pfam ID:PF04563, PF04561, PF04565, PF04566, PF04567, PF00562, PF04560

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3
Gene (Uniprot):RPB3
Chain IDs:C
Chain Length:318
Number of Molecules:1
Biological Source:SACCHAROMYCES CEREVISIAE

UniProt ID:P16370 Pfam ID:PF01193, PF01000

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 1
Gene (Uniprot):RPB5
Chain IDs:D (auth: E)
Chain Length:215
Number of Molecules:1
Biological Source:SACCHAROMYCES CEREVISIAE

UniProt ID:P20434 Pfam ID:PF03871, PF01191

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 2
Gene (Uniprot):RPO26
Chain IDs:E (auth: F)
Chain Length:155
Number of Molecules:1
Biological Source:SACCHAROMYCES CEREVISIAE

UniProt ID:P20435 Pfam ID:PF01192

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 3
Gene (Uniprot):RPB8
Chain IDs:F (auth: H)
Chain Length:146
Number of Molecules:1
Biological Source:SACCHAROMYCES CEREVISIAE

UniProt ID:P20436 Pfam ID:PF03870

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9
Gene (Uniprot):RPB9
Chain IDs:G (auth: I)
Chain Length:122
Number of Molecules:1
Biological Source:SACCHAROMYCES CEREVISIAE

UniProt ID:P27999 Pfam ID:PF02150, PF01096

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 5
Gene (Uniprot):RPB10
Chain IDs:H (auth: J)
Chain Length:70
Number of Molecules:1
Biological Source:SACCHAROMYCES CEREVISIAE

UniProt ID:P22139 Pfam ID:PF01194

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11
Gene (Uniprot):RPB11
Chain IDs:I (auth: K)
Chain Length:120
Number of Molecules:1
Biological Source:SACCHAROMYCES CEREVISIAE

UniProt ID:P38902 Pfam ID:PF13656

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 4
Gene (Uniprot):RPC10
Chain IDs:J (auth: L)
Chain Length:70
Number of Molecules:1
Biological Source:SACCHAROMYCES CEREVISIAE

UniProt ID:P40422 Pfam ID:PF03604

Polymer Type:polydeoxyribonucleotide
Molecule:5'-D(*AP*AP*GP*TP*AP*CP*TP*TP*GP*AP)-3'
Chain IDs:K (auth: N)
Chain Length:10
Number of Molecules:1
Biological Source:SYNTHETIC CONSTRUCT

Polymer Type:polyribonucleotide
Molecule:5'-D(*CP*CP*AP*GP*GP*AP)-3'
Chain IDs:L (auth: P)
Chain Length:6
Number of Molecules:1
Biological Source:SYNTHETIC CONSTRUCT

Polymer Type:polydeoxyribonucleotide
Molecule:5'-D(*TP*CP*AP*AP*GP*TP*AP*CP*TP*TP*TP*TP*TP*CP *CP*BRUP*GP*GP*TP*C)-3'
Chain IDs:M (auth: T)
Chain Length:20
Number of Molecules:1
Biological Source:SYNTHETIC CONSTRUCT

Modified Residue

Compound ID	Chain ID	Parent Comp ID	Details	2D Image
BRU	M	DU	?

Ligand Molecules

Primary Citation

Architecture of the RNA Polymerase II-Mediator Core Initiation Complex.

Plaschka, C, Lariviere, L, Wenzeck, L, Seizl, M, Hemann, M, Tegunov, D, Petrotchenko, E.V, Borchers, C.H, Baumeister, W, Herzog, F, Villa, E, Cramer, P.Show

Nature 518 376 ? (2015)

PMID: 25652824 DOI: 10.1038/NATURE14229

Abstact

The conserved co-activator complex Mediator enables regulated transcription initiation by RNA polymerase (Pol) II. Here we reconstitute an active 15-subunit core Mediator (cMed) comprising all essential Mediator subunits from Saccharomyces cerevisiae. The cryo-electron microscopic structure of cMed bound to a core initiation complex was determined at 9.7 Å resolution. cMed binds Pol II around the Rpb4-Rpb7 stalk near the carboxy-terminal domain (CTD). The Mediator head module binds the Pol II dock and the TFIIB ribbon and stabilizes the initiation complex. The Mediator middle module extends to the Pol II foot with a 'plank' that may influence polymerase conformation. The Mediator subunit Med14 forms a 'beam' between the head and middle modules and connects to the tail module that is predicted to bind transcription activators located on upstream DNA. The Mediator 'arm' and 'hook' domains contribute to a 'cradle' that may position the CTD and TFIIH kinase to stimulate Pol II phosphorylation.

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Primary Citation of related structures