ISDA: 5SVA

Deposition Date 2016-08-05

Release Date 2016-09-28

Last Version Date 2024-11-20

Entry Detail

PDB ID:

5SVA

Keywords:

TRANSCRIPTION, TRANSFERASE/DNA

Title:

Mediator-RNA Polymerase II Pre-Initiation Complex

Biological Source:

Source Organism(s):

Saccharomyces cerevisiae (Taxon ID: 4932)

Expression System(s):

Escherichia coli

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

15.30 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit RPB1
Gene (Uniprot):RPO21
Chain IDs:A
Chain Length:513
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

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

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit RPB2
Gene (Uniprot):RPB2
Chain IDs:B
Chain Length:72
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

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

Structures with similar UniProt ID

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

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit RPB4
Gene (Uniprot):RPB4
Chain IDs:D
Chain Length:221
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P20433 Pfam ID:PF03874

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases I, II, and III subunit RPABC1
Gene (Uniprot):RPB5
Chain IDs:E
Chain Length:215
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P20434 Pfam ID:PF01191, PF03871

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases I, II, and III subunit RPABC2
Gene (Uniprot):RPO26
Chain IDs:F
Chain Length:155
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P20435 Pfam ID:PF01192

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit RPB7
Gene (Uniprot):RPB7
Chain IDs:G
Chain Length:171
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P34087 Pfam ID:PF03876, PF00575

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases I, II, and III subunit RPABC3
Gene (Uniprot):RPB8
Chain IDs:H
Chain Length:146
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P20436 Pfam ID:PF03870

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit RPB9
Gene (Uniprot):RPB9
Chain IDs:I
Chain Length:328
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P27999 Pfam ID:PF02150, PF01096

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases I, II, and III subunit RPABC5
Gene (Uniprot):RPB10
Chain IDs:J
Chain Length:240
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P22139 Pfam ID:PF01194

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit RPB11
Gene (Uniprot):RPB11
Chain IDs:K
Chain Length:120
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P38902 Pfam ID:PF13656

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases I, II, and III subunit RPABC4
Gene (Uniprot):RPC10
Chain IDs:L
Chain Length:70
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P40422 Pfam ID:PF03604

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II transcription subunit 6
Gene (Uniprot):MED6
Chain IDs:M
Chain Length:295
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P38782 Pfam ID:PF04934

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II transcription subunit 8
Gene (Uniprot):MED8
Chain IDs:N
Chain Length:223
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P38304 Pfam ID:PF10232

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II transcription subunit 11
Gene (Uniprot):MED11
Chain IDs:O
Chain Length:115
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:Q99278 Pfam ID:PF10280

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II transcription subunit 17
Gene (Uniprot):SRB4
Chain IDs:P
Chain Length:687
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P32569 Pfam ID:PF10156

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II transcription subunit 18
Gene (Uniprot):SRB5
Chain IDs:Q
Chain Length:307
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P32585 Pfam ID:PF09637

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II transcription subunit 20
Gene (Uniprot):SRB2
Chain IDs:R
Chain Length:210
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P34162 Pfam ID:PF08612

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II transcription subunit 22
Gene (Uniprot):SRB6
Chain IDs:S
Chain Length:121
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P32570 Pfam ID:PF06179

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II transcription subunit 4
Gene (Uniprot):MED4
Chain IDs:T
Chain Length:284
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:Q12343 Pfam ID:PF10018

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II transcription subunit 7
Gene (Uniprot):MED7
Chain IDs:U
Chain Length:222
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:Q08278 Pfam ID:PF05983

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II transcription subunit 9
Gene (Uniprot):CSE2
Chain IDs:V
Chain Length:149
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P33308 Pfam ID:PF07544

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II transcription subunit 21
Gene (Uniprot):SRB7
Chain IDs:W
Chain Length:140
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P47822 Pfam ID:PF11221

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II transcription subunit 31
Gene (Uniprot):SOH1
Chain IDs:X
Chain Length:127
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P38633 Pfam ID:PF05669

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA repair helicase RAD3
Gene (Uniprot):RAD3
Chain IDs:Y
Chain Length:778
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P06839 Pfam ID:PF06777, PF06733, PF13307

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA repair helicase RAD25
Gene (Uniprot):SSL2
Chain IDs:Z
Chain Length:843
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:Q00578 Pfam ID:PF13625, PF04851, PF16203

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:RNA polymerase II transcription factor B subunit 2
Gene (Uniprot):TFB2
Chain IDs:AA (auth: a)
Chain Length:513
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:Q02939 Pfam ID:PF03849, PF18307

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:RNA polymerase II transcription factor B subunit 5
Gene (Uniprot):TFB5
Chain IDs:BA (auth: b)
Chain Length:72
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:Q3E7C1 Pfam ID:PF06331

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Transcription initiation factor IIB
Gene (Uniprot):SUA7
Chain IDs:CA (auth: c)
Chain Length:318
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P29055 Pfam ID:PF08271, PF00382

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Transcription initiation factor IIA large subunit
Gene (Uniprot):TOA1
Chain IDs:DA (auth: d)
Chain Length:221
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P32773 Pfam ID:PF03153

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Transcription initiation factor IIA subunit 2
Gene (Uniprot):TOA2
Chain IDs:EA (auth: e)
Chain Length:215
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P32774 Pfam ID:PF02268, PF02751

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Transcription initiation factor IIF subunit alpha
Gene (Uniprot):TFG1
Chain IDs:FA (auth: f)
Chain Length:155
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P41895 Pfam ID:PF05793

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Transcription initiation factor IIF subunit beta
Gene (Uniprot):TFG2
Chain IDs:GA (auth: g)
Chain Length:171
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P41896 Pfam ID:PF17683, PF02270

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Transcription initiation factor IIE subunit alpha
Gene (Uniprot):TFA1
Chain IDs:HA (auth: h)
Chain Length:146
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P36100 Pfam ID:PF02002

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Transcription initiation factor IIE subunit beta
Gene (Uniprot):TFA2
Chain IDs:IA (auth: i)
Chain Length:328
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P36145 Pfam ID:PF18121, PF22254, PF02186

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:TATA-box-binding protein
Gene (Uniprot):SPT15
Chain IDs:JA (auth: j)
Chain Length:240
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P13393 Pfam ID:PF00352

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit RPB1
Gene (Uniprot):RPO21
Chain IDs:KA (auth: k)
Chain Length:120
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

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

Polymer Type:polydeoxyribonucleotide
Molecule:108bp HIS4 Promoter Non-template Strand (-92/+16)
Chain IDs:LA (auth: l)
Chain Length:70
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Polymer Type:polydeoxyribonucleotide
Molecule:108bp HIS4 Promoter Template Strand (+16/-92)
Chain IDs:MA (auth: m)
Chain Length:295
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Transcription initiation factor TFIID subunit 14
Gene (Uniprot):TAF14
Chain IDs:NA (auth: n)
Chain Length:223
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P35189 Pfam ID:PF03366, PF17035

Ligand Molecules

Primary Citation

Structure of a Complete Mediator-RNA Polymerase II Pre-Initiation Complex.

Robinson, P.J, Trnka, M.J, Bushnell, D.A, Davis, R.E, Mattei, P.J, Burlingame, A.L, Kornberg, R.D.Show

Cell 166 1411 1422.e16 (2016)

PMID: 27610567 DOI: 10.1016/j.cell.2016.08.050

Abstact

A complete, 52-protein, 2.5 million dalton, Mediator-RNA polymerase II pre-initiation complex (Med-PIC) was assembled and analyzed by cryo-electron microscopy and by chemical cross-linking and mass spectrometry. The resulting complete Med-PIC structure reveals two components of functional significance, absent from previous structures, a protein kinase complex and the Mediator-activator interaction region. It thereby shows how the kinase and its target, the C-terminal domain of the polymerase, control Med-PIC interaction and transcription.

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Protein

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Disease

Primary Citation of related structures

Abstact

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