ISDA: 7LBM

Deposition Date 2021-01-08

Release Date 2021-03-24

Last Version Date 2024-10-16

Entry Detail

PDB ID:

7LBM

Keywords:

TRANSCRIPTION/DNA

Title:

Structure of the human Mediator-bound transcription pre-initiation complex

Biological Source:

Source Organism(s):

Homo sapiens (Taxon ID: 9606)

Expression System(s):

Escherichia coli

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

4.80 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:Isoform 2 of Mediator of RNA
Gene (Uniprot):MED16
Chain IDs:A (auth: 0)
Chain Length:841
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9Y2X0 Pfam ID:PF20719, PF00400, PF11635, PF20718

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II
Gene (Uniprot):MED23
Chain IDs:B (auth: 1)
Chain Length:1368
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9ULK4 Pfam ID:PF11573

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II
Gene (Uniprot):MED24
Chain IDs:C (auth: 2)
Chain Length:989
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:O75448 Pfam ID:PF11277

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II
Gene (Uniprot):MED25
Chain IDs:D (auth: 3)
Chain Length:747
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q71SY5 Pfam ID:PF11265, PF11232, PF11235

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase I
Gene (Uniprot):POLR2A
Chain IDs:E (auth: A)
Chain Length:395
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P24928 Pfam ID:PF04997, PF05001, PF00623, PF04983, PF05000, PF04998, PF04992, PF04990

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase I
Gene (Uniprot):POLR2B
Chain IDs:F (auth: B)
Chain Length:308
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P30876 Pfam ID:PF04563, PF04566, PF04560, PF04565, PF00562, PF04561, PF04567

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase I
Gene (Uniprot):POLR2C
Chain IDs:G (auth: C)
Chain Length:71
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P19387 Pfam ID:PF01000, PF01193

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase I
Gene (Uniprot):POLR2D
Chain IDs:H (auth: D)
Chain Length:142
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:O15514 Pfam ID:PF03874

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase I
Gene (Uniprot):POLR2E
Chain IDs:I (auth: E)
Chain Length:210
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P19388 Pfam ID:PF03871, PF01191

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases
Gene (Uniprot):POLR2F
Chain IDs:J (auth: F)
Chain Length:127
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P61218 Pfam ID:PF01192

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase I
Gene (Uniprot):POLR2G
Chain IDs:K (auth: G)
Chain Length:246
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62487 Pfam ID:PF03876, PF00575

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases
Gene (Uniprot):POLR2H
Chain IDs:L (auth: H)
Chain Length:150
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P52434 Pfam ID:PF03870

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase I
Gene (Uniprot):POLR2I
Chain IDs:M (auth: I)
Chain Length:125
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P36954 Pfam ID:PF02150, PF01096

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases
Gene (Uniprot):POLR2L
Chain IDs:N (auth: J)
Chain Length:67
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62875 Pfam ID:PF01194

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase I
Gene (Uniprot):POLR2J
Chain IDs:O (auth: K)
Chain Length:208
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P52435 Pfam ID:PF13656

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases
Gene (Uniprot):POLR2K
Chain IDs:P (auth: L)
Chain Length:58
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P53803 Pfam ID:PF03604

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Transcription initiation fact
Gene (Uniprot):GTF2A1
Chain IDs:Q (auth: M)
Chain Length:200
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P52655 Pfam ID:PF03153

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Transcription initiation fact
Gene (Uniprot):GTF2A2
Chain IDs:R (auth: N)
Chain Length:311
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P52657 Pfam ID:PF02268, PF02751

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Transcription initiation fact
Gene (Uniprot):GTF2B
Chain IDs:S (auth: O)
Chain Length:178
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q00403 Pfam ID:PF08271, PF00382

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:TATA-box-binding protein
Gene (Uniprot):TBP
Chain IDs:T (auth: P)
Chain Length:200
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P20226 Pfam ID:PF00352

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:General transcription factor
Gene (Uniprot):GTF2E1
Chain IDs:U (auth: Q)
Chain Length:178
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P29083 Pfam ID:PF02002, PF08271, PF11521

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Transcription initiation fact
Gene (Uniprot):GTF2E2
Chain IDs:V (auth: R)
Chain Length:291
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P29084 Pfam ID:PF02186, PF18121

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:General transcription factor
Gene (Uniprot):GTF2F1
Chain IDs:W (auth: S)
Chain Length:517
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P35269 Pfam ID:PF05793

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:General transcription factor
Gene (Uniprot):GTF2F2
Chain IDs:X (auth: T)
Chain Length:233
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P13984 Pfam ID:PF17683, PF02270

Polymer Type:polydeoxyribonucleotide
Molecule:super core promoter sense str
Chain IDs:Y (auth: U)
Chain Length:146
Number of Molecules:1
Biological Source:Homo sapiens

Polymer Type:polydeoxyribonucleotide
Molecule:super core promoter antisense
Chain IDs:Z (auth: V)
Chain Length:135
Number of Molecules:1
Biological Source:Homo sapiens

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:TFIIH basal transcription fac
Gene (Uniprot):ERCC3
Chain IDs:AA (auth: W)
Chain Length:244
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P19447 Pfam ID:PF13625, PF04851, PF16203

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:TFIIH basal transcription fac
Gene (Uniprot):ERCC2
Chain IDs:BA (auth: X)
Chain Length:760
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P18074 Pfam ID:PF06733, PF06777, PF13307 EC:3.6.4.12

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:General transcription factor
Gene (Uniprot):GTF2H1
Chain IDs:CA (auth: Y)
Chain Length:131
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P32780 Pfam ID:PF03909, PF08567

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:General transcription factor
Gene (Uniprot):GTF2H4
Chain IDs:DA (auth: Z)
Chain Length:462
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q92759 Pfam ID:PF18307, PF03849

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:General transcription factor
Gene (Uniprot):GTF2H2
Chain IDs:EA (auth: a)
Chain Length:395
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q13888 Pfam ID:PF07975, PF04056

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:General transcription factor
Gene (Uniprot):GTF2H3
Chain IDs:FA (auth: b)
Chain Length:308
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q13889 Pfam ID:PF03850

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:General transcription factor
Gene (Uniprot):GTF2H5
Chain IDs:GA (auth: c)
Chain Length:71
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q6ZYL4 Pfam ID:PF06331

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:CDK-activating kinase assembl
Gene (Uniprot):MNAT1
Chain IDs:HA (auth: d)
Chain Length:142
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P51948 Pfam ID:PF17121, PF06391, PF25811

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Cyclin-dependent kinase 7
Gene (Uniprot):CDK7
Chain IDs:IA (auth: e)
Chain Length:210
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P50613 Pfam ID:PF00069 EC:2.7.11.22

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Cyclin-H
Gene (Uniprot):CCNH
Chain IDs:JA (auth: f)
Chain Length:127
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P51946 Pfam ID:PF16899, PF00134

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II
Gene (Uniprot):MED6
Chain IDs:KA (auth: g)
Chain Length:246
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:O75586 Pfam ID:PF04934

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II
Gene (Uniprot):MED8
Chain IDs:LA (auth: h)
Chain Length:150
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q96G25 Pfam ID:PF10232

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II
Gene (Uniprot):MED11
Chain IDs:MA (auth: i)
Chain Length:125
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9P086 Pfam ID:PF10280

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II
Gene (Uniprot):MED17
Chain IDs:NA (auth: j)
Chain Length:67
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9NVC6 Pfam ID:PF10156

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II
Gene (Uniprot):MED18
Chain IDs:OA (auth: k)
Chain Length:208
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9BUE0 Pfam ID:PF09637

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II
Gene (Uniprot):MED20
Chain IDs:PA (auth: l)
Chain Length:58
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9H944 Pfam ID:PF08612

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II
Gene (Uniprot):MED22
Chain IDs:QA (auth: m)
Chain Length:200
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q15528 Pfam ID:PF06179

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II
Gene (Uniprot):MED27
Chain IDs:RA (auth: n)
Chain Length:311
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q6P2C8 Pfam ID:PF11571

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II
Gene (Uniprot):MED28
Chain IDs:SA (auth: o)
Chain Length:178
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9H204 Pfam ID:PF11594

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II
Gene (Uniprot):MED29
Chain IDs:TA (auth: p)
Chain Length:200
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9NX70 Pfam ID:PF11568

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II
Gene (Uniprot):MED30
Chain IDs:UA (auth: q)
Chain Length:178
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q96HR3 Pfam ID:PF11315

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II
Gene (Uniprot):MED14
Chain IDs:VA (auth: r)
Chain Length:291
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:O60244 Pfam ID:PF22984, PF08638, PF22983, PF22981, PF25065, PF25067, PF25069

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II
Gene (Uniprot):MED4
Chain IDs:WA (auth: s)
Chain Length:517
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9NPJ6 Pfam ID:PF10018

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II
Gene (Uniprot):MED7
Chain IDs:XA (auth: t)
Chain Length:233
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:O43513 Pfam ID:PF05983

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II
Gene (Uniprot):MED9
Chain IDs:YA (auth: u)
Chain Length:146
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9NWA0 Pfam ID:PF07544

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II
Gene (Uniprot):MED10
Chain IDs:ZA (auth: v)
Chain Length:135
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9BTT4 Pfam ID:PF09748

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II
Gene (Uniprot):MED19
Chain IDs:AB (auth: w)
Chain Length:244
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:A0JLT2 Pfam ID:PF10278

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II
Gene (Uniprot):MED21
Chain IDs:BB (auth: x)
Chain Length:760
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q13503 Pfam ID:PF11221

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II
Gene (Uniprot):MED31
Chain IDs:CB (auth: y)
Chain Length:131
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q9Y3C7 Pfam ID:PF05669

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II
Gene (Uniprot):MED15
Chain IDs:DB (auth: z)
Chain Length:462
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q96RN5 Pfam ID:PF09606, PF21538, PF21539

Ligand Molecules

SF4

Primary Citation

Structure of the human Mediator-bound transcription preinitiation complex.

Abdella, R, Talyzina, A, Chen, S, Inouye, C.J, Tjian, R, He, Y.Show

Science 372 52 56 (2021)

PMID: 33707221 DOI: 10.1126/science.abg3074

Abstact

Eukaryotic transcription requires the assembly of a multisubunit preinitiation complex (PIC) composed of RNA polymerase II (Pol II) and the general transcription factors. The coactivator Mediator is recruited by transcription factors, facilitates the assembly of the PIC, and stimulates phosphorylation of the Pol II C-terminal domain (CTD) by the TFIIH subunit CDK7. Here, we present the cryo-electron microscopy structure of the human Mediator-bound PIC at a resolution below 4 angstroms. Transcription factor binding sites within Mediator are primarily flexibly tethered to the tail module. CDK7 is stabilized by multiple contacts with Mediator. Two binding sites exist for the Pol II CTD, one between the head and middle modules of Mediator and the other in the active site of CDK7, providing structural evidence for Pol II CTD phosphorylation within the Mediator-bound PIC.

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Protein

Chemical

Disease

Primary Citation of related structures

Abstact

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