7LBM image
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:
Homo sapiens (Taxon ID: 9606)
Host Organism:
Escherichia coli
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
4.80 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
7LBM validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Isoform 2 of Mediator of RNA polymerase II transcription subunit 16
Gene (Uniprot):MED16
Chain IDs:A (auth: 0)
Chain Length:841
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9Y2X0 Pfam ID:PF00400, PF11635, PF20718, PF20719
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II transcription subunit 23
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II transcription subunit 24
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II transcription subunit 25
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, PF11235, PF11232
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit RPB1
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, PF00623, PF04983, PF05000, PF04998, PF04992, PF04990, PF05001
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit RPB2
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, PF04561, PF04565, PF04566, PF04567, PF00562, PF04560
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit RPB3
Gene (Uniprot):POLR2C
Chain IDs:G (auth: C)
Chain Length:71
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P19387 Pfam ID:PF01193, PF01000
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit RPB4
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit RPB5
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases I, II, and III subunit RPABC2
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit RPB7
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases I, II, and III subunit RPABC3
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit RPB9
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases I, II, and III subunit RPABC5
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit RPB11-a
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases I, II, and III subunit RPABC4
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Transcription initiation factor IIA subunit 1
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Transcription initiation factor IIA subunit 2
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Transcription initiation factor IIB
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
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:General transcription factor IIE subunit 1
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Transcription initiation factor IIE subunit beta
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:General transcription factor IIF subunit 1
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:General transcription factor IIF subunit 2
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 strand
Chain IDs:Y (auth: U)
Chain Length:146
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polydeoxyribonucleotide
Molecule:super core promoter antisense strand
Chain IDs:Z (auth: V)
Chain Length:135
Number of Molecules:1
Biological Source:Homo sapiens
Protein Blast
Polymer Type:polypeptide(L)
Molecule:TFIIH basal transcription factor complex helicase XPB subunit
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:TFIIH basal transcription factor complex helicase XPD subunit
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:General transcription factor IIH subunit 1
Gene (Uniprot):GTF2H1
Chain IDs:CA (auth: Y)
Chain Length:131
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P32780 Pfam ID:PF08567, PF03909
Protein Blast
Polymer Type:polypeptide(L)
Molecule:General transcription factor IIH subunit 4, p52
Gene (Uniprot):GTF2H4
Chain IDs:DA (auth: Z)
Chain Length:462
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q92759 Pfam ID:PF03849, PF18307
Protein Blast
Polymer Type:polypeptide(L)
Molecule:General transcription factor IIH subunit 2
Gene (Uniprot):GTF2H2
Chain IDs:EA (auth: a)
Chain Length:395
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q13888 Pfam ID:PF04056, PF07975
Protein Blast
Polymer Type:polypeptide(L)
Molecule:General transcription factor IIH subunit 3
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:General transcription factor IIH subunit 5
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:CDK-activating kinase assembly factor MAT1
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
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
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:PF00134, PF16899
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II transcription subunit 6
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II transcription subunit 8
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II transcription subunit 11
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II transcription subunit 17
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II transcription subunit 18
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II transcription subunit 20
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II transcription subunit 22
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II transcription subunit 27
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II transcription subunit 28
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II transcription subunit 29
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II transcription subunit 30
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II transcription subunit 14
Gene (Uniprot):MED14
Chain IDs:VA (auth: r)
Chain Length:291
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:O60244 Pfam ID:PF08638, PF22981, PF22984, PF22983
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II transcription subunit 4
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II transcription subunit 7
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II transcription subunit 9
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II transcription subunit 10
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II transcription subunit 19
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II transcription subunit 21
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II transcription subunit 31
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mediator of RNA polymerase II transcription subunit 15
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
MG
SF4
ZN
Primary Citation
Structure of the human Mediator-bound transcription preinitiation complex.
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
7LBM