6I84 image
Deposition Date 2018-11-19
Release Date 2019-01-02
Last Version Date 2024-05-15
Entry Detail
PDB ID:
6I84
Keywords:
TRANSCRIPTION
Title:
Structure of transcribing RNA polymerase II-nucleosome complex
Biological Source:
Source Organism:
Xenopus laevis (Taxon ID: 8355)
synthetic construct (Taxon ID: 32630)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Taxon ID: 559292)
Host Organism:
Escherichia coli
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
4.40 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
6I84 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:K (auth: A)
Chain Length:1733
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P04050 Pfam ID:PF04997, PF00623, PF04983, PF05000, PF04998, PF04992, PF04990, PF05001 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:L (auth: B)
Chain Length:1224
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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:M (auth: C)
Chain Length:348
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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:N (auth: D)
Chain Length:221
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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:O (auth: E)
Chain Length:215
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P20434 Pfam ID:PF03871, PF01191
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:P (auth: F)
Chain Length:155
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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:Q (auth: G)
Chain Length:171
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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:R (auth: H)
Chain Length:146
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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:S (auth: I)
Chain Length:122
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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:T (auth: J)
Chain Length:70
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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:U (auth: K)
Chain Length:120
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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:V (auth: L)
Chain Length:70
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P40422 Pfam ID:PF03604
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone H3.2
Chain IDs:A (auth: M), H (auth: S)
Chain Length:136
Number of Molecules:2
Biological Source:Xenopus laevis
UniProt ID:P84233 Pfam ID:PF00125
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (158-MER)
Chain IDs:E (auth: N)
Chain Length:160
Number of Molecules:1
Biological Source:synthetic construct
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone H4
Chain IDs:F (auth: O), I (auth: U)
Chain Length:103
Number of Molecules:2
Biological Source:Xenopus laevis
UniProt ID:P62799 Pfam ID:PF15511
Polymer Type:polyribonucleotide
Molecule:RNA
Chain IDs:W (auth: P)
Chain Length:10
Number of Molecules:1
Biological Source:synthetic construct
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone H2A type 1
Chain IDs:B (auth: Q), C (auth: V)
Chain Length:130
Number of Molecules:2
Biological Source:Xenopus laevis
UniProt ID:P06897 Pfam ID:PF00125, PF16211
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone H2B 1.1
Chain IDs:G (auth: R), J (auth: W)
Chain Length:123
Number of Molecules:2
Biological Source:Xenopus laevis
UniProt ID:P02281 Pfam ID:PF00125
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (170-MER)
Chain IDs:D (auth: T)
Chain Length:169
Number of Molecules:1
Biological Source:synthetic construct
Ligand Molecules
MG
ZN
Primary Citation
Structure of transcribing RNA polymerase II-nucleosome complex.
Nat Commun 9 5432 5432 (2018)
PMID: 30575770 DOI: 10.1038/s41467-018-07870-y

Abstact

Transcription of eukaryotic protein-coding genes requires passage of RNA polymerase II (Pol II) through nucleosomes, but it is unclear how this is achieved. Here we report the cryo-EM structure of transcribing Saccharomyces cerevisiae Pol II engaged with a downstream nucleosome core particle at an overall resolution of 4.4 Å. Pol II and the nucleosome are observed in a defined relative orientation that is not predicted. Pol II contacts both sides of the nucleosome dyad using its clamp head and lobe domains. Structural comparisons reveal that the elongation factors TFIIS, DSIF, NELF, SPT6, and PAF1 complex can be accommodated on the Pol II surface in the presence of the oriented nucleosome. Our results provide a starting point for analysing the mechanisms of chromatin transcription.

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Primary Citation of related structures
6I84