8JH2 image
Entry Detail
PDB ID:
8JH2
EMDB ID:
Title:
RNA polymerase II elongation complex bound with Elf1, Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome
Biological Source:
PDB Version:
Deposition Date:
2023-05-22
Release Date:
2023-11-29
Method Details:
Experimental Method:
Resolution:
5.70 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polydeoxyribonucleotide
Description:DNA (40-MER)
Chain IDs:A (auth: 0)
Chain Length:40
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polydeoxyribonucleotide
Description:DNA (40-MER)
Chain IDs:B (auth: 1)
Chain Length:40
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polypeptide(L)
Description:DNA-directed RNA polymerase subunit
Chain IDs:C (auth: A)
Chain Length:136
Number of Molecules:1
Biological Source:Komagataella phaffii
Polymer Type:polypeptide(L)
Description:DNA-directed RNA polymerase subunit beta
Chain IDs:D (auth: B)
Chain Length:1227
Number of Molecules:1
Biological Source:Komagataella phaffii
Polymer Type:polypeptide(L)
Description:RNA polymerase II third largest subunit B44, part of central core
Chain IDs:E (auth: C)
Chain Length:130
Number of Molecules:1
Biological Source:Komagataella phaffii
Polymer Type:polypeptide(L)
Description:RNA polymerase II subunit B32
Chain IDs:F (auth: D)
Chain Length:186
Number of Molecules:1
Biological Source:Komagataella phaffii
Polymer Type:polypeptide(L)
Description:RNA polymerase subunit ABC27
Chain IDs:G (auth: E)
Chain Length:136
Number of Molecules:1
Biological Source:Komagataella phaffii
Polymer Type:polypeptide(L)
Description:RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III
Chain IDs:H (auth: F)
Chain Length:103
Number of Molecules:1
Biological Source:Komagataella phaffii
Polymer Type:polypeptide(L)
Description:RNA polymerase II subunit
Chain IDs:I (auth: G)
Chain Length:171
Number of Molecules:1
Biological Source:Komagataella phaffii
Polymer Type:polypeptide(L)
Description:DNA-directed RNA polymerases I, II, and III subunit RPABC3
Chain IDs:J (auth: H)
Chain Length:145
Number of Molecules:1
Biological Source:Komagataella phaffii
Polymer Type:polypeptide(L)
Description:DNA-directed RNA polymerase subunit
Chain IDs:K (auth: I)
Chain Length:115
Number of Molecules:1
Biological Source:Komagataella phaffii
Polymer Type:polypeptide(L)
Description:RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III
Chain IDs:L (auth: J)
Chain Length:72
Number of Molecules:1
Biological Source:Komagataella phaffii
Polymer Type:polypeptide(L)
Description:RNA polymerase II subunit B12.5
Chain IDs:M (auth: K)
Chain Length:118
Number of Molecules:1
Biological Source:Komagataella phaffii
Polymer Type:polypeptide(L)
Description:RNA polymerase subunit ABC10-alpha
Chain IDs:N (auth: L)
Chain Length:72
Number of Molecules:1
Biological Source:Komagataella phaffii
Polymer Type:polypeptide(L)
Description:Transcription elongation factor 1 homolog
Chain IDs:O (auth: M)
Chain Length:110
Number of Molecules:1
Biological Source:Komagataella phaffii
Polymer Type:polydeoxyribonucleotide
Description:DNA (218-MER)
Chain IDs:P (auth: N)
Chain Length:228
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polyribonucleotide
Description:RNA (5'-R(P*CP*CP*UP*GP*GP*UP*GP*UP*CP*UP*UP*GP*GP*GP*UP*G)-3')
Chain IDs:Q (auth: P)
Chain Length:16
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polydeoxyribonucleotide
Description:DNA (218-MER)
Chain IDs:R (auth: T)
Chain Length:228
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polypeptide(L)
Description:Transcription elongation factor SPT4
Chain IDs:S (auth: V)
Chain Length:114
Number of Molecules:1
Biological Source:Komagataella phaffii
Polymer Type:polypeptide(L)
Description:Transcription elongation factor SPT5
Chain IDs:T (auth: W)
Chain Length:908
Number of Molecules:1
Biological Source:Komagataella phaffii
Polymer Type:polypeptide(L)
Description:Histone H3.3
Chain IDs:U (auth: a), Y (auth: e)
Chain Length:136
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Histone H4
Chain IDs:V (auth: b), Z (auth: f)
Chain Length:1227
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Histone H2A type 1-B/E
Chain IDs:W (auth: c), AA (auth: g)
Chain Length:130
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Histone H2B type 1-J
Chain IDs:X (auth: d), BA (auth: h)
Chain Length:186
Number of Molecules:2
Biological Source:Homo sapiens
Primary Citation
Cryo-EM structures of RNA polymerase II-nucleosome complexes rewrapping transcribed DNA.
J.Biol.Chem. 299 105477 105477 (2023)
PMID: 37981206 DOI: 10.1016/j.jbc.2023.105477

Abstact

RNA polymerase II (RNAPII) transcribes DNA wrapped in the nucleosome by stepwise pausing, especially at nucleosomal superhelical locations -5 and -1 [SHL(-5) and SHL(-1), respectively]. In the present study, we performed cryo-electron microscopy analyses of RNAPII-nucleosome complexes paused at a major nucleosomal pausing site, SHL(-1). We determined two previously undetected structures, in which the transcribed DNA behind RNAPII is sharply kinked at the RNAPII exit tunnel and rewrapped around the nucleosomal histones in front of RNAPII by DNA looping. This DNA kink shifts the DNA orientation toward the nucleosome, and the transcribed DNA region interacts with basic amino acid residues of histones H2A, H2B, and H3 exposed by the RNAPII-mediated nucleosomal DNA peeling. The DNA loop structure was not observed in the presence of the transcription elongation factors Spt4/5 and Elf1. These RNAPII-nucleosome structures provide important information for understanding the functional relevance of DNA looping during transcription elongation in the nucleosome.

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