9UJT image
Deposition Date 2025-04-17
Release Date 2026-04-15
Last Version Date 2026-04-15
Entry Detail
PDB ID:
9UJT
Keywords:
TRANSCRIPTION/RNA/DNA
Title:
RNA polymerase II elongation complex stalled at SHL(-0.5) of the H3-H4 octasome (tetrasome)
Biological Source:
Source Organism(s):
Homo sapiens (Taxon ID: 9606)
synthetic construct (Taxon ID: 32630)
Komagataella phaffii GS115 (Taxon ID: 644223)
Expression System(s):
Escherichia coli
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
6.54 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
9UJT validation report missing
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase s
Gene (Uniprot):PAS_chr3_0568
Chain IDs:C (auth: A)
Chain Length:1743
Number of Molecules:1
Biological Source:Komagataella phaffii GS115
UniProt ID:C4R4Y0 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 s
Gene (Uniprot):PAS_chr2-1_0125
Chain IDs:D (auth: B)
Chain Length:1227
Number of Molecules:1
Biological Source:Komagataella phaffii GS115
UniProt ID:C4QZQ7 Pfam ID:PF04563, PF04561, PF04565, PF04566, PF04567, PF00562, PF04560 EC:2.7.7.6
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RNA polymerase II third large
Gene (Uniprot):PAS_chr4_0344
Chain IDs:E (auth: C)
Chain Length:304
Number of Molecules:1
Biological Source:Komagataella phaffii GS115
UniProt ID:C4R7L2 Pfam ID:PF01193, PF01000
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RNA polymerase II subunit B32
Gene (Uniprot):PAS_chr2-2_0104
Chain IDs:F (auth: D)
Chain Length:186
Number of Molecules:1
Biological Source:Komagataella phaffii GS115
UniProt ID:C4R2U9 Pfam ID:PF03874
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RNA polymerase subunit ABC27,
Gene (Uniprot):PAS_chr3_0157
Chain IDs:G (auth: E)
Chain Length:214
Number of Molecules:1
Biological Source:Komagataella phaffii GS115
UniProt ID:C4R3P8 Pfam ID:PF03871, PF01191
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RNA polymerase subunit ABC23,
Gene (Uniprot):PAS_chr2-2_0434
Chain IDs:H (auth: F)
Chain Length:106
Number of Molecules:1
Biological Source:Komagataella phaffii GS115
UniProt ID:C4R1V1 Pfam ID:PF01192
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RNA polymerase II subunit
Gene (Uniprot):PAS_chr4_0906
Chain IDs:I (auth: G)
Chain Length:139
Number of Molecules:1
Biological Source:Komagataella phaffii GS115
UniProt ID:C4R9A1 Pfam ID:PF03876, PF00575
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases
Gene (Uniprot):PAS_chr2-2_0309
Chain IDs:J (auth: H)
Chain Length:106
Number of Molecules:1
Biological Source:Komagataella phaffii GS115
UniProt ID:C4R273 Pfam ID:PF03870
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase s
Gene (Uniprot):RPB9
Chain IDs:K (auth: I)
Chain Length:115
Number of Molecules:1
Biological Source:Komagataella phaffii GS115
UniProt ID:F2QPE6
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RNA polymerase subunit ABC10-
Gene (Uniprot):PAS_chr2-1_0223
Chain IDs:L (auth: J)
Chain Length:72
Number of Molecules:1
Biological Source:Komagataella phaffii GS115
UniProt ID:C4R009 Pfam ID:PF01194
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RNA polymerase II subunit B12
Gene (Uniprot):PAS_chr3_0244
Chain IDs:M (auth: K)
Chain Length:118
Number of Molecules:1
Biological Source:Komagataella phaffii GS115
UniProt ID:C4R3Z5 Pfam ID:PF13656
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RNA polymerase subunit ABC10-
Gene (Uniprot):RPC10
Chain IDs:N (auth: L)
Chain Length:72
Number of Molecules:1
Biological Source:Komagataella phaffii GS115
UniProt ID:F2QMI1
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (198-MER)
Chain IDs:A (auth: N)
Chain Length:198
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polyribonucleotide
Molecule:RNA (5'-R(P*CP*UP*UP*GP*GP*GP
Chain IDs:O (auth: P)
Chain Length:11
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (198-MER)
Chain IDs:B (auth: T)
Chain Length:198
Number of Molecules:1
Biological Source:synthetic construct
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone H3.1
Gene (Uniprot):H3C1, H3C2, H3C3, H3C4, H3C6, H3C7, H3C8, H3C10, H3C11, H3C12
Chain IDs:P (auth: e), R (auth: g)
Chain Length:139
Number of Molecules:2
Biological Source:Homo sapiens
UniProt ID:P68431 Pfam ID:PF00125
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone H4
Gene (Uniprot):H4C1, H4C2, H4C3, H4C4, H4C5, H4C6, H4C8, H4C9, H4C11, H4C12, H4C13, H4C14, H4C15, H4C16
Chain IDs:Q (auth: f), S (auth: h)
Chain Length:106
Number of Molecules:2
Biological Source:Homo sapiens
UniProt ID:P62805 Pfam ID:PF15511
Ligand Molecules
NA
Primary Citation
Structural basis of RNA polymerase II transcription on the histone H3-H4 octasome.
J. Biol. Chem. 302 111340 111340 (2026)
PMID: 41791711 DOI: 10.1016/j.jbc.2026.111340

Abstact

The histone H3-H4 octasome is a nucleosome-like particle in which two DNA gyres are wrapped around each histone (H3-H4)(2) tetramer disk, forming a clamshell-like configuration. In the present study, we performed in vitro RNA polymerase II (RNAPII) transcription assays with the H3-H4 octasome and found that RNAPII transcribed the H3-H4 octasome more efficiently than the nucleosome. RNAPII paused at only one position, superhelical location (SHL(-4)) in the H3-H4 octasome, in contrast to pausing at the SHL(-5), SHL(-2), and SHL(-1) positions in the nucleosome. Cryo-EM analysis revealed that two (H3-H4)(2) tetramer disks are retained when the RNAPII paused at the SHL(-4) position of the H3-H4 octasome. However, when RNAPII reached the SHL(-0.5) position, five base pairs before the dyad position of the H3-H4 octasome, the proximal (H3-H4)(2) tetramer was disassembled, but the distal (H3-H4)(2) tetramer still remained on the DNA. Therefore, RNAPII efficiently transcribes the H3-H4 octasome by stepwise (H3-H4)(2) tetramer disassembly.

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Primary Citation of related structures
9UJS
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