ISDA: 9UXW

Deposition Date 2025-05-14

Release Date 2026-07-01

Last Version Date 2026-07-29

Entry Detail

PDB ID:

9UXW

Keywords:

TRANSCRIPTION

Title:

RNA polymerase II elongation complex stalled at SHL(-0.5) in the hexasome of the overlapping dinucleosome

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, Escherichia coli bl21(de3)

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

3.74 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase s
Chain IDs:A
Chain Length:1743
Number of Molecules:1
Biological Source:Komagataella phaffii GS115

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase s
Chain IDs:B
Chain Length:1227
Number of Molecules:1
Biological Source:Komagataella phaffii GS115

Polymer Type:polypeptide(L)
Molecule:RNA polymerase II third large
Chain IDs:C
Chain Length:133
Number of Molecules:1
Biological Source:Komagataella phaffii GS115

Polymer Type:polypeptide(L)
Molecule:RNA polymerase II subunit B32
Chain IDs:D
Chain Length:186
Number of Molecules:1
Biological Source:Komagataella phaffii GS115

Polymer Type:polypeptide(L)
Molecule:RNA polymerase subunit ABC27,
Chain IDs:E
Chain Length:214
Number of Molecules:1
Biological Source:Komagataella phaffii GS115

Polymer Type:polypeptide(L)
Molecule:RNA polymerase subunit ABC23,
Chain IDs:F
Chain Length:106
Number of Molecules:1
Biological Source:Komagataella phaffii GS115

Polymer Type:polypeptide(L)
Molecule:RNA polymerase II subunit
Chain IDs:G
Chain Length:171
Number of Molecules:1
Biological Source:Komagataella phaffii GS115

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases
Chain IDs:H
Chain Length:145
Number of Molecules:1
Biological Source:Komagataella phaffii GS115

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase s
Chain IDs:I
Chain Length:115
Number of Molecules:1
Biological Source:Komagataella phaffii GS115

Polymer Type:polypeptide(L)
Molecule:RNA polymerase subunit ABC10-
Chain IDs:J
Chain Length:72
Number of Molecules:1
Biological Source:Komagataella phaffii GS115

Polymer Type:polypeptide(L)
Molecule:RNA polymerase II subunit B12
Chain IDs:K
Chain Length:118
Number of Molecules:1
Biological Source:Komagataella phaffii GS115

Polymer Type:polypeptide(L)
Molecule:RNA polymerase subunit ABC10-
Chain IDs:L
Chain Length:106
Number of Molecules:1
Biological Source:Komagataella phaffii GS115

Polymer Type:polydeoxyribonucleotide
Molecule:DNA (254-MER)
Chain IDs:CA (auth: N)
Chain Length:254
Number of Molecules:1
Biological Source:synthetic construct

Polymer Type:polyribonucleotide
Molecule:RNA (5'-R(P*GP*UP*CP*GP*CP*UP
Chain IDs:M (auth: P)
Chain Length:14
Number of Molecules:1
Biological Source:synthetic construct

Polymer Type:polydeoxyribonucleotide
Molecule:DNA (254-MER)
Chain IDs:N (auth: T)
Chain Length:254
Number of Molecules:1
Biological Source:synthetic construct

Polymer Type:polypeptide(L)
Molecule:Histone H3.3
Chain IDs:O (auth: a), S (auth: e), W (auth: k), Y (auth: m)
Chain Length:139
Number of Molecules:4
Biological Source:Homo sapiens

Polymer Type:polypeptide(L)
Molecule:Histone H4
Chain IDs:P (auth: b), T (auth: f), X (auth: l), Z (auth: n)
Chain Length:1227
Number of Molecules:4
Biological Source:Homo sapiens

Polymer Type:polypeptide(L)
Molecule:Histone H2A type 1-B/E
Chain IDs:Q (auth: c), U (auth: g), AA (auth: o)
Chain Length:171
Number of Molecules:3
Biological Source:Homo sapiens

Polymer Type:polypeptide(L)
Molecule:Histone H2B type 1-J
Chain IDs:R (auth: d), V (auth: h), BA (auth: p)
Chain Length:145
Number of Molecules:3
Biological Source:Homo sapiens

Ligand Molecules

Primary Citation

Structural basis of asymmetric transcription through a composite nucleosome formed by a hexasome and an octasome.

Chen, Z, Ho, C.H, Tanaka, H, Kujirai, T, Ogasawara, M, Ehara, H, Sekine, S.I, Takizawa, Y, Kurumizaka, H.Show

Nat.Struct.Mol.Biol. 33 1097 1104 (2026)

PMID: 42350665 DOI: 10.1038/s41594-026-01837-0

Primary Citation of related structures

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