9II7 image
Deposition Date 2024-06-19
Release Date 2025-06-11
Last Version Date 2025-06-11
Entry Detail
PDB ID:
9II7
Keywords:
TRANSCRIPTION
Title:
RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome containing histone variant H2A.B
Biological Source:
Source Organism:
Komagataella phaffii (Taxon ID: 460519)
synthetic construct (Taxon ID: 32630)
Homo sapiens (Taxon ID: 9606)
Host Organism:
Escherichia coli
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.50 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
9II7 validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase subunit
Gene (Uniprot):PAS_chr3_0568
Chain IDs:A
Chain Length:1743
Number of Molecules:1
Biological Source:Komagataella phaffii
UniProt ID:C4R4Y0 Pfam ID:PF04997, PF00623, PF04983, PF05000, PF04998, PF04992, PF04990, PF05001
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase subunit beta
Gene (Uniprot):PAS_chr2-1_0125
Chain IDs:B
Chain Length:103
Number of Molecules:1
Biological Source:Komagataella phaffii
UniProt ID:C4QZQ7 Pfam ID:PF04563, PF04561, PF04565, PF04566, PF04567, PF00562, PF04560
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RNA polymerase II third largest subunit B44, part of central core
Gene (Uniprot):PAS_chr4_0344
Chain IDs:C
Chain Length:304
Number of Molecules:1
Biological Source:Komagataella phaffii
UniProt ID:C4R7L2 Pfam ID:PF01193, PF01000
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RNA polymerase II subunit B32
Gene (Uniprot):PAS_chr2-2_0104
Chain IDs:D
Chain Length:126
Number of Molecules:1
Biological Source:Komagataella phaffii
UniProt ID:C4R2U9 Pfam ID:PF03874
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases I, II, and III subunit RPABC1
Gene (Uniprot):PAS_chr3_0157
Chain IDs:E
Chain Length:214
Number of Molecules:1
Biological Source:Komagataella phaffii
UniProt ID:C4R3P8 Pfam ID:PF03871, PF01191
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III
Gene (Uniprot):PAS_chr2-2_0434
Chain IDs:F
Chain Length:103
Number of Molecules:1
Biological Source:Komagataella phaffii
UniProt ID:C4R1V1 Pfam ID:PF01192
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RNA polymerase II subunit
Gene (Uniprot):PAS_chr4_0906
Chain IDs:G
Chain Length:171
Number of Molecules:1
Biological Source:Komagataella phaffii
UniProt ID:C4R9A1 Pfam ID:PF03876, PF00575
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases I, II, and III subunit RPABC3
Gene (Uniprot):PAS_chr2-2_0309
Chain IDs:H
Chain Length:145
Number of Molecules:1
Biological Source:Komagataella phaffii
UniProt ID:C4R273 Pfam ID:PF03870
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase subunit
Gene (Uniprot):RPB9
Chain IDs:I
Chain Length:115
Number of Molecules:1
Biological Source:Komagataella phaffii
UniProt ID:F2QPE6 Pfam ID:PF02150, PF01096
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III
Gene (Uniprot):PAS_chr2-1_0223
Chain IDs:J
Chain Length:72
Number of Molecules:1
Biological Source:Komagataella phaffii
UniProt ID:C4R009 Pfam ID:PF01194
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RNA polymerase II subunit B12.5
Gene (Uniprot):PAS_chr3_0244
Chain IDs:K
Chain Length:118
Number of Molecules:1
Biological Source:Komagataella phaffii
UniProt ID:C4R3Z5 Pfam ID:PF13656
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RNA polymerase subunit ABC10-alpha
Gene (Uniprot):RPC10
Chain IDs:L
Chain Length:72
Number of Molecules:1
Biological Source:Komagataella phaffii
UniProt ID:F2QMI1 Pfam ID:PF03604
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Transcription elongation factor 1 homolog
Gene (Uniprot):PAS_c121_0006
Chain IDs:M
Chain Length:110
Number of Molecules:1
Biological Source:Komagataella phaffii
UniProt ID:C4QZ45 Pfam ID:PF05129
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (198-MER)
Chain IDs:N
Chain Length:198
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polyribonucleotide
Molecule:RNA (5'-R(P*CP*CP*CP*GP*GP*UP*GP*UP*CP*UP*UP*GP*GP*GP*UP*G)-3')
Chain IDs:O (auth: P)
Chain Length:16
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (198-MER)
Chain IDs:P (auth: T)
Chain Length:198
Number of Molecules:1
Biological Source:synthetic construct
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Transcription elongation factor SPT4
Gene (Uniprot):SPT4
Chain IDs:Q (auth: V)
Chain Length:114
Number of Molecules:1
Biological Source:Komagataella phaffii
UniProt ID:F2QTA2 Pfam ID:PF06093
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Transcription elongation factor SPT5
Gene (Uniprot):PAS_chr3_1136
Chain IDs:R (auth: W)
Chain Length:908
Number of Molecules:1
Biological Source:Komagataella phaffii
UniProt ID:C4R370 Pfam ID:PF11942, PF03439, PF00467, PF12815
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone H3.3
Gene (Uniprot):H3-3A, H3-3B
Chain IDs:S (auth: a), W (auth: e)
Chain Length:1743
Number of Molecules:2
Biological Source:Homo sapiens
UniProt ID:P84243 Pfam ID:PF00125
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:T (auth: b), X (auth: f)
Chain Length:103
Number of Molecules:2
Biological Source:Homo sapiens
UniProt ID:P62805 Pfam ID:PF15511
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone H2A-Bbd type 2/3
Gene (Uniprot):H2AB2, H2AB3
Chain IDs:U (auth: c)
Chain Length:304
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P0C5Z0
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone H2B type 1-J
Gene (Uniprot):H2BC11
Chain IDs:V (auth: d)
Chain Length:126
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P06899 Pfam ID:PF00125
Ligand Molecules
MG
ZN
Primary Citation
Structural basis of RNAPII transcription on the nucleosome containing histone variant H2A.B.
Embo J. ? ? ? (2025)
PMID: 40447801 DOI: 10.1038/s44318-025-00473-6

Abstact

H2A.B is a distant histone H2A variant associated with actively transcribed regions of the genome, suggesting its positive role in promoting transcription. In the present study, we demonstrate that the RNA polymerase II elongation complex (EC) transcribes the nucleosome containing H2A.B more efficiently than that with canonical H2A in vitro. Our cryo-electron microscopy analysis of the H2A.B nucleosome during transcription revealed that the proximal H2A.B-H2B dimer is released from the nucleosome as the EC transcribes the proximal half of the nucleosomal DNA. This dissociation, which is not observed in the canonical H2A nucleosome, likely enhances the EC elongation efficiency in the H2A.B nucleosome. Mutational analyses suggested that the unique short C-terminal region of H2A.B alone enhances EC elongation efficiency when substituted for its counterpart in canonical H2A. Additionally, other regions of H2A.B contribute to this enhancement. These structural and biochemical findings provide new insights into the role of H2A.B in regulating gene expression.

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Disease

Primary Citation of related structures
9II7