6INQ image
Deposition Date 2018-10-26
Release Date 2019-04-03
Last Version Date 2024-03-27
Entry Detail
PDB ID:
6INQ
Keywords:
TRANSCRIPTION/RNA/DNA
Title:
RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA (+1 position)
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
synthetic construct (Taxon ID: 32630)
Komagataella phaffii (strain GS115 / ATCC 20864) (Taxon ID: 644223)
Host Organism:
Escherichia coli
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
6.90 Å
Aggregation State:
PARTICLE
Reconstruction Method:
CRYSTALLOGRAPHY
6INQ validation report
Macromolecular Entities
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (31-MER)
Chain IDs:X (auth: 0)
Chain Length:31
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (31-MER)
Chain IDs:Y (auth: 1)
Chain Length:31
Number of Molecules:1
Biological Source:synthetic construct
Structures with similar UniProt ID
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 (strain GS115 / ATCC 20864)
UniProt ID:C4R4Y0 Pfam ID:PF04997, PF00623, PF04983, PF05000, PF04998, PF04992, PF04990, PF05001
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase subunit beta
Gene (Uniprot):PAS_chr2-1_0125
Chain IDs:B
Chain Length:106
Number of Molecules:1
Biological Source:Komagataella phaffii (strain GS115 / ATCC 20864)
UniProt ID:C4QZQ7 Pfam ID:PF04563, PF04561, PF04565, PF04566, PF04567, PF00562, PF04560
Structures with similar UniProt ID
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 (strain GS115 / ATCC 20864)
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:D
Chain Length:186
Number of Molecules:1
Biological Source:Komagataella phaffii (strain GS115 / ATCC 20864)
UniProt ID:C4R2U9 Pfam ID:PF03874
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III
Gene (Uniprot):PAS_chr3_0157
Chain IDs:E
Chain Length:139
Number of Molecules:1
Biological Source:Komagataella phaffii (strain GS115 / ATCC 20864)
UniProt ID:C4R3P8 Pfam ID:PF03871, PF01191
Structures with similar UniProt ID
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:155
Number of Molecules:1
Biological Source:Komagataella phaffii (strain GS115 / ATCC 20864)
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:G
Chain Length:171
Number of Molecules:1
Biological Source:Komagataella phaffii (strain GS115 / ATCC 20864)
UniProt ID:C4R9A1 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):PAS_chr2-2_0309
Chain IDs:H
Chain Length:129
Number of Molecules:1
Biological Source:Komagataella phaffii (strain GS115 / ATCC 20864)
UniProt ID:C4R273 Pfam ID:PF03870
Structures with similar UniProt ID
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 (strain GS115 / ATCC 20864)
UniProt ID:F2QPE6 Pfam ID:PF02150, PF01096
Structures with similar UniProt ID
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 (strain GS115 / ATCC 20864)
UniProt ID:C4R009 Pfam ID:PF01194
Structures with similar UniProt ID
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 (strain GS115 / ATCC 20864)
UniProt ID:C4R3Z5 Pfam ID:PF13656
Structures with similar UniProt ID
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 (strain GS115 / ATCC 20864)
UniProt ID:F2QMI1 Pfam ID:PF03604
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (198-MER)
Chain IDs:O (auth: N)
Chain Length:198
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polyribonucleotide
Molecule:RNA (5'-R(P*GP*UP*GP*UP*CP*UP*UP*GP*GP*GP*U)-3')
Chain IDs:M (auth: P)
Chain Length:11
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (198-MER)
Chain IDs:N (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 H3.3
Gene (Uniprot):H3-3A, H3-3B
Chain IDs:P (auth: a), T (auth: e)
Chain Length:1743
Number of Molecules:2
Biological Source:Homo sapiens
UniProt ID:P84243 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: b), U (auth: f)
Chain Length:106
Number of Molecules:2
Biological Source:Homo sapiens
UniProt ID:P62805 Pfam ID:PF15511
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone H2A type 1-B/E
Gene (Uniprot):H2AC4, H2AC8
Chain IDs:R (auth: c), V (auth: g)
Chain Length:304
Number of Molecules:2
Biological Source:Homo sapiens
UniProt ID:P04908 Pfam ID:PF00125, PF16211
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone H2B type 1-J
Gene (Uniprot):H2BC11
Chain IDs:S (auth: d), W (auth: h)
Chain Length:186
Number of Molecules:2
Biological Source:Homo sapiens
UniProt ID:P06899 Pfam ID:PF00125
Ligand Molecules
MG
ZN
Primary Citation
Structural basis of the nucleosome transition during RNA polymerase II passage.
Science 362 595 598 (2018)
PMID: 30287617 DOI: 10.1126/science.aau9904

Abstact

Genomic DNA forms chromatin, in which the nucleosome is the repeating unit. The mechanism by which RNA polymerase II (RNAPII) transcribes the nucleosomal DNA remains unclear. Here we report the cryo-electron microscopy structures of RNAPII-nucleosome complexes in which RNAPII pauses at the superhelical locations SHL(-6), SHL(-5), SHL(-2), and SHL(-1) of the nucleosome. RNAPII pauses at the major histone-DNA contact sites, and the nucleosome interactions with the RNAPII subunits stabilize the pause. These structures reveal snapshots of nucleosomal transcription, in which RNAPII gradually tears DNA from the histone surface while preserving the histone octamer. The nucleosomes in the SHL(-1) complexes are bound to a "foreign" DNA segment, which might explain the histone transfer mechanism. These results provide the foundations for understanding chromatin transcription and epigenetic regulation.

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Primary Citation of related structures
6INQ
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