7UND image
Deposition Date 2022-04-10
Release Date 2022-10-19
Last Version Date 2024-10-23
Entry Detail
PDB ID:
7UND
Keywords:
TRANSCRIPTION
Title:
Pol II-DSIF-SPT6-PAF1c-TFIIS-nucleosome complex (stalled at +38)
Biological Source:
Source Organism(s):
Homo sapiens (Taxon ID: 9606)
Xenopus laevis (Taxon ID: 8355)
synthetic construct (Taxon ID: 32630)
Sus scrofa (Taxon ID: 9823)
Expression System(s):
Trichoplusia ni, Escherichia coli
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.00 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
7UND validation report
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase subunit
Chain IDs:A
Chain Length:136
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A7M4DUC2 Pfam ID:PF00623, PF04998, PF05001, PF04997, PF05000, PF04990, PF04983, PF04992
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase subunit beta
Chain IDs:B
Chain Length:103
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A4X1TVZ5 Pfam ID:PF04565, PF00562, PF04561, PF04567, PF04563, PF04566, PF04560
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit RPB3
Chain IDs:C
Chain Length:130
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A481DF93 Pfam ID:PF01000, PF01193
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RPOL4c domain-containing protein
Chain IDs:D
Chain Length:184
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A8D1GCS3 Pfam ID:PF03874
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit E
Gene (Uniprot):POLR2E
Chain IDs:E
Chain Length:210
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A4X1VTX4 Pfam ID:PF01191, PF03871
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases I, II, and III subunit RPABC2
Gene (Uniprot):POLR2F
Chain IDs:F
Chain Length:127
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A4X1VEK9 Pfam ID:PF01192
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit RPB7
Gene (Uniprot):POLR2G
Chain IDs:G
Chain Length:172
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A4X1VKG7 Pfam ID:PF00575, PF03876
Polymer Type:polypeptide(L)
Molecule:RPB8
Chain IDs:H
Chain Length:123
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Molecule:RPB9
Chain IDs:I
Chain Length:125
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Molecule:RPB10
Chain IDs:J
Chain Length:67
Number of Molecules:1
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Molecule:RPB11
Chain IDs:K
Chain Length:117
Number of Molecules:1
Biological Source:Sus scrofa
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RNA polymerase II subunit K
Gene (Uniprot):POLR2K
Chain IDs:L
Chain Length:58
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A4X1TRS6 Pfam ID:PF03604
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Transcription elongation factor SPT6
Gene (Uniprot):SUPT6H
Chain IDs:M
Chain Length:1729
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q7KZ85 Pfam ID:PF14641, PF14635, PF14633, PF14632, PF14639, PF00575, PF22706, PF17674
Polymer Type:polydeoxyribonucleotide
Molecule:Non-template DNA
Chain IDs:N
Chain Length:209
Number of Molecules:1
Biological Source:synthetic construct
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Transcription elongation factor A protein 1
Gene (Uniprot):TCEA1
Chain IDs:O
Chain Length:304
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P23193 Pfam ID:PF01096, PF07500, PF08711
Polymer Type:polyribonucleotide
Molecule:RNA
Chain IDs:P
Chain Length:18
Number of Molecules:1
Biological Source:synthetic construct
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RNA polymerase-associated protein CTR9 homolog
Gene (Uniprot):CTR9
Chain IDs:Q
Chain Length:1179
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q6PD62 Pfam ID:PF13181, PF13374
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RNA polymerase-associated protein RTF1 homolog
Gene (Uniprot):RTF1
Chain IDs:R
Chain Length:713
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q92541 Pfam ID:PF03126
Polymer Type:polydeoxyribonucleotide
Molecule:Template DNA
Chain IDs:S (auth: T)
Chain Length:215
Number of Molecules:1
Biological Source:synthetic construct
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RNA polymerase-associated protein LEO1
Gene (Uniprot):LEO1
Chain IDs:T (auth: U)
Chain Length:666
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q8WVC0 Pfam ID:PF04004
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RNA polymerase II-associated factor 1 homolog
Gene (Uniprot):PAF1
Chain IDs:U (auth: V)
Chain Length:531
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q8N7H5 Pfam ID:PF03985
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:WDR61
Gene (Uniprot):SKIC8
Chain IDs:V (auth: W)
Chain Length:305
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9GZS3 Pfam ID:PF00400
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Parafibromin
Gene (Uniprot):CDC73
Chain IDs:W (auth: X)
Chain Length:531
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q6P1J9 Pfam ID:PF05179, PF16050
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Transcription elongation factor SPT4
Gene (Uniprot):SUPT4H1
Chain IDs:X (auth: Y)
Chain Length:117
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P63272 Pfam ID:PF06093
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Transcription elongation factor SPT5
Gene (Uniprot):SUPT5H
Chain IDs:Y (auth: Z)
Chain Length:1087
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:O00267 Pfam ID:PF00467, PF03439, PF11942, PF23037, PF23288, PF23287
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone H3.2
Mutagens:G102A
Chain IDs:Z (auth: a), DA (auth: e)
Chain Length:136
Number of Molecules:2
Biological Source:Xenopus laevis
UniProt ID:P84233 Pfam ID:PF00125
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone H4
Chain IDs:AA (auth: b), EA (auth: f)
Chain Length:103
Number of Molecules:2
Biological Source:Xenopus laevis
UniProt ID:P62799 Pfam ID:PF15511
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone H2A
Gene (Uniprot):LOC494591
Chain IDs:BA (auth: c), FA (auth: g)
Chain Length:130
Number of Molecules:2
Biological Source:Xenopus laevis
UniProt ID:Q6AZJ8 Pfam ID:PF16211, PF00125
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone H2B 1.1
Mutagens:S29T
Chain IDs:CA (auth: d), GA (auth: h)
Chain Length:184
Number of Molecules:2
Biological Source:Xenopus laevis
UniProt ID:P02281 Pfam ID:PF00125
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
SEP A SER modified residue
TPO A THR modified residue
Ligand Molecules
MG
ZN
Primary Citation
Structural basis of nucleosome retention during transcription elongation.
Science 376 1313 1316 (2022)
PMID: 35709268 DOI: 10.1126/science.abo3851

Abstact

In eukaryotes, RNA polymerase (Pol) II transcribes chromatin and must move past nucleosomes, often resulting in nucleosome displacement. How Pol II unwraps the DNA from nucleosomes to allow transcription and how DNA rewraps to retain nucleosomes has been unclear. Here, we report the 3.0-angstrom cryo-electron microscopy structure of a mammalian Pol II-DSIF-SPT6-PAF1c-TFIIS-nucleosome complex stalled 54 base pairs within the nucleosome. The structure provides a mechanistic basis for nucleosome retention during transcription elongation where upstream DNA emerging from the Pol II cleft has rewrapped the proximal side of the nucleosome. The structure uncovers a direct role for Pol II and transcription elongation factors in nucleosome retention and explains how nucleosomes are retained to prevent the disruption of chromatin structure across actively transcribed genes.

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Disease

Primary Citation of related structures
7UND
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