6J4Z image
Deposition Date 2019-01-10
Release Date 2019-02-20
Last Version Date 2024-03-27
Entry Detail
PDB ID:
6J4Z
Keywords:
TRANSCRIPTION/RNA/DNA
Title:
RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome
Biological Source:
Source Organism:
Komagataella phaffii (strain GS115 / ATCC 20864) (Taxon ID: 644223)
Komagataella pastoris (Taxon ID: 4922)
Homo sapiens (Taxon ID: 9606)
synthetic construct (Taxon ID: 32630)
Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1) (Taxon ID: 981350)
Host Organism:
Escherichia coli
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
4.10 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
6J4Z validation report
Macromolecular Entities
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (42-MER)
Chain IDs:Z (auth: 0)
Chain Length:42
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (42-MER)
Chain IDs:AA (auth: 1)
Chain Length:42
Number of Molecules:1
Biological Source:synthetic construct
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase subunit beta
Gene (Uniprot):PAS_chr2-1_0125
Chain IDs:B
Chain Length:1227
Number of Molecules:1
Biological Source:Komagataella phaffii (strain GS115 / ATCC 20864)
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:133
Number of Molecules:1
Biological Source:Komagataella phaffii (strain GS115 / ATCC 20864)
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:129
Number of Molecules:1
Biological Source:Komagataella phaffii (strain GS115 / ATCC 20864)
UniProt ID:C4R2U9 Pfam ID:PF03874
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
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:106
Number of Molecules:1
Biological Source:Komagataella phaffii (strain GS115 / ATCC 20864)
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 (strain GS115 / ATCC 20864)
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 (strain GS115 / ATCC 20864)
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 (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1)
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 (strain GS115 / ATCC 20864)
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 (strain GS115 / ATCC 20864)
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 (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1)
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*CP*CP*UP*GP*GP*UP*GP*UP*CP*UP*UP*GP*GP*GP*U)-3')
Chain IDs:M (auth: P)
Chain Length:16
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Transcription elongation factor SPT4
Gene (Uniprot):PAS_chr2-1_0350
Chain IDs:P (auth: V)
Chain Length:108
Number of Molecules:1
Biological Source:Komagataella phaffii (strain GS115 / ATCC 20864)
UniProt ID:C4R0E6 Pfam ID:PF06093
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Spt5
Gene (Uniprot):PAS_chr3_1136
Chain IDs:Q (auth: W)
Chain Length:911
Number of Molecules:1
Biological Source:Komagataella pastoris
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:R (auth: a), V (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:S (auth: b), W (auth: f)
Chain Length:1227
Number of Molecules:2
Biological Source:Homo sapiens
UniProt ID:P62805 Pfam ID:PF15511
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone H2A type 1-B/E
Gene (Uniprot):H2AC4, H2AC8
Chain IDs:T (auth: c), X (auth: g)
Chain Length:133
Number of Molecules:2
Biological Source:Homo sapiens
UniProt ID:P04908 Pfam ID:PF00125, PF16211
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone H2B type 1-J
Gene (Uniprot):H2BC11
Chain IDs:U (auth: d), Y (auth: h)
Chain Length:129
Number of Molecules:2
Biological Source:Homo sapiens
UniProt ID:P06899 Pfam ID:PF00125
Ligand Molecules
MG
ZN
Primary Citation
Structural insight into nucleosome transcription by RNA polymerase II with elongation factors.
Science 363 744 747 (2019)
PMID: 30733384 DOI: 10.1126/science.aav8912

Abstact

RNA polymerase II (RNAPII) transcribes chromosomal DNA that contains multiple nucleosomes. The nucleosome forms transcriptional barriers, and nucleosomal transcription requires several additional factors in vivo. We demonstrate that the transcription elongation factors Elf1 and Spt4/5 cooperatively lower the barriers and increase the RNAPII processivity in the nucleosome. The cryo-electron microscopy structures of the nucleosome-transcribing RNAPII elongation complexes (ECs) reveal that Elf1 and Spt4/5 reshape the EC downstream edge and intervene between RNAPII and the nucleosome. They facilitate RNAPII progression through superhelical location SHL(-1) by adjusting the nucleosome in favor of the forward progression. They suppress pausing at SHL(-5) by preventing the stable RNAPII-nucleosome interaction. Thus, the EC overcomes the nucleosomal barriers while providing a platform for various chromatin functions.

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Primary Citation of related structures
6J4Z