7XT7 image
Deposition Date 2022-05-16
Release Date 2022-10-12
Last Version Date 2024-07-03
Entry Detail
PDB ID:
7XT7
Keywords:
TRANSCRIPTION
Title:
RNA polymerase II elongation complex transcribing a nucleosome (EC49B)
Biological Source:
Source Organism:
Komagataella phaffii (Taxon ID: 460519)
Homo sapiens (Taxon ID: 9606)
synthetic construct (Taxon ID: 32630)
Host Organism:
Escherichia coli
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
4.20 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
7XT7 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:1227
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:186
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:155
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:133
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:129
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:1008
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:531
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:1503
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:417
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polyribonucleotide
Molecule:RNA (5'-R(P*GP*AP*CP*CP*CP*GP*GP*GP*UP*GP*UP*CP*UP*UP*CP*CP*CP*CP*A)-3')
Chain IDs:O (auth: P)
Chain Length:19
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):PAS_chr2-1_0350
Chain IDs:Q (auth: V)
Chain Length:108
Number of Molecules:1
Biological Source:Komagataella phaffii
UniProt ID:C4R0E6 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:911
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:Z (auth: a), DA (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:AA (auth: b), EA (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:BA (auth: c), FA (auth: g)
Chain Length:304
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:CA (auth: d), GA (auth: h)
Chain Length:186
Number of Molecules:2
Biological Source:Homo sapiens
UniProt ID:P06899 Pfam ID:PF00125
Protein Blast
Polymer Type:polypeptide(L)
Molecule:FACT complex subunit
Gene (Uniprot):SPT16
Chain IDs:HA (auth: j)
Chain Length:1008
Number of Molecules:1
Biological Source:Komagataella phaffii
UniProt ID:F2QPX0 Pfam ID:PF14826, PF00557, PF08644, PF08512
Protein Blast
Polymer Type:polypeptide(L)
Molecule:FACT complex subunit POB3
Gene (Uniprot):POB3
Chain IDs:IA (auth: k)
Chain Length:531
Number of Molecules:1
Biological Source:Komagataella phaffii
UniProt ID:F2QNN8 Pfam ID:PF17292, PF03531, PF21103, PF08512
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Transcription elongation factor Spt6
Gene (Uniprot):PAS_chr4_0308
Chain IDs:S (auth: m)
Chain Length:1503
Number of Molecules:1
Biological Source:Komagataella phaffii
UniProt ID:C4R7H2 Pfam ID:PF14632, PF14641, PF22706, PF14639, PF14635, PF21710, PF14633
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Protein that interacts with Spt6p and copurifies with Spt5p and RNA polymerase II
Gene (Uniprot):PAS_chr4_0349
Chain IDs:T (auth: n)
Chain Length:417
Number of Molecules:1
Biological Source:Komagataella phaffii
UniProt ID:C4R7L8 Pfam ID:PF08711
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Component of the Paf1p complex
Gene (Uniprot):PAS_chr3_1035
Chain IDs:U (auth: q)
Chain Length:1084
Number of Molecules:1
Biological Source:Komagataella phaffii
UniProt ID:C4R6B2 Pfam ID:PF13432
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RNAPII-associated chromatin remodeling Paf1 complex subunit
Gene (Uniprot):RTF1
Chain IDs:V (auth: r)
Chain Length:544
Number of Molecules:1
Biological Source:Komagataella phaffii
UniProt ID:F2QQ42 Pfam ID:PF03126
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Leo1
Gene (Uniprot):PAS_chr3_1154
Chain IDs:W (auth: u)
Chain Length:459
Number of Molecules:1
Biological Source:Komagataella phaffii
UniProt ID:C4R3K1 Pfam ID:PF04004
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RNAP II-associated protein
Gene (Uniprot):PAS_chr4_0902
Chain IDs:X (auth: v)
Chain Length:108
Number of Molecules:1
Biological Source:Komagataella phaffii
UniProt ID:C4R997 Pfam ID:PF03985
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Constituent of Paf1 complex with RNA polymerase II, Paf1p, Hpr1p, Ctr9, Leo1, Rtf1 and Ccr4p
Gene (Uniprot):PAS_chr2-1_0674
Chain IDs:Y (auth: x)
Chain Length:395
Number of Molecules:1
Biological Source:Komagataella phaffii
UniProt ID:C4R1E6 Pfam ID:PF05179
Ligand Molecules
MG
ZN
Primary Citation
Structural basis of nucleosome disassembly and reassembly by RNAPII elongation complex with FACT.
Science 377 eabp9466 eabp9466 (2022)
PMID: 35981082 DOI: 10.1126/science.abp9466

Abstact

During gene transcription, RNA polymerase II (RNAPII) traverses nucleosomes in chromatin, but the mechanism has remained elusive. Using cryo-electron microscopy, we obtained structures of the RNAPII elongation complex (EC) passing through a nucleosome in the presence of the transcription elongation factors Spt6, Spn1, Elf1, Spt4/5, and Paf1C and the histone chaperone FACT (facilitates chromatin transcription). The structures show snapshots of EC progression on DNA mediating downstream nucleosome disassembly, followed by its reassembly upstream of the EC, which is facilitated by FACT. FACT dynamically adapts to successively occurring subnucleosome intermediates, forming an interface with the EC. Spt6, Spt4/5, and Paf1C form a "cradle" at the EC DNA-exit site and support the upstream nucleosome reassembly. These structures explain the mechanism by which the EC traverses nucleosomes while maintaining the chromatin structure and epigenetic information.

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Disease

Primary Citation of related structures
7XT7