9WMV image
Deposition Date 2025-09-03
Release Date 2025-12-24
Last Version Date 2025-12-24
Entry Detail
PDB ID:
9WMV
Keywords:
TRANSCRIPTION
Title:
Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp130, type B)
Biological Source:
Source Organism:
Komagataella phaffii GS115 (Taxon ID: 644223)
Homo sapiens (Taxon ID: 9606)
synthetic construct (Taxon ID: 32630)
Host Organism:
Escherichia coli
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
4.66 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
9WMV validation report
Macromolecular Entities
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 GS115
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:1227
Number of Molecules:1
Biological Source:Komagataella phaffii GS115
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 GS115
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:129
Number of Molecules:1
Biological Source:Komagataella phaffii GS115
UniProt ID:C4R2U9 Pfam ID:PF03874
Structures with similar UniProt ID
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:139
Number of Molecules:1
Biological Source:Komagataella phaffii GS115
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 GS115
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 GS115
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:145
Number of Molecules:1
Biological Source:Komagataella phaffii GS115
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 GS115
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 GS115
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 GS115
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 GS115
UniProt ID:F2QMI1 Pfam ID:PF03604
Structures with similar UniProt ID
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 GS115
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*GP*UP*CP*CP*UP*UP*UP*UP*GP*UP*GP*CP*GP*GP*CP*CP*UP*CP*G)-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
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Transcription elongation factor SPT4
Gene (Uniprot):PAS_chr2-1_0350
Chain IDs:Q (auth: V)
Chain Length:396
Number of Molecules:1
Biological Source:Komagataella phaffii GS115
UniProt ID:C4R0E6 Pfam ID:PF06093
Structures with similar UniProt ID
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 GS115
UniProt ID:C4R370 Pfam ID:PF11942, PF03439, PF00467, PF12815
Structures with similar UniProt ID
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
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:T (auth: b), X (auth: f)
Chain Length:1227
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:U (auth: c), Y (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:V (auth: d), Z (auth: h)
Chain Length:129
Number of Molecules:2
Biological Source:Homo sapiens
UniProt ID:P06899 Pfam ID:PF00125
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Transcription elongation factor Spt6
Gene (Uniprot):PAS_chr4_0308
Chain IDs:AA (auth: m)
Chain Length:1503
Number of Molecules:1
Biological Source:Komagataella phaffii GS115
UniProt ID:C4R7H2 Pfam ID:PF14632, PF14641, PF22706, PF14639, PF14635, PF21710, PF14633
Structures with similar UniProt ID
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:BA (auth: n)
Chain Length:198
Number of Molecules:1
Biological Source:Komagataella phaffii GS115
UniProt ID:C4R7L8 Pfam ID:PF08711
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Component of the Paf1p complex
Gene (Uniprot):PAS_chr3_1035
Chain IDs:CA (auth: q)
Chain Length:1084
Number of Molecules:1
Biological Source:Komagataella phaffii GS115
UniProt ID:C4R6B2 Pfam ID:PF13432
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RNAPII-associated chromatin remodeling Paf1 complex subunit
Gene (Uniprot):RTF1
Chain IDs:DA (auth: r)
Chain Length:544
Number of Molecules:1
Biological Source:Komagataella phaffii GS115
UniProt ID:F2QQ42 Pfam ID:PF03126
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone-lysine N-methyltransferase, H3 lysine-36 specific
Gene (Uniprot):PAS_chr1-4_0287
Chain IDs:EA (auth: s)
Chain Length:725
Number of Molecules:1
Biological Source:Komagataella phaffii GS115
UniProt ID:C4QY01 Pfam ID:PF17907, PF00856, PF00397, PF08236
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Leo1
Gene (Uniprot):PAS_chr3_1154
Chain IDs:FA (auth: u)
Chain Length:459
Number of Molecules:1
Biological Source:Komagataella phaffii GS115
UniProt ID:C4R3K1 Pfam ID:PF04004
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RNAP II-associated protein
Gene (Uniprot):PAS_chr4_0902
Chain IDs:GA (auth: v)
Chain Length:396
Number of Molecules:1
Biological Source:Komagataella phaffii GS115
UniProt ID:C4R997 Pfam ID:PF03985
Structures with similar UniProt ID
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:HA (auth: x)
Chain Length:395
Number of Molecules:1
Biological Source:Komagataella phaffii GS115
UniProt ID:C4R1E6 Pfam ID:PF05179
Ligand Molecules
MG
SAH
ZN
Primary Citation
Structural basis of transcription-coupled H3K36 trimethylation by Set2 in coordination with FACT
To Be Published ? ? ? (?)
Primary Citation of related structures
9WMV
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