9WMS | pdb_00009wms

Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp115, type B)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history. 


Literature

Structural basis of transcription-coupled H3K36 trimethylation by Set2 in coordination with FACT

Kujirai, T., Ehara, H.

To be published.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit1,743Komagataella phaffii GS115Mutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for C4R4Y0 (Komagataella phaffii (strain GS115 / ATCC 20864))
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta1,227Komagataella phaffii GS115Mutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for C4QZQ7 (Komagataella phaffii (strain GS115 / ATCC 20864))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase II third largest subunit B44, part of central core304Komagataella phaffii GS115Mutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase II subunit B32186Komagataella phaffii GS115Mutation(s): 0 
UniProt
Find proteins for C4R2U9 (Komagataella phaffii (strain GS115 / ATCC 20864))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC1214Komagataella phaffii GS115Mutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III155Komagataella phaffii GS115Mutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase II subunit171Komagataella phaffii GS115Mutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC3145Komagataella phaffii GS115Mutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit115Komagataella phaffii GS115Mutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III72Komagataella phaffii GS115Mutation(s): 0 
UniProt
Find proteins for C4R009 (Komagataella phaffii (strain GS115 / ATCC 20864))
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase II subunit B12.5118Komagataella phaffii GS115Mutation(s): 0 
UniProt
Find proteins for C4R3Z5 (Komagataella phaffii (strain GS115 / ATCC 20864))
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase subunit ABC10-alpha72Komagataella phaffii GS115Mutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription elongation factor 1 homolog113Komagataella phaffii GS115Mutation(s): 0 
Gene Names: PAS_c121_0006
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription elongation factor SPT4Q [auth V]108Komagataella phaffii GS115Mutation(s): 0 
Gene Names: PAS_chr2-1_0350
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription elongation factor SPT5R [auth W]911Komagataella phaffii GS115Mutation(s): 0 
Gene Names: PAS_chr3_1136
UniProt
Find proteins for C4R370 (Komagataella phaffii (strain GS115 / ATCC 20864))
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription elongation factor Spt6S [auth m]1,503Komagataella phaffii GS115Mutation(s): 0 
Gene Names: PAS_chr4_0308
UniProt
Find proteins for C4R7H2 (Komagataella phaffii (strain GS115 / ATCC 20864))
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Protein that interacts with Spt6p and copurifies with Spt5p and RNA polymerase IIT [auth n]417Komagataella phaffii GS115Mutation(s): 0 
Gene Names: PAS_chr4_0349
UniProt
Find proteins for C4R7L8 (Komagataella phaffii (strain GS115 / ATCC 20864))
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Component of the Paf1p complexU [auth q]1,084Komagataella phaffii GS115Mutation(s): 0 
Gene Names: PAS_chr3_1035
UniProt
Find proteins for C4R6B2 (Komagataella phaffii (strain GS115 / ATCC 20864))
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
RNAPII-associated chromatin remodeling Paf1 complex subunitV [auth r]544Komagataella phaffii GS115Mutation(s): 0 
Gene Names: RTF1, PP7435_Chr1-1405
UniProt
Find proteins for F2QQ42 (Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1))
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase, H3 lysine-36 specificW [auth s]725Komagataella phaffii GS115Mutation(s): 0 
Gene Names: PAS_chr1-4_0287
EC: 2.1.1.359
UniProt
Find proteins for C4QY01 (Komagataella phaffii (strain GS115 / ATCC 20864))
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Leo1X [auth u]459Komagataella phaffii GS115Mutation(s): 0 
Gene Names: PAS_chr3_1154
UniProt
Find proteins for C4R3K1 (Komagataella phaffii (strain GS115 / ATCC 20864))
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
RNAP II-associated proteinY [auth v]396Komagataella phaffii GS115Mutation(s): 0 
Gene Names: PAS_chr4_0902
UniProt
Find proteins for C4R997 (Komagataella phaffii (strain GS115 / ATCC 20864))
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Constituent of Paf1 complex with RNA polymerase II, Paf1p, Hpr1p, Ctr9, Leo1, Rtf1 and Ccr4pZ [auth x]395Komagataella phaffii GS115Mutation(s): 0 
Gene Names: PAS_chr2-1_0674
UniProt
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.3AA [auth a],
EA [auth e]		139Homo sapiensMutation(s): 1 
Gene Names: H3-3A, H3.3A, H3F3, H3F3A, PP781, H3-3B, H3.3B, H3F3B
UniProt & NIH Common Fund Data Resources
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PHAROS:  P84243
GTEx:  ENSG00000132475 ENSG00000163041 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4BA [auth b],
FA [auth f]		106Homo sapiensMutation(s): 0 
Gene Names: 
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Find proteins for P62805 (Homo sapiens)
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PHAROS:  P62805
GTEx:  ENSG00000274618 ENSG00000197238 ENSG00000197837 ENSG00000158406 ENSG00000278705 ENSG00000197061 ENSG00000270882 ENSG00000270276 ENSG00000273542 ENSG00000277157 ENSG00000276966 ENSG00000276180 ENSG00000278637 ENSG00000275126 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A type 1-B/ECA [auth c],
GA [auth g]		133Homo sapiensMutation(s): 0 
Gene Names: H2AC4, H2AFM, HIST1H2AB, H2AC8, H2AFA, HIST1H2AE
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GTEx:  ENSG00000277075 ENSG00000278463 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B type 1-JDA [auth d],
HA [auth h]		129Homo sapiensMutation(s): 1 
Gene Names: HIST1H2BJ, H2BFR
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GTEx:  ENSG00000124635 
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Entity ID: 14
MoleculeChains LengthOrganismImage
DNA (198-MER)198synthetic construct
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Entity ID: 15
MoleculeChains LengthOrganismImage
RNA (5'-R(P*GP*CP*UP*UP*GP*UP*GP*CP*UP*GP*UP*CP*UP*UP*CP*GP*UP*CP*CP*A)-3')O [auth P]20synthetic construct
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Entity ID: 16
MoleculeChains LengthOrganismImage
DNA (198-MER)P [auth T]198synthetic construct
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH
Download Ideal Coordinates CCD File 
WA [auth s]S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
ZN
Query on ZN
Download Ideal Coordinates CCD File 
IA [auth A]
JA [auth A]
LA [auth B]
MA [auth C]
NA [auth I]
IA [auth A],
JA [auth A],
LA [auth B],
MA [auth C],
NA [auth I],
OA [auth I],
PA [auth J],
QA [auth L],
RA [auth M],
SA [auth V],
TA [auth s],
UA [auth s],
VA [auth s]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG
Download Ideal Coordinates CCD File 
KA [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.1_5286:

Structure Validation

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View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Japan Agency for Medical Research and Development (AMED)JapanJP24ama121009
Japan Society for the Promotion of Science (JSPS)JapanJP20H05690
Japan Society for the Promotion of Science (JSPS)JapanJP24H00062
Japan Society for the Promotion of Science (JSPS)JapanJP20H03201
Japan Society for the Promotion of Science (JSPS)JapanJP23K17392
Japan Society for the Promotion of Science (JSPS)JapanJP22K15033
Japan Society for the Promotion of Science (JSPS)JapanJP24H02328
Japan Society for the Promotion of Science (JSPS)JapanJP23H05475
Japan Society for the Promotion of Science (JSPS)JapanJP20H05906
Japan Science and TechnologyJapanJPMJER1901
Japan Science and TechnologyJapanJPMJCR24T3
Other privateDaiichi Sankyo Foundation for Life Science

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-24
    Type: Initial release