[English] 日本語
Yorodumi
- PDB-9wmt: Co-transcriptional histone H3K36 methylation complex containing R... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9wmt
TitleCo-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp115, type A)
Components
  • (DNA (198-MER)) x 2
  • (DNA-directed RNA polymerase ...) x 3
  • (DNA-directed RNA polymerases I, II, and III subunit ...) x 2
  • (RNA polymerase II ...) x 4
  • (RNA polymerase subunit ABC10- ...) x 2
  • (Transcription elongation factor ...) x 4
  • Component of the Paf1p complex
  • Constituent of Paf1 complex with RNA polymerase II, Paf1p, Hpr1p, Ctr9, Leo1, Rtf1 and Ccr4p
  • Histone H2A type 1-B/E
  • Histone H2B type 1-J
  • Histone H3.3
  • Histone H4
  • Histone-lysine N-methyltransferase, H3 lysine-36 specific
  • Leo1
  • Protein that interacts with Spt6p and copurifies with Spt5p and RNA polymerase II
  • 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')
  • RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III
  • RNAP II-associated protein
  • RNAPII-associated chromatin remodeling Paf1 complex subunit
KeywordsTRANSCRIPTION / chromatin / nucleosome
Function / homology
Function and homology information


snoRNA transcription by RNA polymerase II / sno(s)RNA transcription / negative regulation of antisense RNA transcription / regulation of transcription initiation by RNA polymerase II / negative regulation of transcription elongation by RNA polymerase I / sno(s)RNA 3'-end processing / negative regulation of reciprocal meiotic recombination / positive regulation of transcription elongation by RNA polymerase I / mating-type region heterochromatin / histone H3K36 dimethyltransferase activity ...snoRNA transcription by RNA polymerase II / sno(s)RNA transcription / negative regulation of antisense RNA transcription / regulation of transcription initiation by RNA polymerase II / negative regulation of transcription elongation by RNA polymerase I / sno(s)RNA 3'-end processing / negative regulation of reciprocal meiotic recombination / positive regulation of transcription elongation by RNA polymerase I / mating-type region heterochromatin / histone H3K36 dimethyltransferase activity / transcription antitermination factor activity, DNA binding / regulation of septum digestion after cytokinesis / RNA polymerase II C-terminal domain phosphoserine binding / [histone H3]-lysine36 N-trimethyltransferase / ascospore formation / regulation of transcription-coupled nucleotide-excision repair / triplex DNA binding / Cdc73/Paf1 complex / co-transcriptional lncRNA 3' end processing, cleavage and polyadenylation pathway / histone H3K36 trimethyltransferase activity / regulation of mRNA 3'-end processing / siRNA-mediated pericentric heterochromatin formation / RNA polymerase I core binding / DSIF complex / regulation of rRNA processing / RNA polymerase I general transcription initiation factor binding / intracellular mRNA localization / rDNA binding / rDNA heterochromatin / negative regulation of DNA recombination / intracellular phosphate ion homeostasis / RPB4-RPB7 complex / snRNP binding / transcription elongation-coupled chromatin remodeling / mRNA 3'-end processing / DNA-templated transcription elongation / U4 snRNA binding / transcription elongation factor activity / kinetochore assembly / chromatin-protein adaptor activity / regulation of DNA-templated DNA replication initiation / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / poly(A)+ mRNA export from nucleus / nucleosomal DNA binding / Regulation of PD-L1(CD274) transcription / cellular response to stress / termination of RNA polymerase II transcription / negative regulation of mitophagy / mitotic metaphase chromosome alignment / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / termination of RNA polymerase III transcription / spliceosomal complex assembly / termination of RNA polymerase I transcription / transcription initiation at RNA polymerase III promoter / RNA polymerase II complex binding / transcription initiation at RNA polymerase I promoter / U5 snRNA binding / 7-methylguanosine mRNA capping / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / positive regulation of translational initiation / U2 snRNA binding / nuclear-transcribed mRNA catabolic process / U6 snRNA binding / negative regulation of tumor necrosis factor-mediated signaling pathway / translation elongation factor activity / U1 snRNA binding / RNA polymerase II core promoter sequence-specific DNA binding / pericentric heterochromatin / nucleosome binding / RNA polymerase I complex / RNA polymerase III complex / negative regulation of megakaryocyte differentiation / transcription elongation by RNA polymerase I / protein localization to CENP-A containing chromatin / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / transcription by RNA polymerase I / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / translesion synthesis / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / transcription-coupled nucleotide-excision repair / positive regulation of autophagy / translation initiation factor binding / Deposition of new CENPA-containing nucleosomes at the centromere / telomere organization / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / RNA Polymerase I Promoter Opening / transcription initiation-coupled chromatin remodeling / Inhibition of DNA recombination at telomere / Assembly of the ORC complex at the origin of replication / Meiotic synapsis / SUMOylation of chromatin organization proteins / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / negative regulation of autophagy / DNA methylation / Condensation of Prophase Chromosomes
Similarity search - Function
Histone-lysine N-methyltransferase, Set2, fungi / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / : / Spt6, S1/OB domain / : / Plus-3 domain / Plus3-like superfamily / Plus-3 domain / Plus3 domain profile. / Short conserved domain in transcriptional regulators. ...Histone-lysine N-methyltransferase, Set2, fungi / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / : / Spt6, S1/OB domain / : / Plus-3 domain / Plus3-like superfamily / Plus-3 domain / Plus3 domain profile. / Short conserved domain in transcriptional regulators. / Leo1-like protein / Leo1-like protein / Spt5 C-terminal nonapeptide repeat binding Spt4 / RNA polymerase II associated factor Paf1 / Paf1 / Cdc73/Parafibromin / RNA polymerase-associated protein Ctr9 / Cell division control protein 73, C-terminal / Cell division control protein 73, C-terminal domain superfamily / RNA pol II accessory factor, Cdc73 family, C-terminal / Set2 Rpb1 interacting domain superfamily / SETD2/Set2, SET domain / Transcription elongation factor 1 / Transcription elongation factor 1 superfamily / Transcription elongation factor Elf1 like / : / Spt6 acidic, N-terminal domain / Helix-turn-helix DNA-binding domain of Spt6 / Transcription elongation factor Spt6, YqgF domain / Transcription elongation factor Spt6, helix-hairpin-helix motif / Spt6, SH2 domain, C terminus / Acidic N-terminal SPT6 / Helix-hairpin-helix motif / Holliday-junction resolvase-like of SPT6 / Helix-turn-helix DNA-binding domain of SPT6 / Tex-like protein, HTH domain superfamily / Tex-like domain superfamily / Spt6, Death-like domain / : / Tex central region-like / Transcription elongation factor Spt6 / Spt6, SH2 domain, N terminus / Spt6, SH2 domain / SH2 domain / YqgF/RNase H-like domain superfamily / Set2 Rpb1 interacting domain / SRI (Set2 Rpb1 interacting) domain / Transcription initiation Spt4 / Spt4 superfamily / TFIIS N-terminal domain profile. / TFIIS helical bundle-like domain / Transcription factor IIS, N-terminal / Spt4/RpoE2 zinc finger / Spt4/RpoE2 zinc finger / Spt4/RpoE2 zinc finger / AWS domain / AWS domain / AWS domain profile. / associated with SET domains / : / Transcription elongation factor SPT5, KOWx domain / Transcription elongation factor SPT5, second KOW domain / Transcription elongation factor SPT5, fifth KOW domain / Transcription elongation factor SPT5, KOW1 domain / Transcription elongation factor SPT5, fourth KOW domain / Transcription elongation factor Spt5, eukaryote / Spt5 transcription elongation factor, N-terminal / Spt5, KOW domain repeat 2 / Spt5, KOW domain repeat 3 / Spt5, KOW domain repeat 5 / Spt5 transcription elongation factor, acidic N-terminal / NGN domain, eukaryotic / Spt5, KOW domain repeat 1 / Spt5, KOW domain repeat 4 / NGN domain / Transcription elongation factor SPT5 / Early transcription elongation factor of RNA pol II, NGN section / Cysteine-rich motif following a subset of SET domains / RuvA domain 2-like / TFIIS/LEDGF domain superfamily / Post-SET domain / Post-SET domain profile. / Tetratricopeptide repeat / NusG, N-terminal domain superfamily / WW domain / WW/rsp5/WWP domain signature. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / SET domain / WW domain / SET domain profile. / SET domain superfamily / SET domain / DNA-directed RNA polymerase II subunit Rpb4-like / RNA polymerase Rpb4/RPC9, core / RNA polymerase Rpb1 C-terminal repeat / DNA-directed RNA-polymerase II subunit / RNA polymerase II, heptapeptide repeat, eukaryotic
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / DNA / DNA (> 10) / DNA (> 100) / RNA / RNA (> 10) / Histone-lysine N-methyltransferase, H3 lysine-36 specific / Transcription elongation factor 1 homolog / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerases I, II, and III subunit RPABC5 ...S-ADENOSYL-L-HOMOCYSTEINE / DNA / DNA (> 10) / DNA (> 100) / RNA / RNA (> 10) / Histone-lysine N-methyltransferase, H3 lysine-36 specific / Transcription elongation factor 1 homolog / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / Transcription elongation factor SPT4 / Constituent of Paf1 complex with RNA polymerase II, Paf1p, Hpr1p, Ctr9, Leo1, Rtf1 and Ccr4p / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / RNA polymerase II subunit B32 / Transcription elongation factor SPT5 / RNA polymerase-associated protein LEO1 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / RNA polymerase II subunit B12.5 / DNA-directed RNA polymerase subunit / Component of the Paf1p complex / Transcription elongation factor Spt6 / DNA-directed RNA polymerase II subunit RPB3 / Protein that interacts with Spt6p and copurifies with Spt5p and RNA polymerase II / RNAP II-associated protein / DNA-directed RNA polymerase subunit / RNA polymerase subunit ABC10-alpha / DNA-directed RNA polymerase subunit / RNAPII-associated chromatin remodeling Paf1 complex subunit / Histone H2A type 1-B/E / Histone H2B type 1-J / Histone H4 / Histone H3.3
Similarity search - Component
Biological speciesKomagataella phaffii GS115 (fungus)
Homo sapiens (human)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.59 Å
AuthorsKujirai, T. / Ehara, H. / Ito, T. / Henmi, M. / Sekine, S. / Kurumizaka, H.
Funding support Japan, 12items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP24ama121009 Japan
Japan Society for the Promotion of Science (JSPS)JP20H05690 Japan
Japan Society for the Promotion of Science (JSPS)JP24H00062 Japan
Japan Society for the Promotion of Science (JSPS)JP20H03201 Japan
Japan Society for the Promotion of Science (JSPS)JP23K17392 Japan
Japan Society for the Promotion of Science (JSPS)JP22K15033 Japan
Japan Society for the Promotion of Science (JSPS)JP24H02328 Japan
Japan Society for the Promotion of Science (JSPS)JP23H05475 Japan
Japan Society for the Promotion of Science (JSPS)JP20H05906 Japan
Japan Science and TechnologyJPMJER1901 Japan
Japan Science and TechnologyJPMJCR24T3 Japan
Other privateDaiichi Sankyo Foundation for Life Science
CitationJournal: Sci Adv / Year: 2026
Title: Structural basis of transcription-coupled H3K36 trimethylation by Set2 in coordination with FACT.
Authors: Tomoya Kujirai / Haruhiko Ehara / Tomoko Ito / Masami Henmi / Eriko Oya / Takehiko Kobayashi / Shun-Ichi Sekine / Hitoshi Kurumizaka /
Abstract: Trimethylation of the histone H3K36 residue (H3K36me3) plays an indispensable role in ensuring transcription fidelity by suppressing undesired cryptic transcription in chromatin. H3K36me3 ...Trimethylation of the histone H3K36 residue (H3K36me3) plays an indispensable role in ensuring transcription fidelity by suppressing undesired cryptic transcription in chromatin. H3K36me3 modification is accomplished by Set2/SETD2 during transcription elongation by the RNA polymerase II elongation complex (EC). Here, we found that Set2-mediated H3K36me3 deposition occurs on the nucleosome reassembling behind the EC. The histone chaperone FACT suppresses H3K36me3 deposition on the downstream nucleosome, thereby ensuring that Set2 targets specifically on the reassembling upstream nucleosome. Cryo-electron microscopy structures of the nucleosome-transcribing EC complexed with Set2 revealed that Set2 is anchored by the Spt6 subunit of the EC to capture both of the H3 N-terminal tails in a stepwise manner during the nucleosome reassembly process. Abrogation of the Set2-EC interaction leads to defective transcription-coupled H3K36me3 deposition. These insights elucidate the structure-based mechanism of transcription-coupled H3K36me3 deposition in chromatin.
History
DepositionSep 3, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 24, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Additional map / Part number: 2 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update
Revision 1.1Mar 4, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA-directed RNA polymerase subunit
B: DNA-directed RNA polymerase subunit beta
C: RNA polymerase II third largest subunit B44, part of central core
D: RNA polymerase II subunit B32
E: DNA-directed RNA polymerases I, II, and III subunit RPABC1
F: RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III
G: RNA polymerase II subunit
H: DNA-directed RNA polymerases I, II, and III subunit RPABC3
I: DNA-directed RNA polymerase subunit
J: RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III
K: RNA polymerase II subunit B12.5
L: RNA polymerase subunit ABC10-alpha
M: Transcription elongation factor 1 homolog
N: DNA (198-MER)
P: 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')
T: DNA (198-MER)
V: Transcription elongation factor SPT4
W: Transcription elongation factor SPT5
m: Transcription elongation factor Spt6
n: Protein that interacts with Spt6p and copurifies with Spt5p and RNA polymerase II
q: Component of the Paf1p complex
r: RNAPII-associated chromatin remodeling Paf1 complex subunit
s: Histone-lysine N-methyltransferase, H3 lysine-36 specific
u: Leo1
v: RNAP II-associated protein
x: Constituent of Paf1 complex with RNA polymerase II, Paf1p, Hpr1p, Ctr9, Leo1, Rtf1 and Ccr4p
a: Histone H3.3
b: Histone H4
c: Histone H2A type 1-B/E
d: Histone H2B type 1-J
e: Histone H3.3
f: Histone H4
g: Histone H2A type 1-B/E
h: Histone H2B type 1-J
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,512,55149
Polymers1,511,29234
Non-polymers1,25915
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
DNA-directed RNA polymerase ... , 3 types, 3 molecules ABI

#1: Protein DNA-directed RNA polymerase subunit / RNA polymerase II subunit Rpb1


Mass: 194107.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella phaffii GS115 (fungus) / References: UniProt: C4R4Y0, DNA-directed RNA polymerase
#2: Protein DNA-directed RNA polymerase subunit beta / RNA polymerase II subunit Rpb2


Mass: 139746.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella phaffii GS115 (fungus) / References: UniProt: C4QZQ7, DNA-directed RNA polymerase
#9: Protein DNA-directed RNA polymerase subunit


Mass: 13612.320 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella phaffii GS115 (fungus) / References: UniProt: F2QPE6

-
RNA polymerase II ... , 4 types, 4 molecules CDGK

#3: Protein RNA polymerase II third largest subunit B44, part of central core / RNA polymerase II subunit Rpb3


Mass: 34216.293 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella phaffii GS115 (fungus) / References: UniProt: C4R7L2
#4: Protein RNA polymerase II subunit B32 / RNA polymerase II subunit Rpb4


Mass: 20622.980 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella phaffii GS115 (fungus) / References: UniProt: C4R2U9
#7: Protein RNA polymerase II subunit / RNA polymerase II subunit Rpb7


Mass: 18802.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella phaffii GS115 (fungus) / References: UniProt: C4R9A1
#11: Protein RNA polymerase II subunit B12.5 / RNA polymerase II subunit Rpb11


Mass: 13832.896 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella phaffii GS115 (fungus) / References: UniProt: C4R3Z5

-
DNA-directed RNA polymerases I, II, and III subunit ... , 2 types, 2 molecules EH

#5: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC1 / RNA polymerase II subunit Rpb5


Mass: 24962.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella phaffii GS115 (fungus) / References: UniProt: C4R3P8
#8: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC3 / RNA polymerase II subunit Rpb8


Mass: 16249.220 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella phaffii GS115 (fungus) / References: UniProt: C4R273

-
Protein , 12 types, 16 molecules Fnqrsuvxaebfcgdh

#6: Protein RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III / RNA polymerase II subunit Rpb6


Mass: 17803.588 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella phaffii GS115 (fungus) / References: UniProt: C4R1V1
#20: Protein Protein that interacts with Spt6p and copurifies with Spt5p and RNA polymerase II


Mass: 46907.785 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Komagataella phaffii GS115 (fungus) / Gene: PAS_chr4_0349 / Production host: Escherichia coli (E. coli) / References: UniProt: C4R7L8
#21: Protein Component of the Paf1p complex


Mass: 124979.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Komagataella phaffii GS115 (fungus) / Gene: PAS_chr3_1035 / Production host: Escherichia coli (E. coli) / References: UniProt: C4R6B2
#22: Protein RNAPII-associated chromatin remodeling Paf1 complex subunit


Mass: 62301.246 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Komagataella phaffii GS115 (fungus) / Gene: RTF1, PP7435_Chr1-1405 / Production host: Escherichia coli (E. coli) / References: UniProt: F2QQ42
#23: Protein Histone-lysine N-methyltransferase, H3 lysine-36 specific / SET domain-containing protein 2


Mass: 83724.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Komagataella phaffii GS115 (fungus) / Gene: PAS_chr1-4_0287 / Production host: Escherichia coli (E. coli)
References: UniProt: C4QY01, [histone H3]-lysine36 N-trimethyltransferase
#24: Protein Leo1


Mass: 52387.715 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Komagataella phaffii GS115 (fungus) / Gene: PAS_chr3_1154 / Production host: Escherichia coli (E. coli) / References: UniProt: C4R3K1
#25: Protein RNAP II-associated protein


Mass: 46045.980 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Komagataella phaffii GS115 (fungus) / Gene: PAS_chr4_0902 / Production host: Escherichia coli (E. coli) / References: UniProt: C4R997
#26: Protein Constituent of Paf1 complex with RNA polymerase II, Paf1p, Hpr1p, Ctr9, Leo1, Rtf1 and Ccr4p


Mass: 44760.652 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Komagataella phaffii GS115 (fungus) / Gene: PAS_chr2-1_0674 / Production host: Escherichia coli (E. coli) / References: UniProt: C4R1E6
#27: Protein Histone H3.3


Mass: 15645.277 Da / Num. of mol.: 2 / Mutation: K36M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: H3-3A, H3.3A, H3F3, H3F3A, PP781, H3-3B, H3.3B, H3F3B / Production host: Escherichia coli (E. coli) / References: UniProt: P84243
#28: Protein Histone H4


Mass: 11676.703 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: H4C1, H4/A, H4FA, HIST1H4A, H4C2, H4/I, H4FI, HIST1H4B, H4C3, H4/G, H4FG, HIST1H4C, H4C4, H4/B, H4FB, HIST1H4D, H4C5, H4/J, H4FJ, HIST1H4E, H4C6, H4/C, H4FC, HIST1H4F, H4C8, H4/H, H4FH, ...Gene: H4C1, H4/A, H4FA, HIST1H4A, H4C2, H4/I, H4FI, HIST1H4B, H4C3, H4/G, H4FG, HIST1H4C, H4C4, H4/B, H4FB, HIST1H4D, H4C5, H4/J, H4FJ, HIST1H4E, H4C6, H4/C, H4FC, HIST1H4F, H4C8, H4/H, H4FH, HIST1H4H, H4C9, H4/M, H4FM, HIST1H4I, H4C11, H4/E, H4FE, HIST1H4J, H4C12, H4/D, H4FD, HIST1H4K, H4C13, H4/K, H4FK, HIST1H4L, H4C14, H4/N, H4F2, H4FN, HIST2H4, HIST2H4A, H4C15, H4/O, H4FO, HIST2H4B, H4C16, H4-16, HIST4H4
Production host: Escherichia coli (E. coli) / References: UniProt: P62805
#29: Protein Histone H2A type 1-B/E / Histone H2A.2 / Histone H2A/a / Histone H2A/m


Mass: 14447.825 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: H2AC4, H2AFM, HIST1H2AB, H2AC8, H2AFA, HIST1H2AE / Production host: Escherichia coli (E. coli) / References: UniProt: P04908
#30: Protein Histone H2B type 1-J / Histone H2B.1 / Histone H2B.r / H2B/r


Mass: 14191.479 Da / Num. of mol.: 2 / Mutation: K121C-ubiquitination mimic
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIST1H2BJ, H2BFR / Production host: Escherichia coli (E. coli) / References: UniProt: P06899

-
RNA polymerase subunit ABC10- ... , 2 types, 2 molecules JL

#10: Protein RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III / RNA polymerase II subunit Rpb10


Mass: 8554.064 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella phaffii GS115 (fungus) / References: UniProt: C4R009
#12: Protein RNA polymerase subunit ABC10-alpha / RNA polymerase II subunit Rpb12


Mass: 7862.048 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Komagataella phaffii GS115 (fungus) / References: UniProt: F2QMI1

-
Transcription elongation factor ... , 4 types, 4 molecules MVWm

#13: Protein Transcription elongation factor 1 homolog


Mass: 12606.896 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Komagataella phaffii GS115 (fungus) / Gene: PAS_c121_0006 / Production host: Escherichia coli (E. coli) / References: UniProt: C4QZ45
#17: Protein Transcription elongation factor SPT4


Mass: 12039.614 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Komagataella phaffii GS115 (fungus) / Gene: PAS_chr2-1_0350 / Production host: Escherichia coli (E. coli) / References: UniProt: C4R0E6
#18: Protein Transcription elongation factor SPT5 / Chromatin Elongation factor SPT5 / Transcription elongation factor spt5


Mass: 101459.422 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Komagataella phaffii GS115 (fungus) / Gene: PAS_chr3_1136 / Production host: Escherichia coli (E. coli) / References: UniProt: C4R370
#19: Protein Transcription elongation factor Spt6


Mass: 173241.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Komagataella phaffii GS115 (fungus) / Gene: PAS_chr4_0308 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: C4R7H2

-
DNA chain , 2 types, 2 molecules NT

#14: DNA chain DNA (198-MER)


Mass: 61264.703 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#16: DNA chain DNA (198-MER)


Mass: 60987.176 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
RNA chain , 1 types, 1 molecules P

#15: RNA chain 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')


Mass: 6290.695 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Non-polymers , 3 types, 15 molecules

#31: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Zn
#32: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#33: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S

-
Details

Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp115, type A)
Type: COMPLEX / Entity ID: #1-#30 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
11Komagataella phaffii GS115 (fungus)644223
21Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
11Escherichia coli (E. coli)562
21Spodoptera frugiperda (fall armyworm)7108
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 58 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

-
Processing

EM softwareName: PHENIX / Version: 1.21.1_5286: / Category: model refinement
CTF correctionType: NONE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.59 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 35823 / Symmetry type: POINT

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more