6J4Z

RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Structural insight into nucleosome transcription by RNA polymerase II with elongation factors.

Ehara, H., Kujirai, T., Fujino, Y., Shirouzu, M., Kurumizaka, H., Sekine, S.I.

(2019) Science 363: 744-747

  • DOI: https://doi.org/10.1126/science.aav8912
  • Primary Citation of Related Structures:  
    6IR9, 6J4W, 6J4X, 6J4Y, 6J4Z, 6J50, 6J51

  • PubMed Abstract: 

    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.

    • Organizational Affiliation: 

    RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.


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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UniProt GroupC4R4Y0
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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
Find proteins for C4R7L2 (Komagataella phaffii (strain GS115 / ATCC 20864))
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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
RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III214Komagataella phaffii GS115Mutation(s): 0 
UniProt
Find proteins for C4R3P8 (Komagataella phaffii (strain GS115 / ATCC 20864))
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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 CBS 7435Mutation(s): 0 
UniProt
Find proteins for F2QPE6 (Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1))
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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
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase II subunit B12.5118Komagataella phaffii GS115Mutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase subunit ABC10-alpha72Komagataella phaffii CBS 7435Mutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription elongation factor SPT4P [auth V]108Komagataella phaffii GS115Mutation(s): 0 
Gene Names: PAS_chr2-1_0350
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Spt5Q [auth W]911Komagataella pastorisMutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.3R [auth a],
V [auth e]		139Homo sapiensMutation(s): 0 
Gene Names: H3F3A, H3.3A, H3F3, PP781, H3F3B, H3.3B
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GTEx:  ENSG00000132475 ENSG00000163041 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4S [auth b],
W [auth f]		106Homo sapiensMutation(s): 0 
Gene Names: 
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GTEx:  ENSG00000274618 ENSG00000197238 ENSG00000197837 ENSG00000158406 ENSG00000278705 ENSG00000197061 ENSG00000270882 ENSG00000270276 ENSG00000273542 ENSG00000277157 ENSG00000276966 ENSG00000276180 ENSG00000278637 ENSG00000275126 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A type 1-B/ET [auth c],
X [auth g]		133Homo sapiensMutation(s): 0 
Gene Names: HIST1H2AB, H2AFM, HIST1H2AE, H2AFA
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GTEx:  ENSG00000277075 ENSG00000278463 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B type 1-JU [auth d],
Y [auth h]		129Homo sapiensMutation(s): 0 
Gene Names: HIST1H2BJ, H2BFR
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GTEx:  ENSG00000124635 
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Entity ID: 13
MoleculeChains LengthOrganismImage
RNA (5'-R(P*GP*CP*CP*UP*GP*GP*UP*GP*UP*CP*UP*UP*GP*GP*GP*U)-3')M [auth P]16synthetic construct
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Entity ID: 14
MoleculeChains LengthOrganismImage
DNA (198-MER)N [auth T]198synthetic construct
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Entity ID: 15
MoleculeChains LengthOrganismImage
DNA (198-MER)O [auth N]198synthetic construct
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Entity ID: 22
MoleculeChains LengthOrganismImage
DNA (42-MER)Z [auth 0]42synthetic construct
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Entity ID: 23
MoleculeChains LengthOrganismImage
DNA (42-MER)AA [auth 1]42synthetic construct
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download Ideal Coordinates CCD File 
BA [auth A]
CA [auth A]
EA [auth B]
FA [auth C]
GA [auth I]
BA [auth A],
CA [auth A],
EA [auth B],
FA [auth C],
GA [auth I],
HA [auth I],
IA [auth J],
JA [auth L],
KA [auth V]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG
Download Ideal Coordinates CCD File 
DA [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0-beta2

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapanJP25116002
Japan Society for the Promotion of ScienceJapanJP15H04344
Japan Agency for Medical Research and Development (AMED)JapanJP18am0101076
Japan Agency for Medical Research and Development (AMED)JapanJP18am0101082
Japan Science and TechnologyJapanJPMJCR16G1
Other governmentJapanRIKEN Dynamic Structural Biology project

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-20
    Type: Initial release
  • Version 1.1: 2019-02-27
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-06
    Changes: Data collection, Other
  • Version 1.3: 2024-03-27
    Changes: Data collection, Database references, Derived calculations