6IR9

RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1126/science.aav8912
  • Structures With Same Primary Citation

  • 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 ...

    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. shunichi.sekine@riken.jp kurumizaka@iam.u-tokyo.ac.jp.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunitA1743Linanthus concinnusMutation(s): 0 
EC: 2.7.7.6
Find proteins for C4R4Y0 (Komagataella phaffii (strain GS115 / ATCC 20864))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit betaB1227Komagataella phaffii GS115Mutation(s): 0 
Gene Names: PAS_chr2-1_0125
EC: 2.7.7.6
Find proteins for C4QZQ7 (Komagataella phaffii (strain GS115 / ATCC 20864))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase II third largest subunit B44, part of central coreC304Komagataella phaffii GS115Mutation(s): 0 
Gene Names: PAS_chr4_0344
Find proteins for C4R7L2 (Komagataella phaffii (strain GS115 / ATCC 20864))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase II subunit B32D186Komagataella phaffii GS115Mutation(s): 0 
Gene Names: PAS_chr2-2_0104
Find proteins for C4R2U9 (Komagataella phaffii (strain GS115 / ATCC 20864))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase subunit ABC27, common to RNA polymerases I, II, and IIIE214Komagataella phaffii GS115Mutation(s): 0 
Gene Names: PAS_chr3_0157
Find proteins for C4R3P8 (Komagataella phaffii (strain GS115 / ATCC 20864))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase subunit ABC23, common to RNA polymerases I, II, and IIIF155Komagataella phaffii GS115Mutation(s): 0 
Gene Names: PAS_chr2-2_0434
Find proteins for C4R1V1 (Komagataella phaffii (strain GS115 / ATCC 20864))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase II subunitG171Komagataella phaffii GS115Mutation(s): 0 
Gene Names: PAS_chr4_0906
Find proteins for C4R9A1 (Komagataella phaffii (strain GS115 / ATCC 20864))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC3H145Komagataella phaffii GS115Mutation(s): 0 
Gene Names: PAS_chr2-2_0309
Find proteins for C4R273 (Komagataella phaffii (strain GS115 / ATCC 20864))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunitI115Komagataella phaffii CBS 7435Mutation(s): 0 
Gene Names: RPB9PP7435_Chr1-1144
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
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and IIIJ72Komagataella phaffii GS115Mutation(s): 0 
Gene Names: PAS_chr2-1_0223
Find proteins for C4R009 (Komagataella phaffii (strain GS115 / ATCC 20864))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase II subunit B12.5K118Komagataella phaffii GS115Mutation(s): 0 
Gene Names: PAS_chr3_0244
Find proteins for C4R3Z5 (Komagataella phaffii (strain GS115 / ATCC 20864))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase subunit ABC10-alphaL72Komagataella phaffii CBS 7435Mutation(s): 0 
Gene Names: RPC10PP7435_Chr1-0476
Find proteins for F2QMI1 (Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Transcription elongation factor 1 homologM113Komagataella phaffii GS115Mutation(s): 0 
Gene Names: PAS_c121_0006
Find proteins for C4QZ45 (Komagataella phaffii (strain GS115 / ATCC 20864))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
Transcription elongation factor SPT4V108Komagataella phaffii GS115Mutation(s): 0 
Gene Names: PAS_chr2-1_0350
Find proteins for C4R0E6 (Komagataella phaffii (strain GS115 / ATCC 20864))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
Histone H4b, f106Homo sapiensMutation(s): 0 
Gene Names: 
Find proteins for P62805 (Homo sapiens)
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NIH Common Fund Data Resources
PHAROS  P62805
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
Histone H2A type 1-B/Ec, g133Homo sapiensMutation(s): 0 
Gene Names: HIST1H2ABH2AFMHIST1H2AEH2AFAH2AC4H2AC8
Find proteins for P04908 (Homo sapiens)
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PHAROS  P04908
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
Spt5W911Komagataella phaffii GS115Mutation(s): 0 
Gene Names: PAS_chr3_1136
Find proteins for C4R370 (Komagataella phaffii (strain GS115 / ATCC 20864))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
Histone H3.3a, e139Homo sapiensMutation(s): 0 
Gene Names: H3F3AH3.3AH3F3PP781H3F3BH3.3BH3-3AH3-3B
Find proteins for P84243 (Homo sapiens)
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PHAROS  P84243
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Histone H2B type 1-Jd, h129Homo sapiensMutation(s): 0 
Gene Names: HIST1H2BJH2BFRH2BC11
Find proteins for P06899 (Homo sapiens)
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PHAROS  P06899
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  • Reference Sequence

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Entity ID: 14
MoleculeChainsLengthOrganism
DNA (198-MER)T198synthetic construct
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Entity ID: 13
MoleculeChainsLengthOrganism
RNA (5'-R(P*GP*CP*CP*UP*GP*GP*UP*GP*UP*CP*UP*UP*GP*GP*GP*U)-3')P16synthetic construct

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Entity ID: 15
MoleculeChainsLengthOrganism
DNA (198-MER)N198synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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A, B, C, I, J, L, M, V
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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
RIKEN Dynamic Structural Biology projectJapan--

Revision History 

  • 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