6A5U

RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA, tilt conformation

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.6 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 basis of the nucleosome transition during RNA polymerase II passage.

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

(2018) Science 362: 595-598

  • DOI: 10.1126/science.aau9904
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Genomic DNA forms chromatin, in which the nucleosome is the repeating unit. The mechanism by which RNA polymerase II (RNAPII) transcribes the nucleosomal DNA remains unclear. Here we report the cryo-electron microscopy structures of RNAPII-nucleosome ...

    Genomic DNA forms chromatin, in which the nucleosome is the repeating unit. The mechanism by which RNA polymerase II (RNAPII) transcribes the nucleosomal DNA remains unclear. Here we report the cryo-electron microscopy structures of RNAPII-nucleosome complexes in which RNAPII pauses at the superhelical locations SHL(-6), SHL(-5), SHL(-2), and SHL(-1) of the nucleosome. RNAPII pauses at the major histone-DNA contact sites, and the nucleosome interactions with the RNAPII subunits stabilize the pause. These structures reveal snapshots of nucleosomal transcription, in which RNAPII gradually tears DNA from the histone surface while preserving the histone octamer. The nucleosomes in the SHL(-1) complexes are bound to a "foreign" DNA segment, which might explain the histone transfer mechanism. These results provide the foundations for understanding chromatin transcription and epigenetic regulation.

    Organizational Affiliation: 

    RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.,Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.,RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan. kurumizaka@iam.u-tokyo.ac.jp shunichi.sekine@riken.jp.,Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.,Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan. kurumizaka@iam.u-tokyo.ac.jp shunichi.sekine@riken.jp.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit
A
1743Komagataella phaffii (strain GS115 / ATCC 20864)Mutation(s): 0 
EC: 2.7.7.6
Find proteins for C4R4Y0 (Komagataella phaffii (strain GS115 / ATCC 20864))
Go to UniProtKB:  C4R4Y0
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit beta
B
1227Komagataella phaffii (strain GS115 / ATCC 20864)Mutation(s): 0 
EC: 2.7.7.6
Find proteins for C4QZQ7 (Komagataella phaffii (strain GS115 / ATCC 20864))
Go to UniProtKB:  C4QZQ7
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase II third largest subunit B44, part of central core
C
304Komagataella phaffii (strain GS115 / ATCC 20864)Mutation(s): 0 
Find proteins for C4R7L2 (Komagataella phaffii (strain GS115 / ATCC 20864))
Go to UniProtKB:  C4R7L2
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase II subunit B32
D
186Komagataella phaffii (strain GS115 / ATCC 20864)Mutation(s): 0 
Find proteins for C4R2U9 (Komagataella phaffii (strain GS115 / ATCC 20864))
Go to UniProtKB:  C4R2U9
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III
E
214Komagataella phaffii (strain GS115 / ATCC 20864)Mutation(s): 0 
Find proteins for C4R3P8 (Komagataella phaffii (strain GS115 / ATCC 20864))
Go to UniProtKB:  C4R3P8
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III
F
155Komagataella phaffii (strain GS115 / ATCC 20864)Mutation(s): 0 
Find proteins for C4R1V1 (Komagataella phaffii (strain GS115 / ATCC 20864))
Go to UniProtKB:  C4R1V1
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase II subunit
G
171Komagataella phaffii (strain GS115 / ATCC 20864)Mutation(s): 0 
Find proteins for C4R9A1 (Komagataella phaffii (strain GS115 / ATCC 20864))
Go to UniProtKB:  C4R9A1
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC3
H
145Komagataella phaffii (strain GS115 / ATCC 20864)Mutation(s): 0 
Find proteins for C4R273 (Komagataella phaffii (strain GS115 / ATCC 20864))
Go to UniProtKB:  C4R273
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit
I
115Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1)Mutation(s): 0 
Gene Names: RPB9
Find proteins for F2QPE6 (Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1))
Go to UniProtKB:  F2QPE6
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III
J
72Komagataella phaffii (strain GS115 / ATCC 20864)Mutation(s): 0 
Find proteins for C4R009 (Komagataella phaffii (strain GS115 / ATCC 20864))
Go to UniProtKB:  C4R009
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase II subunit B12.5
K
118Komagataella phaffii (strain GS115 / ATCC 20864)Mutation(s): 0 
Find proteins for C4R3Z5 (Komagataella phaffii (strain GS115 / ATCC 20864))
Go to UniProtKB:  C4R3Z5
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase subunit ABC10-alpha
L
72Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1)Mutation(s): 0 
Gene Names: RPC10
Find proteins for F2QMI1 (Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1))
Go to UniProtKB:  F2QMI1
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Histone H3.3
a, e
139Homo sapiensMutation(s): 0 
Gene Names: H3-3A, H3-3B (H3.3A, H3F3, H3F3A, H3.3B, H3F3B)
Find proteins for P84243 (Homo sapiens)
Go to UniProtKB:  P84243
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
Histone H4
b, f
106Homo sapiensMutation(s): 0 
Gene Names: H4C1, H4C2, H4C3, H4C4, H4C5, H4C6, H4C8, H4C9, H4C11, H4C12, H4C13, H4C14, H4C15, H4-16 (H4/A, H4FA, HIST1H4A, H4/I, H4FI, HIST1H4B, H4/G, H4FG, HIST1H4C, H4/B, H4FB, HIST1H4D, H4/J, H4FJ, HIST1H4E, H4/C, H4FC, HIST1H4F, H4/H, H4FH, HIST1H4H, H4/M, H4FM, HIST1H4I, H4/E, H4FE, HIST1H4J, H4/D, H4FD, HIST1H4K, H4/K, H4FK, HIST1H4L, H4/N, H4F2, H4FN, HIST2H4, HIST2H4A, H4/O, H4FO, HIST2H4B, HIST4H4)
Find proteins for P62805 (Homo sapiens)
Go to UniProtKB:  P62805
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
Histone H2A, Histone H2A type 1-B/E
c, g
133Homo sapiensMutation(s): 0 
Gene Names: H2AC4, H2AC8 (H2AFM, HIST1H2AB, H2AFA, HIST1H2AE)
Find proteins for P04908 (Homo sapiens)
Go to UniProtKB:  P04908
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
Histone H2B, Histone H2B type 1-J
d, h
129Homo sapiensMutation(s): 0 
Gene Names: H2BC11 (H2BFR, HIST1H2BJ)
Find proteins for P06899 (Homo sapiens)
Go to UniProtKB:  P06899
Entity ID: 13
MoleculeChainsLengthOrganism
RNA (5'-R(P*GP*GP*UP*GP*UP*CP*UP*UP*GP*GP*G)-3')P11synthetic construct
Entity ID: 14
MoleculeChainsLengthOrganism
DNA (198-MER)T198synthetic construct
Entity ID: 15
MoleculeChainsLengthOrganism
DNA (198-MER)N198synthetic construct
Entity ID: 20
MoleculeChainsLengthOrganism
DNA (40-MER)040synthetic construct
Entity ID: 21
MoleculeChainsLengthOrganism
DNA (40-MER)140synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download SDF File 
Download CCD File 
A, B, C, I, J, L
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG
Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.6 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

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: 2018-10-03
    Type: Initial release
  • Version 1.1: 2018-10-24
    Type: Data collection, Database references
  • Version 1.2: 2018-11-14
    Type: Data collection, Database references
  • Version 1.3: 2019-11-06
    Type: Data collection, Other