7XN7

RNA polymerase II elongation complex containing Spt4/5, Elf1, Spt6, Spn1 and Paf1C


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 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 basis of nucleosome disassembly and reassembly by RNAPII elongation complex with FACT.

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

(2022) Science 377: eabp9466-eabp9466

  • DOI: https://doi.org/10.1126/science.abp9466
  • Primary Citation of Related Structures:  
    7XN7, 7XSE, 7XSX, 7XSZ, 7XT7, 7XTD, 7XTI

  • PubMed Abstract: 

    During gene transcription, RNA polymerase II (RNAPII) traverses nucleosomes in chromatin, but the mechanism has remained elusive. Using cryo-electron microscopy, we obtained structures of the RNAPII elongation complex (EC) passing through a nucleosome in the presence of the transcription elongation factors Spt6, Spn1, Elf1, Spt4/5, and Paf1C and the histone chaperone FACT (facilitates chromatin transcription). The structures show snapshots of EC progression on DNA mediating downstream nucleosome disassembly, followed by its reassembly upstream of the EC, which is facilitated by FACT. FACT dynamically adapts to successively occurring subnucleosome intermediates, forming an interface with the EC. Spt6, Spt4/5, and Paf1C form a "cradle" at the EC DNA-exit site and support the upstream nucleosome reassembly. These structures explain the mechanism by which the EC traverses nucleosomes while maintaining the chromatin structure and epigenetic information.


  • Organizational Affiliation

    RIKEN Center for Biosystems Dynamics Research, Tsurumi-ku, Yokohama 230-0045, Japan.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit1,743Komagataella phaffiiMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for C4R4Y0 (Komagataella phaffii (strain GS115 / ATCC 20864))
Explore C4R4Y0 
Go to UniProtKB:  C4R4Y0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC4R4Y0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta1,227Komagataella phaffiiMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for C4QZQ7 (Komagataella phaffii (strain GS115 / ATCC 20864))
Explore C4QZQ7 
Go to UniProtKB:  C4QZQ7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC4QZQ7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase II third largest subunit B44, part of central core304Komagataella phaffiiMutation(s): 0 
UniProt
Find proteins for C4R7L2 (Komagataella phaffii (strain GS115 / ATCC 20864))
Explore C4R7L2 
Go to UniProtKB:  C4R7L2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC4R7L2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase II subunit B32186Komagataella phaffiiMutation(s): 0 
UniProt
Find proteins for C4R2U9 (Komagataella phaffii (strain GS115 / ATCC 20864))
Explore C4R2U9 
Go to UniProtKB:  C4R2U9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC4R2U9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC1214Komagataella phaffiiMutation(s): 0 
UniProt
Find proteins for F2QX94 (Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1))
Explore F2QX94 
Go to UniProtKB:  F2QX94
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF2QX94
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III155Komagataella phaffiiMutation(s): 0 
UniProt
Find proteins for C4R1V1 (Komagataella phaffii (strain GS115 / ATCC 20864))
Explore C4R1V1 
Go to UniProtKB:  C4R1V1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC4R1V1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase II subunit171Komagataella phaffiiMutation(s): 0 
UniProt
Find proteins for C4R9A1 (Komagataella phaffii (strain GS115 / ATCC 20864))
Explore C4R9A1 
Go to UniProtKB:  C4R9A1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC4R9A1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC3145Komagataella phaffiiMutation(s): 0 
UniProt
Find proteins for C4R273 (Komagataella phaffii (strain GS115 / ATCC 20864))
Explore C4R273 
Go to UniProtKB:  C4R273
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC4R273
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit115Komagataella phaffiiMutation(s): 0 
UniProt
Find proteins for F2QPE6 (Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1))
Explore F2QPE6 
Go to UniProtKB:  F2QPE6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF2QPE6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III72Komagataella phaffiiMutation(s): 0 
UniProt
Find proteins for C4R009 (Komagataella phaffii (strain GS115 / ATCC 20864))
Explore C4R009 
Go to UniProtKB:  C4R009
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC4R009
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase II subunit B12.5118Komagataella phaffiiMutation(s): 0 
UniProt
Find proteins for C4R3Z5 (Komagataella phaffii (strain GS115 / ATCC 20864))
Explore C4R3Z5 
Go to UniProtKB:  C4R3Z5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC4R3Z5
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase subunit ABC10-alpha72Komagataella phaffiiMutation(s): 0 
UniProt
Find proteins for F2QMI1 (Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1))
Explore F2QMI1 
Go to UniProtKB:  F2QMI1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF2QMI1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription elongation factor 1 homolog113Komagataella phaffiiMutation(s): 0 
Gene Names: PAS_c121_0006
UniProt
Find proteins for C4QZ45 (Komagataella phaffii (strain GS115 / ATCC 20864))
Explore C4QZ45 
Go to UniProtKB:  C4QZ45
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC4QZ45
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription elongation factor SPT4Q [auth V]108Komagataella phaffiiMutation(s): 0 
Gene Names: PAS_chr2-1_0350
UniProt
Find proteins for C4R0E6 (Komagataella phaffii (strain GS115 / ATCC 20864))
Explore C4R0E6 
Go to UniProtKB:  C4R0E6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC4R0E6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Chromatin elongation factor SPT5R [auth W]911Komagataella phaffiiMutation(s): 0 
Gene Names: PAS_chr3_1136
UniProt
Find proteins for C4R370 (Komagataella phaffii (strain GS115 / ATCC 20864))
Explore C4R370 
Go to UniProtKB:  C4R370
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC4R370
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription elongation factor Spt6S [auth m]1,503Komagataella phaffiiMutation(s): 0 
Gene Names: PAS_chr4_0308
UniProt
Find proteins for C4R7H2 (Komagataella phaffii (strain GS115 / ATCC 20864))
Explore C4R7H2 
Go to UniProtKB:  C4R7H2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC4R7H2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Protein that interacts with Spt6p and copurifies with Spt5p and RNA polymerase IIT [auth n]417Komagataella phaffiiMutation(s): 0 
Gene Names: PAS_chr4_0349
UniProt
Find proteins for C4R7L8 (Komagataella phaffii (strain GS115 / ATCC 20864))
Explore C4R7L8 
Go to UniProtKB:  C4R7L8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC4R7L8
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Component of the Paf1p complexU [auth q]1,084Komagataella phaffiiMutation(s): 0 
Gene Names: PAS_chr3_1035
UniProt
Find proteins for C4R6B2 (Komagataella phaffii (strain GS115 / ATCC 20864))
Explore C4R6B2 
Go to UniProtKB:  C4R6B2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC4R6B2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
RNAPII-associated chromatin remodeling Paf1 complex subunitV [auth r]544Komagataella phaffiiMutation(s): 0 
Gene Names: RTF1PP7435_Chr1-1405
UniProt
Find proteins for F2QQ42 (Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1))
Explore F2QQ42 
Go to UniProtKB:  F2QQ42
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF2QQ42
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Leo1W [auth u]459Komagataella phaffiiMutation(s): 0 
Gene Names: PAS_chr3_1154
UniProt
Find proteins for C4R3K1 (Komagataella phaffii (strain GS115 / ATCC 20864))
Explore C4R3K1 
Go to UniProtKB:  C4R3K1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC4R3K1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
RNAP II-associated proteinX [auth v]396Komagataella phaffiiMutation(s): 0 
Gene Names: PAS_chr4_0902
UniProt
Find proteins for C4R997 (Komagataella phaffii (strain GS115 / ATCC 20864))
Explore C4R997 
Go to UniProtKB:  C4R997
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC4R997
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Constituent of Paf1 complex with RNA polymerase II, Paf1p, Hpr1p, Ctr9, Leo1, Rtf1 and Ccr4pY [auth x]395Komagataella phaffiiMutation(s): 0 
Gene Names: PAS_chr2-1_0674
UniProt
Find proteins for C4R1E6 (Komagataella phaffii (strain GS115 / ATCC 20864))
Explore C4R1E6 
Go to UniProtKB:  C4R1E6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC4R1E6
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 14
MoleculeChains LengthOrganismImage
DNA (198-mer)198synthetic construct
Sequence Annotations
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 15
MoleculeChains LengthOrganismImage
RNA (5'-R(P*AP*AP*GP*CP*CP*UP*GP*GP*UP*GP*UP*CP*UP*UP*GP*GP*GP*UP*G)-3')O [auth P]19synthetic construct
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 16
MoleculeChains LengthOrganismImage
DNA (198-mer)P [auth T]198synthetic construct
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth A]
CA [auth B]
DA [auth C]
EA [auth I]
FA [auth I]
AA [auth A],
CA [auth B],
DA [auth C],
EA [auth I],
FA [auth I],
GA [auth J],
HA [auth L],
IA [auth M],
JA [auth V],
Z [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
BA [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)JapanJP20H03201
Japan Society for the Promotion of Science (JSPS)JapanJP20H05690
Japan Society for the Promotion of Science (JSPS)JapanJP20H00449
Japan Society for the Promotion of Science (JSPS)JapanJP18H05534
Japan Agency for Medical Research and Development (AMED)JapanJP20am0101082
Japan Agency for Medical Research and Development (AMED)JapanJP21am0101076
Japan Science and TechnologyJapanJPMJER1901

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-07
    Type: Initial release
  • Version 1.1: 2022-09-21
    Changes: Database references
  • Version 1.2: 2022-10-12
    Changes: Database references