5XON

RNA Polymerase II elongation complex bound with Spt4/5 and TFIIS


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.83 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

Structure of the complete elongation complex of RNA polymerase II with basal factors

Ehara, H.Yokoyama, T.Shigematsu, H.Yokoyama, S.Shirouzu, M.Sekine, S.I.

(2017) Science 357: 921-924

  • DOI: 10.1126/science.aan8552
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • In the early stage of transcription, eukaryotic RNA polymerase II (Pol II) exchanges initiation factors with elongation factors to form an elongation complex for processive transcription. Here we report the structure of the Pol II elongation complex ...

    In the early stage of transcription, eukaryotic RNA polymerase II (Pol II) exchanges initiation factors with elongation factors to form an elongation complex for processive transcription. Here we report the structure of the Pol II elongation complex bound with the basal elongation factors Spt4/5, Elf1, and TFIIS. Spt4/5 (the Spt4/Spt5 complex) and Elf1 modify a wide area of the Pol II surface. Elf1 bridges the Pol II central cleft, completing a "DNA entry tunnel" for downstream DNA. Spt4 and the Spt5 NGN and KOW1 domains encircle the upstream DNA, constituting a "DNA exit tunnel." The Spt5 KOW4 and KOW5 domains augment the "RNA exit tunnel," directing the exiting nascent RNA. Thus, the elongation complex establishes a completely different transcription and regulation platform from that of the initiation complexes.


    Organizational Affiliation

    RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan. shunichi.sekine@riken.jp.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunitA1743Komagataella phaffii GS115Mutation(s): 0 
Gene Names: PAS_chr3_0568
EC: 2.7.7.6
Find proteins for C4R4Y0 (Komagataella phaffii (strain GS115 / ATCC 20864))
Explore C4R4Y0 
Go to UniProtKB:  C4R4Y0
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

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))
Explore C4QZQ7 
Go to UniProtKB:  C4QZQ7
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

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))
Explore C4R7L2 
Go to UniProtKB:  C4R7L2
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

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))
Explore C4R2U9 
Go to UniProtKB:  C4R2U9
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

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))
Explore C4R1V1 
Go to UniProtKB:  C4R1V1
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

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))
Explore C4R9A1 
Go to UniProtKB:  C4R9A1
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase subunit ABC14.5, common to RNA polymerases I, II, and IIIH145Komagataella phaffii GS115Mutation(s): 0 
Gene Names: PAS_chr2-2_0309
Find proteins for C4R273 (Komagataella phaffii (strain GS115 / ATCC 20864))
Explore C4R273 
Go to UniProtKB:  C4R273
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

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))
Explore C4R009 
Go to UniProtKB:  C4R009
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

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))
Explore C4R3Z5 
Go to UniProtKB:  C4R3Z5
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase subunit, found in RNA polymerase complexes I, II, and IIIL72Komagataella phaffii GS115Mutation(s): 0 
Gene Names: PAS_chr1-1_0166
Find proteins for C4QWA8 (Komagataella phaffii (strain GS115 / ATCC 20864))
Explore C4QWA8 
Go to UniProtKB:  C4QWA8
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
General transcription elongation factor TFIISU190Komagataella phaffii GS115Mutation(s): 0 
Gene Names: PAS_chr2-2_0135
Find proteins for C4R2R6 (Komagataella phaffii (strain GS115 / ATCC 20864))
Explore C4R2R6 
Go to UniProtKB:  C4R2R6
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

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))
Explore C4R0E6 
Go to UniProtKB:  C4R0E6
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
Protein that forms a complex with Spt4pW612Komagataella phaffii GS115Mutation(s): 0 
Gene Names: PAS_chr3_1136
Find proteins for C4R370 (Komagataella phaffii (strain GS115 / ATCC 20864))
Explore C4R370 
Go to UniProtKB:  C4R370
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

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))
Explore C4R3P8 
Go to UniProtKB:  C4R3P8
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunitI115Komagataella phaffii GS115Mutation(s): 0 
Gene Names: PAS_chr1-4_0359
Find proteins for C4QY79 (Komagataella phaffii (strain GS115 / ATCC 20864))
Explore C4QY79 
Go to UniProtKB:  C4QY79
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar nucleic acids by: Sequence   |  Structure

Entity ID: 13
MoleculeChainsLengthOrganism
RNA (30-MER)P30synthetic construct

Find similar nucleic acids by: Sequence  |  Structure

Entity ID: 14
MoleculeChainsLengthOrganism
DNA (48-MER)T48synthetic construct

Find similar nucleic acids by: Sequence  |  Structure

Entity ID: 15
MoleculeChainsLengthOrganism
DNA (48-MER)N48synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

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

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.83 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-08-16
    Type: Initial release
  • Version 1.1: 2017-09-13
    Changes: Database references
  • Version 1.2: 2019-11-06
    Changes: Data collection, Other