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 1.3 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: https://doi.org/10.1126/science.aan8552
  • Primary Citation of Related Structures:  
    5XOG, 5XON

  • 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 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.


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
Find proteins for C4R1V1 (Komagataella phaffii (strain GS115 / ATCC 20864))
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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
RNA polymerase subunit ABC14.5, common to RNA polymerases I, II, and III145Komagataella phaffii GS115Mutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit115Komagataella phaffii GS115Mutation(s): 0 
UniProt
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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
Find proteins for C4R009 (Komagataella phaffii (strain GS115 / ATCC 20864))
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase II subunit B12.5118Komagataella phaffii GS115Mutation(s): 0 
UniProt
Find proteins for C4R3Z5 (Komagataella phaffii (strain GS115 / ATCC 20864))
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UniProt GroupC4R3Z5
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase subunit, found in RNA polymerase complexes I, II, and III72Komagataella phaffii GS115Mutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription elongation factor TFIISP [auth U]190Komagataella phaffii GS115Mutation(s): 0 
Gene Names: PAS_chr2-2_0135
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription elongation factor SPT4Q [auth V]108Komagataella phaffii GS115Mutation(s): 0 
Gene Names: PAS_chr2-1_0350
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Protein that forms a complex with Spt4pR [auth W]612Komagataella phaffii GS115Mutation(s): 0 
Gene Names: PAS_chr3_1136
UniProt
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Entity ID: 13
MoleculeChains LengthOrganismImage
RNA (30-MER)M [auth P]30synthetic construct
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Entity ID: 14
MoleculeChains LengthOrganismImage
DNA (48-MER)N [auth T]48synthetic construct
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Entity ID: 15
MoleculeChains LengthOrganismImage
DNA (48-MER)O [auth N]48synthetic 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 
AA [auth L]
BA [auth U]
CA [auth V]
S [auth A]
T [auth A]
AA [auth L],
BA [auth U],
CA [auth V],
S [auth A],
T [auth A],
V [auth B],
W [auth C],
X [auth I],
Y [auth I],
Z [auth J]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG
Download Ideal Coordinates CCD File 
U [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.83 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION2.0.2
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2024-03-27
    Changes: Data collection, Database references, Derived calculations