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 1.1 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
  • Primary Citation of Related Structures:  

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




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
RNA polymerase subunit ABC14.5, common to RNA polymerases I, II, and III
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 GS115 / ATCC 20864)Mutation(s): 0 
Find proteins for C4QY79 (Komagataella phaffii (strain GS115 / ATCC 20864))
Go to UniProtKB:  C4QY79
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, found in RNA polymerase complexes I, II, and III
L
72Komagataella phaffii (strain GS115 / ATCC 20864)Mutation(s): 0 
Find proteins for C4QWA8 (Komagataella phaffii (strain GS115 / ATCC 20864))
Go to UniProtKB:  C4QWA8
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
General transcription elongation factor TFIIS
U
190Komagataella phaffii (strain GS115 / ATCC 20864)Mutation(s): 0 
Find proteins for C4R2R6 (Komagataella phaffii (strain GS115 / ATCC 20864))
Go to UniProtKB:  C4R2R6
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
Transcription elongation factor SPT4
V
108Komagataella phaffii (strain GS115 / ATCC 20864)Mutation(s): 0 
Find proteins for C4R0E6 (Komagataella phaffii (strain GS115 / ATCC 20864))
Go to UniProtKB:  C4R0E6
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
Protein that forms a complex with Spt4p
W
612Komagataella phaffii (strain GS115 / ATCC 20864)Mutation(s): 0 
Find proteins for C4R370 (Komagataella phaffii (strain GS115 / ATCC 20864))
Go to UniProtKB:  C4R370
Entity ID: 13
MoleculeChainsLengthOrganism
RNA (30-MER)P30synthetic construct
Entity ID: 14
MoleculeChainsLengthOrganism
DNA (48-MER)T48synthetic construct
Entity ID: 15
MoleculeChainsLengthOrganism
DNA (48-MER)N48synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

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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 or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-08-16
    Type: Initial release
  • Version 1.1: 2017-09-13
    Type: Database references