5XOG

RNA Polymerase II elongation complex bound with Spt5 KOW5 and Elf1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.195 

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
  • 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 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
Transcription elongation factor 1 homolog
M
85Komagataella pastorisMutation(s): 3 
Gene Names: ELF1
Find proteins for A0A1B2JER8 (Komagataella pastoris)
Go to Gene View: ELF1
Go to UniProtKB:  A0A1B2JER8
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
Spt4/5 complex component
W
83Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1)Mutation(s): 0 
Gene Names: SPT5
Find proteins for F2QUC3 (Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1))
Go to UniProtKB:  F2QUC3
Entity ID: 13
MoleculeChainsLengthOrganism
RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*AP*UP*CP*GP*AP*GP*AP*GP*GP*U)-3')P17synthetic construct
Entity ID: 14
MoleculeChainsLengthOrganism
DNA (39-MER)T39synthetic construct
Entity ID: 15
MoleculeChainsLengthOrganism
DNA (30-MER)N30synthetic construct
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

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Download CCD File 
A
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE
C11 H18 N5 O12 P3
CAWZRIXWFRFUQB-IOSLPCCCSA-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: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 155.250α = 90.00
b = 159.910β = 90.00
c = 268.930γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata reduction
PHENIXphasing
XSCALEdata scaling
PHENIXrefinement

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: 2017-08-23
    Type: Database references
  • Version 1.2: 2017-09-13
    Type: Database references