5XOG

RNA Polymerase II elongation complex bound with Spt5 KOW5 and Elf1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 

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

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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))
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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))
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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))
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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))
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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))
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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))
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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))
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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))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunitI115Komagataella phaffii CBS 7435Mutation(s): 0 
Gene Names: RPB9PP7435_Chr1-1144
Find proteins for F2QPE6 (Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1))
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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))
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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))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase subunit ABC10-alphaL72Komagataella phaffii CBS 7435Mutation(s): 0 
Gene Names: RPC10PP7435_Chr1-0476
Find proteins for F2QMI1 (Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Transcription elongation factor 1 homologM85Komagataella pastorisMutation(s): 3 
Gene Names: ELF1ATY40_BA7504229
Find proteins for A0A1B2JER8 (Komagataella pastoris)
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
Spt4/5 complex componentW83Komagataella phaffii CBS 7435Mutation(s): 0 
Gene Names: SPT5PP7435_Chr3-0027
Find proteins for F2QUC3 (Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1))
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  • Reference Sequence
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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

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Entity ID: 14
MoleculeChainsLengthOrganism
DNA (39-MER)T39synthetic construct

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Entity ID: 15
MoleculeChainsLengthOrganism
DNA (30-MER)N30synthetic construct
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
APC
Query on APC

Download CCD File 
A
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
C11 H18 N5 O12 P3
CAWZRIXWFRFUQB-IOSLPCCCSA-N
 Ligand Interaction
ZN
Query on ZN

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A, B, C, I, J, L, M
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 155.25α = 90
b = 159.91β = 90
c = 268.93γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-08-16
    Type: Initial release
  • Version 1.1: 2017-08-23
    Changes: Database references
  • Version 1.2: 2017-09-13
    Changes: Database references