5X51

RNA Polymerase II from Komagataella Pastoris (Type-3 crystal)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 7.00 Å
  • R-Value Free: 0.335 
  • R-Value Work: 0.338 
  • R-Value Observed: 0.337 

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Literature

Crystal structure of RNA polymerase II from Komagataella pastoris

Ehara, H.Umehara, T.Sekine, S.I.Yokoyama, S.

(2017) Biochem Biophys Res Commun 487: 230-235

  • DOI: https://doi.org/10.1016/j.bbrc.2017.04.039
  • Primary Citation of Related Structures:  
    5X4Z, 5X50, 5X51

  • PubMed Abstract: 

    RNA polymerase II (Pol II) is a 12-subunit protein complex that conducts the transcription of mRNA and some small RNAs. In this work, the crystal structure of Pol II from the methylotropic yeast Komagataella pastoris (Pichia pastoris) was determined. While the structure is highly homologous to that of Pol II from the budding yeast Saccharomyces cerevisiae, the stalk and clamp modules of the K. pastoris Pol II displayed large inward rotations, closing the central cleft to a greater extent than in the known S. cerevisiae Pol II structures. The conformational differences reflect the inherent flexibilities of the stalk and the clamp, as additional low-resolution structures of K. pastoris Pol II in different crystal forms revealed diverse stalk and clamp orientations. Comparisons with other eukaryotic/archaeal RNA polymerase structures in the Protein Data Bank revealed the distributions of the stalk and clamp orientations. The conformational plasticity should be essential for transcriptional functions and binding various regulatory factors.


  • Organizational Affiliation

    Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan; RIKEN Center for Life Science Technologies, Division of Structural and Synthetic Biology, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit
A, M
1,743Komagataella 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 beta
B, N
1,227Komagataella 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 core
C, O
304Komagataella 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 B32
D, P
186Komagataella 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 III
E, Q
214Komagataella phaffii GS115Mutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III
F, R
155Komagataella phaffii GS115Mutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase II subunit
G, S
171Komagataella 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 III
H, T
145Komagataella phaffii GS115Mutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit
I, U
115Komagataella phaffii CBS 7435Mutation(s): 0 
UniProt
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
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III
J, V
72Komagataella phaffii GS115Mutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase II subunit B12.5
K, W
118Komagataella phaffii GS115Mutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase subunit, found in RNA polymerase complexes I, II, and III
L, X
73Komagataella phaffii GS115Mutation(s): 0 
UniProt
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth B]
BA [auth C]
CA [auth I]
DA [auth I]
EA [auth J]
AA [auth B],
BA [auth C],
CA [auth I],
DA [auth I],
EA [auth J],
FA [auth L],
GA [auth M],
HA [auth M],
IA [auth N],
JA [auth O],
KA [auth U],
LA [auth U],
MA [auth V],
NA [auth X],
Y [auth A],
Z [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 7.00 Å
  • R-Value Free: 0.335 
  • R-Value Work: 0.338 
  • R-Value Observed: 0.337 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 148.77α = 90
b = 158.05β = 92.54
c = 254.96γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-17
    Type: Initial release
  • Version 1.1: 2024-10-30
    Changes: Data collection, Database references, Structure summary