5X50

RNA Polymerase II from Komagataella Pastoris (Type-2 crystal)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.293 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.235 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

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: 10.1016/j.bbrc.2017.04.039
  • Primary Citation of Related Structures:  

  • 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. ...

    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.,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 Structural Biology Laboratory, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan. Electronic address: yokoyama@riken.jp.,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

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, found in RNA polymerase complexes I, II, and III
L
73Komagataella phaffii (strain GS115 / ATCC 20864)Mutation(s): 0 
Find proteins for C4QWA8 (Komagataella phaffii (strain GS115 / ATCC 20864))
Go to UniProtKB:  C4QWA8
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, I, J, L
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.293 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.235 
  • Space Group: P 31
Unit Cell:
Length (Å)Angle (°)
a = 211.750α = 90.00
b = 211.750β = 90.00
c = 132.280γ = 120.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
XDSdata reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-05-17
    Type: Initial release