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 

wwPDB Validation 3D Report Full Report



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
  • Structures With Same Primary Citation

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



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunitA, M1743Komagataella 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 betaB, N1227Komagataella 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 coreC, O304Komagataella 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 B32D, P186Komagataella 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 IIIE, Q214Komagataella 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 IIIF, R155Komagataella 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 subunitG, S171Komagataella 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 IIIH, T145Komagataella 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 subunitI, U115Komagataella 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 IIIJ, V72Komagataella 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 B12.5K, W118Komagataella 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, found in RNA polymerase complexes I, II, and IIIL, X73Komagataella phaffii GS115Mutation(s): 0 
Gene Names: PAS_chr1-1_0166
Find proteins for C4QWA8 (Komagataella phaffii (strain GS115 / ATCC 20864))
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
A, B, C, I, J, L, M, N, O, U, V, X
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
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 

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