5U5Q

12 Subunit RNA Polymerase II at Room Temperature collected using SFX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.219 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Double-flow focused liquid injector for efficient serial femtosecond crystallography.

Oberthuer, D.Knoska, J.Wiedorn, M.O.Beyerlein, K.R.Bushnell, D.A.Kovaleva, E.G.Heymann, M.Gumprecht, L.Kirian, R.A.Barty, A.Mariani, V.Tolstikova, A.Adriano, L.Awel, S.Barthelmess, M.Dorner, K.Xavier, P.L.Yefanov, O.James, D.R.Nelson, G.Wang, D.Calvey, G.Chen, Y.Schmidt, A.Szczepek, M.Frielingsdorf, S.Lenz, O.Snell, E.Robinson, P.J.Sarler, B.Belsak, G.Macek, M.Wilde, F.Aquila, A.Boutet, S.Liang, M.Hunter, M.S.Scheerer, P.Lipscomb, J.D.Weierstall, U.Kornberg, R.D.Spence, J.C.Pollack, L.Chapman, H.N.Bajt, S.

(2017) Sci Rep 7: 44628-44628

  • DOI: https://doi.org/10.1038/srep44628
  • Primary Citation of Related Structures:  
    5MND, 5U5Q

  • PubMed Abstract: 

    Serial femtosecond crystallography requires reliable and efficient delivery of fresh crystals across the beam of an X-ray free-electron laser over the course of an experiment. We introduce a double-flow focusing nozzle to meet this challenge, with significantly reduced sample consumption, while improving jet stability over previous generations of nozzles. We demonstrate its use to determine the first room-temperature structure of RNA polymerase II at high resolution, revealing new structural details. Moreover, the double-flow focusing nozzles were successfully tested with three other protein samples and the first room temperature structure of an extradiol ring-cleaving dioxygenase was solved by utilizing the improved operation and characteristics of these devices [corrected].


  • Organizational Affiliation

    Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB11,733Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 2.7.7.6
UniProt
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB21,224Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for P08518 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB3318Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB4221Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC1215Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC2155Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB7171Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC3146Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB9122Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC570Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB11120Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P38902 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC470Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P40422 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.219 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 223.4α = 90
b = 396.8β = 90
c = 287.9γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CrystFELdata reduction
CrystFELdata scaling
Cootmodel building

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesNSF-1231306

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-29
    Type: Initial release
  • Version 1.1: 2017-09-06
    Changes: Author supporting evidence
  • Version 1.2: 2017-11-01
    Changes: Author supporting evidence
  • Version 1.3: 2018-02-14
    Changes: Data collection
  • Version 1.4: 2018-09-19
    Changes: Data collection
  • Version 1.5: 2019-11-27
    Changes: Author supporting evidence