4YM7

RNA polymerase I structure with an alternative dimer hinge

  • Classification: TRANSFERASE
  • Organism(s): Saccharomyces cerevisiae
  • Mutation(s): No 

  • Deposited: 2015-03-06 Released: 2015-09-09 
  • Deposition Author(s): Kostrewa, D., Kuhn, C.-D., Engel, C., Cramer, P.
  • Funding Organization(s): Fonds der Chemischen Industrie, Elite Network of Bavaria, Boehringer Ingelheim Fonds, Graduate Research Academy RNA Biology of SFB960, German Research Foundation, Advanced Grant TRANSIT of the European Research Council

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.50 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

An alternative RNA polymerase I structure reveals a dimer hinge.

Kostrewa, D.Kuhn, C.D.Engel, C.Cramer, P.

(2015) Acta Crystallogr D Biol Crystallogr 71: 1850-1855

  • DOI: 10.1107/S1399004715012651
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • RNA polymerase I (Pol I) is the central, 14-subunit enzyme that synthesizes the ribosomal RNA (rRNA) precursor in eukaryotic cells. The recent crystal structure of Pol I at 2.8 Å resolution revealed two novel elements: the `expander' in the active-ce ...

    RNA polymerase I (Pol I) is the central, 14-subunit enzyme that synthesizes the ribosomal RNA (rRNA) precursor in eukaryotic cells. The recent crystal structure of Pol I at 2.8 Å resolution revealed two novel elements: the `expander' in the active-centre cleft and the `connector' that mediates Pol I dimerization [Engel et al. (2013), Nature (London), 502, 650-655]. Here, a Pol I structure in an alternative crystal form that was solved by molecular replacement using the original atomic Pol I structure is reported. The resulting alternative structure lacks the expander but still shows an expanded active-centre cleft. The neighbouring Pol I monomers form a homodimer with a relative orientation distinct from that observed previously, establishing the connector as a hinge between Pol I monomers.


    Organizational Affiliation

    Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.



Macromolecules

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase I subunit RPA14AD, BD, CD, DD, ED, FD137Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P50106 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC3AH, BH, CH, DH, EH, FH146Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P20436 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase I subunit RPA12AI, BI, CI, DI, EI, FI125Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P32529 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase I subunit RPA34AN, BN, CN, DN, EN, FN233Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P47006 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase I subunit RPA190AA, BA, CA, DA, EA, FA1664Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
Find proteins for P10964 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC5AJ, BJ, CJ, DJ, EJ, FJ70Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P22139 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I and III subunit RPAC2AK, BK, CK, DK, EK, FK142Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC4AL, BL, CL, DL, EL, FL70Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P40422 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase I subunit RPA49AM, BM, CM, DM, EM, FM415Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase I subunit RPA135AB, BB, CB, DB, EB, FB1203Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I and III subunit RPAC1AC, BC, CC, DC, EC, FC335Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC1AE, BE, CE, DE, EE, FE215Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P20434 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC2AF, BF, CF, DF, EF, FF155Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P20435 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase I subunit RPA43AG, AO, BG, BO, CG, CO, DG, DO, EG, EO, FG, FO326Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P46669 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
AA, AB, AI, AJ, AL, BA, BB, BI, BJ, BL, CA, CB, CI, CJ, CL, DA, DB, DI, DJ, DL, EA, EB, EI, EJ, EL, FA, FB, FI, FJ, FL
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.50 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.196 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 619.48α = 90
b = 306.62β = 97.5
c = 251.78γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Fonds der Chemischen IndustrieGermany--
Elite Network of BavariaGermany--
Boehringer Ingelheim FondsGermany--
Graduate Research Academy RNA Biology of SFB960Germany--
German Research FoundationGermany--
Advanced Grant TRANSIT of the European Research CouncilGermany--

Revision History 

  • Version 1.0: 2015-09-09
    Type: Initial release
  • Version 1.1: 2015-09-16
    Changes: Database references
  • Version 1.2: 2017-09-06
    Changes: Author supporting evidence