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 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 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: https://doi.org/10.1107/S1399004715012651
  • Primary Citation of Related Structures:  
    4YM7

  • 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-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: 

    Gene Center Munich and Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase I subunit RPA1901,664Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
UniProt
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase I subunit RPA1351,203Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I and III subunit RPAC1335Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase I subunit RPA14137Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC1215Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC2155Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase I subunit RPA43326Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC3146Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase I subunit RPA12125Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC570Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I and III subunit RPAC2142Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC470Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase I subunit RPA49415Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase I subunit RPA34233Saccharomyces cerevisiaeMutation(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 
AD [auth CA]
AE [auth FJ]
BD [auth CA]
BE [auth FL]
CD [auth CB]
AD [auth CA],
AE [auth FJ],
BD [auth CA],
BE [auth FL],
CD [auth CB],
DD [auth CI],
ED [auth CI],
FD [auth CJ],
GD [auth CL],
HD [auth DA],
ID [auth DA],
JD [auth DB],
KD [auth DI],
LD [auth DI],
MC [auth AA],
MD [auth DJ],
NC [auth AA],
ND [auth DL],
OC [auth AB],
OD [auth EA],
PC [auth AI],
PD [auth EA],
QC [auth AI],
QD [auth EB],
RC [auth AJ],
RD [auth EI],
SC [auth AL],
SD [auth EI],
TC [auth BA],
TD [auth EJ],
UC [auth BA],
UD [auth EL],
VC [auth BB],
VD [auth FA],
WC [auth BI],
WD [auth FA],
XC [auth BI],
XD [auth FB],
YC [auth BJ],
YD [auth FI],
ZC [auth BL],
ZD [auth FI]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
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  (Full details and data files)

  • 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
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Refinement description
  • Version 1.4: 2024-11-20
    Changes: Structure summary