4YM7 image
Deposition Date 2015-03-06
Release Date 2015-09-09
Last Version Date 2024-11-20
Entry Detail
PDB ID:
4YM7
Keywords:
TRANSFERASE
Title:
RNA polymerase I structure with an alternative dimer hinge
Biological Source:
Source Organism:
Saccharomyces cerevisiae (Taxon ID: 4932)
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
5.50 Å
R-Value Free:
0.23
R-Value Work:
0.19
R-Value Observed:
0.19
Space Group:
C 1 2 1
4YM7 validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase I subunit RPA190
Gene (Uniprot):RPA190
Chain IDs:A (auth: AA), P (auth: BA), EA (auth: CA), TA (auth: DA), IB (auth: EA), XB (auth: FA)
Chain Length:1664
Number of Molecules:6
Biological Source:Saccharomyces cerevisiae
UniProt ID:P10964 Pfam ID:PF04997, PF00623, PF04983, PF05000, PF04998
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase I subunit RPA135
Gene (Uniprot):RPA135
Chain IDs:B (auth: AB), Q (auth: BB), FA (auth: CB), UA (auth: DB), JB (auth: EB), YB (auth: FB)
Chain Length:1203
Number of Molecules:6
Biological Source:Saccharomyces cerevisiae
UniProt ID:P22138 Pfam ID:PF04563, PF04561, PF04565, PF06883, PF00562, PF04560
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases I and III subunit RPAC1
Gene (Uniprot):RPC40
Chain IDs:C (auth: AC), R (auth: BC), GA (auth: CC), VA (auth: DC), KB (auth: EC), ZB (auth: FC)
Chain Length:335
Number of Molecules:6
Biological Source:Saccharomyces cerevisiae
UniProt ID:P07703 Pfam ID:PF01193, PF01000
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase I subunit RPA14
Gene (Uniprot):RPA14
Chain IDs:D (auth: AD), S (auth: BD), HA (auth: CD), WA (auth: DD), LB (auth: ED), AC (auth: FD)
Chain Length:137
Number of Molecules:6
Biological Source:Saccharomyces cerevisiae
UniProt ID:P50106 Pfam ID:PF08203
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases I, II, and III subunit RPABC1
Gene (Uniprot):RPB5
Chain IDs:E (auth: AE), T (auth: BE), IA (auth: CE), XA (auth: DE), MB (auth: EE), BC (auth: FE)
Chain Length:215
Number of Molecules:6
Biological Source:Saccharomyces cerevisiae
UniProt ID:P20434 Pfam ID:PF03871, PF01191
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases I, II, and III subunit RPABC2
Gene (Uniprot):RPO26
Chain IDs:F (auth: AF), U (auth: BF), JA (auth: CF), YA (auth: DF), NB (auth: EF), CC (auth: FF)
Chain Length:155
Number of Molecules:6
Biological Source:Saccharomyces cerevisiae
UniProt ID:P20435 Pfam ID:PF01192
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase I subunit RPA43
Gene (Uniprot):RPA43
Chain IDs:G (auth: AG), O (auth: AO), V (auth: BG), DA (auth: BO), KA (auth: CG), SA (auth: CO), ZA (auth: DG), HB (auth: DO), OB (auth: EG), WB (auth: EO), DC (auth: FG), LC (auth: FO)
Chain Length:326
Number of Molecules:12
Biological Source:Saccharomyces cerevisiae
UniProt ID:P46669 Pfam ID:PF03876, PF17875
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases I, II, and III subunit RPABC3
Gene (Uniprot):RPB8
Chain IDs:H (auth: AH), W (auth: BH), LA (auth: CH), AB (auth: DH), PB (auth: EH), EC (auth: FH)
Chain Length:146
Number of Molecules:6
Biological Source:Saccharomyces cerevisiae
UniProt ID:P20436 Pfam ID:PF03870
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase I subunit RPA12
Gene (Uniprot):RPA12
Chain IDs:I (auth: AI), X (auth: BI), MA (auth: CI), BB (auth: DI), QB (auth: EI), FC (auth: FI)
Chain Length:125
Number of Molecules:6
Biological Source:Saccharomyces cerevisiae
UniProt ID:P32529 Pfam ID:PF02150, PF01096
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases I, II, and III subunit RPABC5
Gene (Uniprot):RPB10
Chain IDs:J (auth: AJ), Y (auth: BJ), NA (auth: CJ), CB (auth: DJ), RB (auth: EJ), GC (auth: FJ)
Chain Length:70
Number of Molecules:6
Biological Source:Saccharomyces cerevisiae
UniProt ID:P22139 Pfam ID:PF01194
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases I and III subunit RPAC2
Gene (Uniprot):RPC19
Chain IDs:K (auth: AK), Z (auth: BK), OA (auth: CK), DB (auth: DK), SB (auth: EK), HC (auth: FK)
Chain Length:142
Number of Molecules:6
Biological Source:Saccharomyces cerevisiae
UniProt ID:P28000 Pfam ID:PF13656
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases I, II, and III subunit RPABC4
Gene (Uniprot):RPC10
Chain IDs:L (auth: AL), AA (auth: BL), PA (auth: CL), EB (auth: DL), TB (auth: EL), IC (auth: FL)
Chain Length:70
Number of Molecules:6
Biological Source:Saccharomyces cerevisiae
UniProt ID:P40422 Pfam ID:PF03604
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase I subunit RPA49
Gene (Uniprot):RPA49
Chain IDs:M (auth: AM), BA (auth: BM), QA (auth: CM), FB (auth: DM), UB (auth: EM), JC (auth: FM)
Chain Length:415
Number of Molecules:6
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q01080 Pfam ID:PF06870
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase I subunit RPA34
Gene (Uniprot):RPA34
Chain IDs:N (auth: AN), CA (auth: BN), RA (auth: CN), GB (auth: DN), VB (auth: EN), KC (auth: FN)
Chain Length:233
Number of Molecules:6
Biological Source:Saccharomyces cerevisiae
UniProt ID:P47006 Pfam ID:PF08208
Ligand Molecules
ZN
Primary Citation
An alternative RNA polymerase I structure reveals a dimer hinge.
Acta Crystallogr.,Sect.D 71 1850 1855 (2015)
PMID: 26327374 DOI: 10.1107/S1399004715012651

Abstact

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.

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Disease

Primary Citation of related structures
4YM7