5M3M

Free monomeric RNA polymerase I at 4.0A resolution

> Summary

Summary for 5M3M

EMDB informationEMD-4148
DescriptorDNA-directed RNA polymerase I subunit RPA190 (E.C.2.7.7.6), DNA-directed RNA polymerase I subunit RPA135 (E.C.2.7.7.6), DNA-directed RNA polymerases I and III subunit RPAC1, DNA-directed RNA polymerases I, II, and III subunit RPABC1, DNA-directed RNA polymerases I, II, and III subunit RPABC2, DNA-directed RNA polymerases I, II, and III subunit RPABC3, DNA-directed RNA polymerase I subunit RPA12, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerases I and III subunit RPAC2, DNA-directed RNA polymerases I, II, and III subunit RPABC4, DNA-directed RNA polymerase I subunit RPA49, DNA-directed RNA polymerase I subunit RPA34, DNA-directed RNA polymerase I subunit RPA14, DNA-directed RNA polymerase I subunit RPA43
Functional Keywordsrna polymerase i, transcription
Biological sourceSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Cellular locationNucleus, nucleolus  P10964 P22138 P07703 P32529 P22139 P28000 P40422 Q01080 P47006 P50106 P46669
Nucleus P20434 P20436
Cytoplasm  P20435
Total number of polymer chains14
Total molecular weight590832.46
Authors
Neyer, S.,Kunz, M.,Geiss, C.,Hantsche, M.,Hodirnau, V.-V.,Seybert, A.,Engel, C.,Scheffer, M.P.,Cramer, P.,Frangakis, A.S. (deposition date: 2016-10-15, release date: 2016-11-23, modification date: 2016-12-28)
Primary citation
Neyer, S.,Kunz, M.,Geiss, C.,Hantsche, M.,Hodirnau, V.V.,Seybert, A.,Engel, C.,Scheffer, M.P.,Cramer, P.,Frangakis, A.S.
Structure of RNA polymerase I transcribing ribosomal DNA genes.
Nature, 540:607-610, 2016
PubMed: 27842382
DOI: 10.1038/nature20561
MImport into Mendeley
Experimental method
ELECTRON MICROSCOPY
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Structure validation

ClashscoreRamachandran outliersSidechain outliers240.7%1.0%MetricValuePercentile RanksWorseBetterPercentile relative to all structuresPercentile relative to all EM structures

More Asymmetric unit images

Molmil generated image of 5m3m
no rotation
Molmil generated image of 5m3m
rotated about x axis by 90°
Molmil generated image of 5m3m
rotated about y axis by 90°

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
ADNA-directed RNA polymerase I subunit RPA190polymer1664186677.01
UniProt (P10964)
Pfam (PF00623)
Pfam (PF04983)
Pfam (PF04997)
Pfam (PF04998)
Pfam (PF05000)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)DNA-directed RNA polymerase I 190 kDa polypeptide,A190,DNA-directed RNA polymerase I largest subunit
BDNA-directed RNA polymerase I subunit RPA135polymer1203135910.31
UniProt (P22138)
Pfam (PF00562)
Pfam (PF04560)
Pfam (PF04563)
Pfam (PF04565)
Pfam (PF06883)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)DNA-directed RNA polymerase I 135 kDa polypeptide,A135,DNA-directed RNA polymerase I polypeptide 2,RNA polymerase I subunit 2
CDNA-directed RNA polymerases I and III subunit RPAC1polymer33537732.61
UniProt (P07703)
Pfam (PF01193)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RNA polymerases I and III subunit AC1,C37,DNA-directed RNA polymerases I and III 40 kDa polypeptide,C40
EDNA-directed RNA polymerases I, II, and III subunit RPABC1polymer21525117.11
UniProt (P20434)
Pfam (PF01191)
Pfam (PF03871)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RNA polymerases I,II,and III subunit ABC1,ABC27,DNA-directed RNA polymerases I,and III 27 kDa polypeptide
FDNA-directed RNA polymerases I, II, and III subunit RPABC2polymer15517931.81
UniProt (P20435)
Pfam (PF01192)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RNA polymerases I,II,and III subunit ABC2,ABC23,DNA-directed RNA polymerases I,and III 23 kDa polypeptide
HDNA-directed RNA polymerases I, II, and III subunit RPABC3polymer14616525.41
UniProt (P20436)
Pfam (PF03870)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RNA polymerases I,II,and III subunit ABC3,ABC14.4,ABC14.5,DNA-directed RNA polymerases I,and III 14.5 kDa polypeptide
IDNA-directed RNA polymerase I subunit RPA12polymer12513676.61
UniProt (P32529)
Pfam (PF01096)
Pfam (PF02150)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)A12,A12.2,DNA-directed RNA polymerase I 13.7 kDa polypeptide
JDNA-directed RNA polymerases I, II, and III subunit RPABC5polymer708290.71
UniProt (P22139)
Pfam (PF01194)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RNA polymerases I,II,and III subunit ABC5,ABC10-beta,ABC8,DNA-directed RNA polymerases I,and III 8.3 kDa polypeptide
KDNA-directed RNA polymerases I and III subunit RPAC2polymer14216167.91
UniProt (P28000)
Pfam (PF13656)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RNA polymerases I and III subunit AC2,AC19,DNA-directed RNA polymerases I and III 16 kDa polypeptide,RPA19
LDNA-directed RNA polymerases I, II, and III subunit RPABC4polymer707730.01
UniProt (P40422)
Pfam (PF03604)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RNA polymerases I,II,and III subunit ABC4,ABC10-alpha
MDNA-directed RNA polymerase I subunit RPA49polymer41546721.71
UniProt (Q01080)
Pfam (PF06870)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)A49,DNA-directed RNA polymerase I 49 kDa polypeptide
NDNA-directed RNA polymerase I subunit RPA34polymer23326933.51
UniProt (P47006)
Pfam (PF08208)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)A34,DNA-directed DNA-dependent RNA polymerase 34.5 kDa polypeptide,A34.5
DDNA-directed RNA polymerase I subunit RPA14polymer13714599.11
UniProt (P50106)
Pfam (PF08203)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)A14,DNA-directed RNA polymerase I 14 kDa polypeptide
GDNA-directed RNA polymerase I subunit RPA43polymer32636264.91
UniProt (P46669)
Pfam (PF03876)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)A43,DNA-directed DNA-dependent RNA polymerase 36 kDa polypeptide
ZINC IONnon-polymer65.47
SULFATE IONnon-polymer96.11

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains14
Total molecular weight590278.5
Non-Polymers*Number of molecules8
Total molecular weight553.9
All*Total molecular weight590832.5
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:ELECTRON MICROSCOPY

Cell axes1.0001.0001.000
Cell angles90.0090.0090.00
SpacegroupP 1
Resolution limits -
the highest resolution shell value -

Data Collection Statistics

Resolution limits -
the highest resolution shell value -

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
Annotated Information is extracted from Literature Info*

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
I0005736cellular_componentDNA-directed RNA polymerase I complex
I0003676molecular_functionnucleic acid binding
I0001054molecular_functionRNA polymerase I activity
I0061629molecular_functionRNA polymerase II sequence-specific DNA binding transcription factor binding
I0008270molecular_functionzinc ion binding
I0006379biological_processmRNA cleavage
I0000122biological_processnegative regulation of transcription from RNA polymerase II promoter
I0042254biological_processribosome biogenesis
I0006363biological_processtermination of RNA polymerase I transcription
I0006360biological_processtranscription from RNA polymerase I promoter
I0042790biological_processtranscription of nuclear large rRNA transcript from RNA polymerase I promoter
D0005736cellular_componentDNA-directed RNA polymerase I complex
D0001054molecular_functionRNA polymerase I activity
D0042254biological_processribosome biogenesis
D0006360biological_processtranscription from RNA polymerase I promoter
D0042790biological_processtranscription of nuclear large rRNA transcript from RNA polymerase I promoter
A0005736cellular_componentDNA-directed RNA polymerase I complex
A0005730cellular_componentnucleolus
A0003677molecular_functionDNA binding
A1990841molecular_functionpromoter-specific chromatin binding
A0001054molecular_functionRNA polymerase I activity
A0008270molecular_functionzinc ion binding
A0042254biological_processribosome biogenesis
A0006360biological_processtranscription from RNA polymerase I promoter
A0042790biological_processtranscription of nuclear large rRNA transcript from RNA polymerase I promoter
B0005829cellular_componentcytosol
B0005736cellular_componentDNA-directed RNA polymerase I complex
B0003677molecular_functionDNA binding
B0046872molecular_functionmetal ion binding
B0032549molecular_functionribonucleoside binding
B0001054molecular_functionRNA polymerase I activity
B0042254biological_processribosome biogenesis
B0006360biological_processtranscription from RNA polymerase I promoter
B0042790biological_processtranscription of nuclear large rRNA transcript from RNA polymerase I promoter
N0005736cellular_componentDNA-directed RNA polymerase I complex
N0005730cellular_componentnucleolus
N0005634cellular_componentnucleus
N0001054molecular_functionRNA polymerase I activity
N0042254biological_processribosome biogenesis
N0006362biological_processtranscription elongation from RNA polymerase I promoter
N0006360biological_processtranscription from RNA polymerase I promoter
N0042790biological_processtranscription of nuclear large rRNA transcript from RNA polymerase I promoter
G0005736cellular_componentDNA-directed RNA polymerase I complex
G0001054molecular_functionRNA polymerase I activity
G0042254biological_processribosome biogenesis
G0006360biological_processtranscription from RNA polymerase I promoter
G0042790biological_processtranscription of nuclear large rRNA transcript from RNA polymerase I promoter
M0005736cellular_componentDNA-directed RNA polymerase I complex
M0005730cellular_componentnucleolus
M0003677molecular_functionDNA binding
M0001054molecular_functionRNA polymerase I activity
M0042254biological_processribosome biogenesis
M0006362biological_processtranscription elongation from RNA polymerase I promoter
M0006360biological_processtranscription from RNA polymerase I promoter
M0042790biological_processtranscription of nuclear large rRNA transcript from RNA polymerase I promoter
E0005736cellular_componentDNA-directed RNA polymerase I complex
E0005665cellular_componentDNA-directed RNA polymerase II, core complex
E0005666cellular_componentDNA-directed RNA polymerase III complex
E0005654cellular_componentnucleoplasm
E0003677molecular_functionDNA binding
E0001054molecular_functionRNA polymerase I activity
E0042254biological_processribosome biogenesis
E0006386biological_processtermination of RNA polymerase III transcription
E0006385biological_processtranscription elongation from RNA polymerase III promoter
E0006360biological_processtranscription from RNA polymerase I promoter
E0006366biological_processtranscription from RNA polymerase II promoter
E0006383biological_processtranscription from RNA polymerase III promoter
E0001172biological_processtranscription, RNA-templated
E0042797biological_processtRNA transcription from RNA polymerase III promoter
F0005737cellular_componentcytoplasm
F0005736cellular_componentDNA-directed RNA polymerase I complex
F0005665cellular_componentDNA-directed RNA polymerase II, core complex
F0005666cellular_componentDNA-directed RNA polymerase III complex
F0005654cellular_componentnucleoplasm
F0003677molecular_functionDNA binding
F0001054molecular_functionRNA polymerase I activity
F0042254biological_processribosome biogenesis
F0006386biological_processtermination of RNA polymerase III transcription
F0006385biological_processtranscription elongation from RNA polymerase III promoter
F0006360biological_processtranscription from RNA polymerase I promoter
F0006366biological_processtranscription from RNA polymerase II promoter
F0006383biological_processtranscription from RNA polymerase III promoter
F0001172biological_processtranscription, RNA-templated
F0042797biological_processtRNA transcription from RNA polymerase III promoter
H0005736cellular_componentDNA-directed RNA polymerase I complex
H0005665cellular_componentDNA-directed RNA polymerase II, core complex
H0005666cellular_componentDNA-directed RNA polymerase III complex
H0005654cellular_componentnucleoplasm
H0003677molecular_functionDNA binding
H0001054molecular_functionRNA polymerase I activity
H0042254biological_processribosome biogenesis
H0006386biological_processtermination of RNA polymerase III transcription
H0006385biological_processtranscription elongation from RNA polymerase III promoter
H0006360biological_processtranscription from RNA polymerase I promoter
H0006366biological_processtranscription from RNA polymerase II promoter
H0006383biological_processtranscription from RNA polymerase III promoter
H0001172biological_processtranscription, RNA-templated
H0042797biological_processtRNA transcription from RNA polymerase III promoter
L0005736cellular_componentDNA-directed RNA polymerase I complex
L0005665cellular_componentDNA-directed RNA polymerase II, core complex
L0005666cellular_componentDNA-directed RNA polymerase III complex
L0005654cellular_componentnucleoplasm
L0003677molecular_functionDNA binding
L0001054molecular_functionRNA polymerase I activity
L0008270molecular_functionzinc ion binding
L0042254biological_processribosome biogenesis
L0006386biological_processtermination of RNA polymerase III transcription
L0006385biological_processtranscription elongation from RNA polymerase III promoter
L0006360biological_processtranscription from RNA polymerase I promoter
L0006366biological_processtranscription from RNA polymerase II promoter
L0006383biological_processtranscription from RNA polymerase III promoter
L0001172biological_processtranscription, RNA-templated
L0042797biological_processtRNA transcription from RNA polymerase III promoter
J0005736cellular_componentDNA-directed RNA polymerase I complex
J0005665cellular_componentDNA-directed RNA polymerase II, core complex
J0005666cellular_componentDNA-directed RNA polymerase III complex
J0005654cellular_componentnucleoplasm
J0003677molecular_functionDNA binding
J0001054molecular_functionRNA polymerase I activity
J0008270molecular_functionzinc ion binding
J0042254biological_processribosome biogenesis
J0006386biological_processtermination of RNA polymerase III transcription
J0006385biological_processtranscription elongation from RNA polymerase III promoter
J0006360biological_processtranscription from RNA polymerase I promoter
J0006366biological_processtranscription from RNA polymerase II promoter
J0006383biological_processtranscription from RNA polymerase III promoter
J0001172biological_processtranscription, RNA-templated
J0042797biological_processtRNA transcription from RNA polymerase III promoter
C0005736cellular_componentDNA-directed RNA polymerase I complex
C0005666cellular_componentDNA-directed RNA polymerase III complex
C0005654cellular_componentnucleoplasm
C0003677molecular_functionDNA binding
C0001054molecular_functionRNA polymerase I activity
C0042254biological_processribosome biogenesis
C0006386biological_processtermination of RNA polymerase III transcription
C0006385biological_processtranscription elongation from RNA polymerase III promoter
C0006360biological_processtranscription from RNA polymerase I promoter
C0006383biological_processtranscription from RNA polymerase III promoter
C0070893biological_processtransposon integration
C0042797biological_processtRNA transcription from RNA polymerase III promoter
K0005736cellular_componentDNA-directed RNA polymerase I complex
K0005666cellular_componentDNA-directed RNA polymerase III complex
K0005654cellular_componentnucleoplasm
K0003677molecular_functionDNA binding
K0001054molecular_functionRNA polymerase I activity
K0042254biological_processribosome biogenesis
K0006386biological_processtermination of RNA polymerase III transcription
K0006385biological_processtranscription elongation from RNA polymerase III promoter
K0006360biological_processtranscription from RNA polymerase I promoter
K0006383biological_processtranscription from RNA polymerase III promoter
K0042797biological_processtRNA transcription from RNA polymerase III promoter
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC15binding site for residue ZN A 3001
ChainResidue
ACYS65
ALEU67
APHE71
ACYS72
APRO73

AC25binding site for residue ZN A 3002
ChainResidue
ACYS102
ALEU103
APHE104
ACYS105
AHIS106

AC35binding site for residue SO4 B 1301
ChainResidue
BHIS532
BSER698
BILE699
BLEU700
BALA701

AC45binding site for residue ZN B 1302
ChainResidue
BCYS1104
BARG1105
BGLU1106
BCYS1107
BGLU1172

AC54binding site for residue ZN I 3001
ChainResidue
ICYS10
ILEU11
IASP12
ICYS13

AC65binding site for residue ZN I 3002
ChainResidue
ICYS86
IMET94
ICYS114
ICYS117
ITYR119

AC74binding site for residue ZN J 3001
ChainResidue
JCYS7
JCYS10
JCYS45
JCYS46

AC84binding site for residue ZN L 3001
ChainResidue
LCYS31
LCYS34
LCYS48
LCYS51

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Functional Information from PDB atom coordinates for the "HETATM" binding sites

site_idNumber of ResiduesDetails
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Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
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Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
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Catalytic Information from CSA

site_idNumber of ResiduesDetails

> Sequence Neighbor

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