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- PDB-5oa1: RNA polymerase I pre-initiation complex -

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Entry
Database: PDB / ID: 5oa1
TitleRNA polymerase I pre-initiation complex
DescriptorALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA
(DNA-directed RNA polymerase I subunit ...) x 7
(DNA-directed RNA polymerases I and III subunit ...) x 2
(DNA-directed RNA polymerases I/II/III subunit ...) x 5
(RNA polymerase I-specific transcription initiation factor ...) x 4
(ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA- ...) x 10
KeywordsTRANSCRIPTION / RNA polymerase I / pre-initiation complex / transcription
Specimen sourceSaccharomyces cerevisiae s288c / yeast / image: Saccharomyces cerevisiae
MethodElectron microscopy (4.4 Å resolution / Particle / Single particle)
AuthorsSadian, Y. / Tafur, L. / Kosinski, J. / Jakobi, A.J. / Muller, C.W.
CitationEMBO J., 2017

EMBO J., 2017 StrPapers
Structural insights into transcription initiation by yeast RNA polymerase I.
Yashar Sadian / Lucas Tafur / Jan Kosinski / Arjen J Jakobi / Rene Wetzel / Katarzyna Buczak / Wim Jh Hagen / Martin Beck / Carsten Sachse / Christoph W Müller

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jun 20, 2017 / Release: Jul 26, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jul 26, 2017Structure modelrepositoryInitial release
1.1Aug 2, 2017Structure modelDatabase referencescitation_author_citation_author.name

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Assembly

Deposited unit
A: DNA-directed RNA polymerase I subunit RPA190
B: DNA-directed RNA polymerase I subunit RPA135
C: DNA-directed RNA polymerases I and III subunit RPAC1
D: DNA-directed RNA polymerase I subunit RPA14
E: DNA-directed RNA polymerases I, II, and III subunit RPABC1
F: DNA-directed RNA polymerases I, II, and III subunit RPABC2
G: DNA-directed RNA polymerase I subunit RPA43
H: DNA-directed RNA polymerases I, II, and III subunit RPABC3
I: DNA-directed RNA polymerase I subunit RPA12
J: DNA-directed RNA polymerases I, II, and III subunit RPABC5
K: DNA-directed RNA polymerases I and III subunit RPAC2
L: DNA-directed RNA polymerases I, II, and III subunit RPABC4
M: DNA-directed RNA polymerase I subunit RPA49
N: DNA-directed RNA polymerase I subunit RPA34
O: RNA polymerase I-specific transcription initiation factor RRN3
S: DNA (49-MER)
T: DNA (56-MER)
U: RNA polymerase I-specific transcription initiation factor RRN7
V: RNA polymerase I-specific transcription initiation factor RRN6
W: RNA polymerase I-specific transcription initiation factor RRN11
1: ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA
2: ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA
3: ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA
4: ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA
5: ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA
6: ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA
7: ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA
8: ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA
9: ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA
Q: ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA
P: ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA
Z: ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA
Y: ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA
R: ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)944,73141
Polyers944,27334
Non-polymers4587
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_5551
MethodPISA

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Components

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DNA-directed RNA polymerase I subunit ... , 7 types, 7 molecules ABDGIMN

#1: Polypeptide(L)DNA-directed RNA polymerase I subunit RPA190 / DNA-directed RNA polymerase I 190 kDa polypeptide / A190 / DNA-directed RNA polymerase I largest subunit


Mass: 186676.969 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288C / References: UniProt: P10964, EC: 2.7.7.6
#2: Polypeptide(L)DNA-directed RNA polymerase I subunit RPA135 / DNA-directed RNA polymerase I 135 kDa polypeptide / A135 / DNA-directed RNA polymerase I polypeptide 2 / RNA polymerase I subunit 2


Mass: 135910.328 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288C / References: UniProt: P22138, EC: 2.7.7.6
#4: Polypeptide(L)DNA-directed RNA polymerase I subunit RPA14 / A14 / DNA-directed RNA polymerase I 14 kDa polypeptide


Mass: 14599.128 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288C / References: UniProt: P50106
#7: Polypeptide(L)DNA-directed RNA polymerase I subunit RPA43 / A43 / DNA-directed DNA-dependent RNA polymerase 36 kDa polypeptide


Mass: 36264.852 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288C / References: UniProt: P46669
#9: Polypeptide(L)DNA-directed RNA polymerase I subunit RPA12 / A12 / A12.2 / DNA-directed RNA polymerase I 13.7 kDa polypeptide


Mass: 13676.566 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288C / References: UniProt: P32529
#13: Polypeptide(L)DNA-directed RNA polymerase I subunit RPA49 / A49 / DNA-directed RNA polymerase I 49 kDa polypeptide


Mass: 46721.707 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288C / References: UniProt: Q01080
#14: Polypeptide(L)DNA-directed RNA polymerase I subunit RPA34 / A34 / DNA-directed DNA-dependent RNA polymerase 34.5 kDa polypeptide / A34.5


Mass: 26933.518 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288C / References: UniProt: P47006

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DNA-directed RNA polymerases I and III subunit ... , 2 types, 2 molecules CK

#3: Polypeptide(L)DNA-directed RNA polymerases I and III subunit RPAC1 / RNA polymerases I and III subunit AC1 / C37 / DNA-directed RNA polymerases I and III 40 kDa polypeptide / C40


Mass: 37732.613 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288C / References: UniProt: P07703
#11: Polypeptide(L)DNA-directed RNA polymerases I and III subunit RPAC2 / RNA polymerases I and III subunit AC2 / AC19 / DNA-directed RNA polymerases I and III 16 kDa polypeptide / RPA19


Mass: 16167.860 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288C / References: UniProt: P28000

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DNA-directed RNA polymerases I, II, and III subunit ... , 5 types, 5 molecules EFHJL

#5: Polypeptide(L)DNA-directed RNA polymerases I, II, and III subunit RPABC1 / RNA polymerases I / II / and III subunit ABC1 / ABC27 / DNA-directed RNA polymerases I / and III 27 kDa polypeptide


Mass: 25117.094 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288C / References: UniProt: P20434
#6: Polypeptide(L)DNA-directed RNA polymerases I, II, and III subunit RPABC2 / RNA polymerases I / II / and III subunit ABC2 / ABC23 / DNA-directed RNA polymerases I / and III 23 kDa polypeptide


Mass: 17931.834 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288C / References: UniProt: P20435
#8: Polypeptide(L)DNA-directed RNA polymerases I, II, and III subunit RPABC3 / RNA polymerases I / II / and III subunit ABC3 / ABC14.4 / ABC14.5 / DNA-directed RNA polymerases I / and III 14.5 kDa polypeptide


Mass: 16525.363 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288C / References: UniProt: P20436
#10: Polypeptide(L)DNA-directed RNA polymerases I, II, and III subunit RPABC5 / RNA polymerases I / II / and III subunit ABC5 / ABC10-beta / ABC8 / DNA-directed RNA polymerases I / and III 8.3 kDa polypeptide


Mass: 8290.732 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288C / References: UniProt: P22139
#12: Polypeptide(L)DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerases I / II / and III subunit ABC4 / ABC10-alpha


Mass: 7729.969 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288C / References: UniProt: P40422

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RNA polymerase I-specific transcription initiation factor ... , 4 types, 4 molecules OUVW

#15: Polypeptide(L)RNA polymerase I-specific transcription initiation factor RRN3


Mass: 72458.258 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288C / References: UniProt: P36070
#18: Polypeptide(L)RNA polymerase I-specific transcription initiation factor RRN7


Mass: 60435.195 Da / Num. of mol.: 1 / Source: (gene. exp.) Saccharomyces cerevisiae S288C / References: UniProt: P40992
#19: Polypeptide(L)RNA polymerase I-specific transcription initiation factor RRN6


Mass: 102163.227 Da / Num. of mol.: 1 / Source: (gene. exp.) Saccharomyces cerevisiae S288C / References: UniProt: P32786
#20: Polypeptide(L)RNA polymerase I-specific transcription initiation factor RRN11


Mass: 59334.262 Da / Num. of mol.: 1 / Source: (gene. exp.) Saccharomyces cerevisiae S288C / References: UniProt: Q04712

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DNA chain , 2 types, 2 molecules ST

#16: DNA chainDNA (49-MER)


Mass: 22000.131 Da / Num. of mol.: 1 / Source: (synth.) Saccharomyces cerevisiae S288c
#17: DNA chainDNA (56-MER)


Mass: 21216.605 Da / Num. of mol.: 1 / Source: (synth.) Saccharomyces cerevisiae S288c

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ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA- ... , 10 types, 12 molecules 1245Q687PZYR

#21: Polypeptide(L)ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA


Mass: 942.027 Da / Num. of mol.: 1 / Source: (gene. exp.) Saccharomyces cerevisiae S288c
#22: Polypeptide(L)ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA


Mass: 1368.494 Da / Num. of mol.: 1 / Source: (gene. exp.) Saccharomyces cerevisiae S288c
#24: Polypeptide(L)ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA


Mass: 1723.883 Da / Num. of mol.: 1 / Source: (gene. exp.) Saccharomyces cerevisiae S288c
#25: Polypeptide(L)ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA


Mass: 1155.260 Da / Num. of mol.: 2 / Source: (gene. exp.) Saccharomyces cerevisiae S288c
#26: Polypeptide(L)ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA


Mass: 728.793 Da / Num. of mol.: 2 / Source: (gene. exp.) Saccharomyces cerevisiae S288c
#27: Polypeptide(L)ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA


Mass: 1794.960 Da / Num. of mol.: 1 / Source: (gene. exp.) Saccharomyces cerevisiae S288c
#28: Polypeptide(L)ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA


Mass: 1581.727 Da / Num. of mol.: 1 / Source: (gene. exp.) Saccharomyces cerevisiae S288c
#29: Polypeptide(L)ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA


Mass: 1084.182 Da / Num. of mol.: 1 / Source: (gene. exp.) Saccharomyces cerevisiae S288c
#30: Polypeptide(L)ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA


Mass: 870.949 Da / Num. of mol.: 1 / Source: (gene. exp.) Saccharomyces cerevisiae S288c
#31: Polypeptide(L)ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA


Mass: 1937.116 Da / Num. of mol.: 1 / Source: (gene. exp.) Saccharomyces cerevisiae S288c

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Polypeptide(L) / Non-polymers , 2 types, 9 molecules 39

#23: Polypeptide(L)ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA


Mass: 657.715 Da / Num. of mol.: 2 / Source: (gene. exp.) Saccharomyces cerevisiae S288c
#32: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

Component
IDNameTypeEntity IDParent IDSource
1RNA polymerase I pre-initiation complexCOMPLEX1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 310MULTIPLE SOURCES
2RNA polymerase I pre-initiation complexCOMPLEX1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 151NATURAL
3RNA polymerase I pre-initiation complexCOMPLEX16, 171RECOMBINANT
4RNA polymerase I pre-initiation complexCOMPLEX18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 311RECOMBINANT
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
12559292Saccharomyces cerevisiae S288C
23559292Saccharomyces cerevisiae S288C
34559292Saccharomyces cerevisiae S288C
Source (recombinant)
IDEntity assembly IDNcbi tax IDOrganism
14562Escherichia coli
2332630synthetic construct
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 2 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 38589 / Symmetry type: POINT
Atomic model buildingDetails: PLEASE NOTE: This entry represents a model built based on a 4.4 Angstrom cryo-EM map. Due to the limited resolution, the sequence in several regions of Rrn6, Rrn7, and Rrn11 subunits is only tentatively assigned and may contain sequence register shifts. To account for these uncertainties, the coordinates of the Core Factor subunits Rrn6, Rrn7, and Rrn11 subunits in this entry only contain backbone atoms and unassigned helices located in the EM density are built as poly-alanines. For more details regarding the model and its limitations please refer to the publication (Sadian et al., EMBO J, 2017) associated with this entry.
Ref protocol: FLEXIBLE FIT

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