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- PDB-5vvr: Ternary complex of RNA Pol II, transcription scaffold and Rad26 -

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Basic information

Entry
Database: PDB / ID: 5vvr
TitleTernary complex of RNA Pol II, transcription scaffold and Rad26
DescriptorDNA repair and recombination protein RAD26/DNA Complex
(DNA-directed RNA polymerase II subunit ...) x 7
(DNA-directed RNA polymerases I/II/III subunit ...) x 5
KeywordsTRANSCRIPTION/RNA/DNA / complex / RNA polymerase / CSB / transcription / TRANSCRIPTION-RNA-DNA complex
Specimen sourceSaccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast / Baker's yeast /
Saccharomyces cerevisiae / yeast / Baker's yeast / サッカロミセス・セレビシエ /
MethodElectron microscopy (5.8 Å resolution / Particle / Single particle)
AuthorsLahiri, I. / Leschziner, A.E.
CitationNature, 2017, 551, 653-657

Nature, 2017, 551, 653-657 Yorodumi Papers
Structural basis for the initiation of eukaryotic transcription-coupled DNA repair.
Jun Xu / Indrajit Lahiri / Wei Wang / Adam Wier / Michael A Cianfrocco / Jenny Chong / Alissa A Hare / Peter B Dervan / Frank DiMaio / Andres E Leschziner / Dong Wang

Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 19, 2017 / Release: Nov 22, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Nov 22, 2017Structure modelrepositoryInitial release
1.1Dec 6, 2017Structure modelDatabase referencescitation / citation_author_citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
1.2Dec 13, 2017Structure modelDatabase referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last

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Assembly

Deposited unit
A: DNA-directed RNA polymerase II subunit RPB1
B: DNA-directed RNA polymerase II subunit RPB2
C: DNA-directed RNA polymerase II subunit RPB3
D: DNA-directed RNA polymerase II subunit RPB4
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 II subunit RPB7
H: DNA-directed RNA polymerases I, II, and III subunit RPABC3
I: DNA-directed RNA polymerase II subunit RPB9
J: DNA-directed RNA polymerases I, II, and III subunit RPABC5
K: DNA-directed RNA polymerase II subunit RPB11
L: DNA-directed RNA polymerases I, II, and III subunit RPABC4
M: DNA repair and recombination protein RAD26
N: DNA (NTS)
R: RNA
T: DNA (TS)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)671,44425
Polyers670,89616
Non-polymers5489
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)71430
ΔGint (kcal/M)-448
Surface area (Å2)214860
MethodPISA

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Components

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DNA-directed RNA polymerase II subunit ... , 7 types, 7 molecules ABCDGIK

#1: Polypeptide(L)DNA-directed RNA polymerase II subunit RPB1 / RNA polymerase II subunit B1 / DNA-directed RNA polymerase III largest subunit / RNA polymerase II subunit B220


Mass: 191821.578 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P04050, EC: 2.7.7.6
#2: Polypeptide(L)DNA-directed RNA polymerase II subunit RPB2 / RNA polymerase II subunit 2 / B150 / DNA-directed RNA polymerase II 140 kDa polypeptide


Mass: 138937.297 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P08518, EC: 2.7.7.6
#3: Polypeptide(L)DNA-directed RNA polymerase II subunit RPB3 / RNA polymerase II subunit B3 / B44.5 / DNA-directed RNA polymerase II 45 kDa polypeptide


Mass: 35330.457 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P16370
#4: Polypeptide(L)DNA-directed RNA polymerase II subunit RPB4 / RNA polymerase II subunit B4 / B32 / DNA-directed RNA polymerase II 32 kDa polypeptide


Mass: 25451.191 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P20433
#7: Polypeptide(L)DNA-directed RNA polymerase II subunit RPB7 / RNA polymerase II subunit B7 / B16


Mass: 19081.053 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P34087
#9: Polypeptide(L)DNA-directed RNA polymerase II subunit RPB9 / RNA polymerase II subunit B9 / B12.6 / DNA-directed RNA polymerase II 14.2 kDa polypeptide / DNA-directed RNA polymerase II subunit 9


Mass: 14308.161 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P27999
#11: Polypeptide(L)DNA-directed RNA polymerase II subunit RPB11 / RNA polymerase II subunit B11 / B13.6 / DNA-directed RNA polymerase II 13.6 kDa polypeptide


Mass: 13633.493 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P38902

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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 (strain ATCC 204508 / 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 (strain ATCC 204508 / 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 (strain ATCC 204508 / 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 (strain ATCC 204508 / 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 (strain ATCC 204508 / S288c)
References: UniProt: P40422

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DNA chain , 2 types, 2 molecules NT

#14: DNA chainDNA (NTS)


Mass: 14494.314 Da / Num. of mol.: 1 / Source: (synth.) Saccharomyces cerevisiae
#16: DNA chainDNA (TS)


Mass: 14269.129 Da / Num. of mol.: 1 / Source: (synth.) Saccharomyces cerevisiae

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Polypeptide(L) / RNA chain , 2 types, 2 molecules MR

#13: Polypeptide(L)DNA repair and recombination protein RAD26 / ATP-dependent helicase RAD26


Mass: 124710.570 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P40352, EC: 3.6.4.12
#15: RNA chainRNA


Mass: 3264.036 Da / Num. of mol.: 1 / Source: (synth.) Saccharomyces cerevisiae

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Non-polymers , 2 types, 9 molecules

#17: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Formula: Zn
#18: ChemicalChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Formula: Mg

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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

ComponentName: Ternary complex of RNA Pol II, transcription scaffold and Rad26
Type: COMPLEX
Entity ID: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16
Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Strain: ATCC 204508 / S288c
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 277.15 kelvins

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 7.7 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameCategoryFitting IDImage processing ID
7RosettaMODEL FITTING1
12RELIONRECONSTRUCTION1
13RosettaMODEL REFINEMENT1
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 5.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 19331 / Symmetry type: POINT

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