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- PDB-6i84: Structure of transcribing RNA polymerase II-nucleosome complex -

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Entry
Database: PDB / ID: 6i84
TitleStructure of transcribing RNA polymerase II-nucleosome complex
Components
  • (DNA-directed RNA polymerase II subunit ...Polymerase) x 7
  • (DNA-directed RNA polymerases I, II, and III subunit ...RNA polymerase) x 5
  • DNA (158-MER)
  • DNA (170-MER)
  • Histone H2A type 1
  • Histone H2B 1.1
  • Histone H3.2
  • Histone H4
  • RNA
KeywordsTRANSCRIPTION / Nucleosome / elongation / chromatin / RNA polymerase II
Function / homologyRNA-binding domain, S1 / RNA polymerase Rpb5, N-terminal domain superfamily / Histone H2A conserved site / Pol II subunit B9, C-terminal zinc ribbon / CENP-T/Histone H4, histone fold / RPB5-like RNA polymerase subunit superfamily / RPB6/omega subunit-like superfamily / RNA polymerase, RBP11-like subunit / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase Rpb7-like, N-terminal domain superfamily ...RNA-binding domain, S1 / RNA polymerase Rpb5, N-terminal domain superfamily / Histone H2A conserved site / Pol II subunit B9, C-terminal zinc ribbon / CENP-T/Histone H4, histone fold / RPB5-like RNA polymerase subunit superfamily / RPB6/omega subunit-like superfamily / RNA polymerase, RBP11-like subunit / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase Rpb7-like, N-terminal domain superfamily / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase RBP11 / RNA polymerase Rpb1, funnel domain superfamily / Rpb4/RPC9 superfamily / RNA polymerase Rpb1, domain 7 superfamily / DNA-directed RNA polymerase subunit Rpb5-like / Histone H2A, C-terminal domain / DNA-directed RNA polymerase, subunit RPB6 / Core histone H2A/H2B/H3/H4 / DNA-directed RNA polymerase RPB5 subunit, eukaryote/virus / Histone-fold / HRDC-like superfamily / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / DNA-directed RNA polymerase subunit/transcription factor S / RNA polymerase subunit, RPB6/omega / Nucleic acid-binding, OB-fold / RNA polymerase Rpb2, OB-fold / RNA polymerase subunit RPB10 / DNA-directed RNA polymerase, subunit 2 / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / Histone H4, conserved site / RNA polymerase, subunit H/Rpb5, conserved site / Archaeal RpoH /eukaryotic RPB5 RNA polymerase subunit / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerases, subunit N, zinc binding site / RNA polymerases K / 14 to 18 Kd subunits signature. / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerase Rpb2, domain 6 / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / C-terminus of histone H2A / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1 C-terminal repeat / RNA polymerase Rpb3/Rpb11 dimerisation domain / Centromere kinetochore component CENP-T histone fold / Histone H2A signature. / RNA polymerase Rpb1, domain 3 / Histone H4 signature. / Eukaryotic RNA polymerase II heptapeptide repeat. / Histone H3 signature 1. / Histone H2B signature. / RNA polymerases D / 30 to 40 Kd subunits signature. / Zinc finger TFIIS-type signature. / Histone H3 signature 2. / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb2, domain 5 / S1 RNA binding domain / RNA polymerases M/15 Kd subunit / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb3/RpoA insert domain / Transcription factor S-II (TFIIS) / RNA polymerase Rpb5, C-terminal domain / RNA polymerase Rpb6 / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases N / 8 kDa subunit / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb8 / RNA polymerase Rpb5, N-terminal domain / RNA polymerase Rpb4 / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 2 / RNA polymerase beta subunit / RNA polymerase Rpb2, domain 3 / DNA-directed RNA polymerase, RBP11-like dimerisation domain / RNA polymerase Rpb2, domain 5 / RNA polymerases H / 23 Kd subunits signature. / Formation of TC-NER Pre-Incision Complex / RNA polymerase, alpha subunit / RNA polymerase II, heptapeptide repeat, eukaryotic / Histone H2B / DNA-directed RNA polymerase, subunit N/Rpb10 / Histone H3/CENP-A / RNA polymerases N / 8 Kd subunits signature. / RNA polymerases L / 13 to 16 Kd subunits signature. / RNA polymerases beta chain signature. / RNA polymerase Rpb2, domain 4 / Zinc finger TFIIS-type profile. / Formation of the Early Elongation Complex / RNA Polymerase II Pre-transcription Events / Dual incision in TC-NER / Zinc finger, TFIIS-type / Gap-filling DNA repair synthesis and ligation in TC-NER / TP53 Regulates Transcription of DNA Repair Genes
Function and homology information
Specimen sourceXenopus laevis (African clawed frog)
Saccharomyces cerevisiae (baker's yeast)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4.4 Å resolution
AuthorsFarnung, L. / Vos, S.M. / Cramer, P.
CitationJournal: Nat Commun / Year: 2018
Title: Structure of transcribing RNA polymerase II-nucleosome complex.
Authors: Lucas Farnung / Seychelle M Vos / Patrick Cramer
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 19, 2018 / Release: Jan 2, 2019

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Structure visualization

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Assembly

Deposited unit
M: Histone H3.2
Q: Histone H2A type 1
V: Histone H2A type 1
T: DNA (170-MER)
N: DNA (158-MER)
O: Histone H4
R: Histone H2B 1.1
S: Histone H3.2
U: Histone H4
W: Histone H2B 1.1
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
P: RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)732,09132
Polyers731,54323
Non-polymers5489
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
MethodPISA

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Components

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Protein/peptide , 4 types, 8 molecules MSQVOURW

#1: Protein/peptide Histone H3.2


Mass: 15435.126 Da / Num. of mol.: 2 / Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P84233
#2: Protein/peptide Histone H2A type 1


Mass: 14109.436 Da / Num. of mol.: 2 / Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P06897
#5: Protein/peptide Histone H4 /


Mass: 11394.426 Da / Num. of mol.: 2 / Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P62799
#6: Protein/peptide Histone H2B 1.1 / H2B1.1


Mass: 13655.948 Da / Num. of mol.: 2 / Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P02281

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DNA chain , 2 types, 2 molecules TN

#3: DNA chain DNA (170-MER)


Mass: 52041.215 Da / Num. of mol.: 1 / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (158-MER)


Mass: 49537.551 Da / Num. of mol.: 1 / Source: (synth.) synthetic construct (others)

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

#7: Protein/peptide DNA-directed RNA polymerase II subunit RPB1 / Polymerase / 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) (yeast)
References: UniProt: P04050, DNA-directed RNA polymerase
#8: Protein/peptide DNA-directed RNA polymerase II subunit RPB2 / Polymerase / 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) (yeast)
References: UniProt: P08518, DNA-directed RNA polymerase
#9: Protein/peptide DNA-directed RNA polymerase II subunit RPB3 / Polymerase / RNA polymerase II subunit B3 / B44.5 / DNA-directed RNA polymerase II 45 kDa polypeptide


Mass: 38809.113 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P16370
#10: Protein/peptide DNA-directed RNA polymerase II subunit RPB4 / Polymerase / 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) (yeast)
References: UniProt: P20433
#13: Protein/peptide DNA-directed RNA polymerase II subunit RPB7 / Polymerase / RNA polymerase II subunit B7 / B16


Mass: 19081.053 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P34087
#15: Protein/peptide DNA-directed RNA polymerase II subunit RPB9 / Polymerase / 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) (yeast)
References: UniProt: P27999
#17: Protein/peptide DNA-directed RNA polymerase II subunit RPB11 / Polymerase / 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) (yeast)
References: UniProt: P38902

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

#11: Protein/peptide DNA-directed RNA polymerases I, II, and III subunit RPABC1 / RNA polymerase / 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) (yeast)
References: UniProt: P20434
#12: Protein/peptide DNA-directed RNA polymerases I, II, and III subunit RPABC2 / RNA polymerase / 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) (yeast)
References: UniProt: P20435
#14: Protein/peptide DNA-directed RNA polymerases I, II, and III subunit RPABC3 / RNA polymerase / 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) (yeast)
References: UniProt: P20436
#16: Protein/peptide DNA-directed RNA polymerases I, II, and III subunit RPABC5 / RNA polymerase / 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) (yeast)
References: UniProt: P22139
#18: Protein/peptide DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerase / 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) (yeast)
References: UniProt: P40422

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RNA chain , 1 types, 1 molecules P

#19: RNA chain RNA /


Mass: 3137.908 Da / Num. of mol.: 1 / Source: (synth.) synthetic construct (others)

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Non-polymers , 2 types, 9 molecules

#20: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Formula: Zn / Zinc
#21: Chemical ChemComp-MG / MAGNESIUM ION


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

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent IDSource
1Complex of S. cerevisiae RNA polymerase II and X. leaves NCPCOMPLEX1,2,3,4,5,6,7, 9,10,11,12,13,14,16,17,18,19,8,150MULTIPLE SOURCES
2Complex of S. cerevisiae RNA polymerase II and X. leaves NCPCOMPLEX1,2,5,61RECOMBINANT
3Complex of S. cerevisiae RNA polymerase II and X. leaves NCPCOMPLEX7,8,9,10,11,12,13,14,16,17,18,151NATURAL
4Complex of S. cerevisiae RNA polymerase II and X. leaves NCPCOMPLEX3,4,191NATURAL
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
128355Xenopus laevis (African clawed frog)
23559292Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
3432630synthetic construct (others)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid type: UltrAuFoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 kelvins

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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: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 46 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.14_3260: / Classification: refinement
EM software
IDNameVersionCategory
2EPUimage acquisition
4Warp1.0.5CTF correction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1
3D reconstructionResolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 49703 / Symmetry type: POINT

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