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- PDB-9mu9: Structure of a native Drosophila melanogaster Nucleosome Elongati... -

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Entry
Database: PDB / ID: 9mu9
TitleStructure of a native Drosophila melanogaster Nucleosome Elongation Complex (Pol II EC-nucleosome). Composite map
Components
  • (DNA-directed RNA polymerase II subunit ...) x 7
  • (DNA-directed RNA polymerases I, II, and III subunit ...) x 3
  • Histone H2A
  • Histone H2B
  • Histone H3
  • Histone H4
  • Non-template DNA
  • RNA
  • Template DNA
KeywordsTRANSCRIPTION / polymerase / Pol II / mRNA
Function / homology
Function and homology information


Formation of the Early Elongation Complex / mRNA Capping / mRNA Splicing - Minor Pathway / RNA Polymerase I Transcription Initiation / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / Formation of RNA Pol II elongation complex / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Transcription Elongation ...Formation of the Early Elongation Complex / mRNA Capping / mRNA Splicing - Minor Pathway / RNA Polymerase I Transcription Initiation / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / Formation of RNA Pol II elongation complex / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Transcription Elongation / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Polymerase II Pre-transcription Events / Gap-filling DNA repair synthesis and ligation in TC-NER / Formation of TC-NER Pre-Incision Complex / Processing of Capped Intron-Containing Pre-mRNA / Dual incision in TC-NER / polytene chromosome puff / RNA polymerase II transcribes snRNA genes / mRNA Splicing - Major Pathway / HDMs demethylate histones / PKMTs methylate histone lysines / Interleukin-7 signaling / Chromatin modifying enzymes / Condensation of Prophase Chromosomes / SUMOylation of chromatin organization proteins / Metalloprotease DUBs / E3 ubiquitin ligases ubiquitinate target proteins / Factors involved in megakaryocyte development and platelet production / RCAF complex / RMTs methylate histone arginines / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / polytene chromosome band / SIRT1 negatively regulates rRNA expression / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Formation of the beta-catenin:TCF transactivating complex / PRC2 methylates histones and DNA / HDACs deacetylate histones / Ub-specific processing proteases / RNA Polymerase I Promoter Escape / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Regulation of endogenous retroelements by KRAB-ZFP proteins / larval somatic muscle development / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Senescence-Associated Secretory Phenotype (SASP) / Transcriptional regulation by small RNAs / Estrogen-dependent gene expression / HATs acetylate histones / UCH proteinases / Assembly of the ORC complex at the origin of replication / Oxidative Stress Induced Senescence / polytene chromosome / nucleosomal DNA binding / nuclear chromosome / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / transcription by RNA polymerase I / RNA polymerase I complex / transcription elongation by RNA polymerase I / RNA polymerase III complex / transcription-coupled nucleotide-excision repair / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / : / DNA-directed RNA polymerase activity / transcription initiation at RNA polymerase II promoter / ribonucleoside binding / : / : / : / : / : / : / DNA-directed RNA polymerase / structural constituent of chromatin / nucleosome / heterochromatin formation / nucleosome assembly / mitotic cell cycle / chromatin organization / chromosome / cellular response to heat / transcription by RNA polymerase II / nucleic acid binding / protein dimerization activity / protein heterodimerization activity / protein-containing complex binding / chromatin / nucleolus / DNA binding / zinc ion binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
RNA polymerase II, heptapeptide repeat, eukaryotic / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / Zinc finger TFIIS-type signature. ...RNA polymerase II, heptapeptide repeat, eukaryotic / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / Zinc finger TFIIS-type signature. / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / DNA-directed RNA polymerase, M/15kDa subunit / RNA polymerases M/15 Kd subunit / RNA polymerase subunit 9 / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / RNA polymerases M / 15 Kd subunits signature. / DNA-directed RNA polymerase subunit/transcription factor S / : / RNA polymerase, Rpb8 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerase Rpb8 / RNA polymerase subunit 8 / RNA polymerase, Rpb5, N-terminal / RNA polymerase Rpb5, N-terminal domain superfamily / RNA polymerase Rpb5, N-terminal domain / DNA-directed RNA polymerase, subunit RPB6 / DNA-directed RNA polymerase subunit RPABC5/Rpb10 / RNA polymerases, subunit N, zinc binding site / RNA polymerase subunit RPB10 / RNA polymerases N / 8 kDa subunit / RNA polymerases N / 8 Kd subunits signature. / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / RNA polymerase, subunit H/Rpb5, conserved site / RNA polymerases H / 23 Kd subunits signature. / RNA polymerase subunit CX / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo3/Rpb3/RPAC1 / RNA polymerases D / 30 to 40 Kd subunits signature. / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo11 / RNA polymerases L / 13 to 16 Kd subunits signature. / Zinc finger, TFIIS-type / Transcription factor S-II (TFIIS) / Zinc finger TFIIS-type profile. / C2C2 Zinc finger / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / DNA-directed RNA polymerase, RBP11-like dimerisation domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase, subunit H/Rpb5 C-terminal / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / RPB5-like RNA polymerase subunit superfamily / RNA polymerase Rpb5, C-terminal domain / Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerases K / 14 to 18 Kd subunits signature. / : / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 superfamily / RPB6/omega subunit-like superfamily / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases D / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / RNA / GH07456p / Histone H2B / Histone H3 / DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB9 ...DNA / DNA (> 10) / DNA (> 100) / RNA / GH07456p / Histone H2B / Histone H3 / DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB9 / Histone H4 / Histone H2A / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / GEO11084p1 / RPB5 homolog / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase II subunit RPB11 / DNA-directed RNA polymerases I, II, and III subunit RPABC3
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.8 Å
AuthorsVenette-Smith, N.L. / Vishwakarma, R.K. / Dollinger, R. / Schultz, J. / Venkatakrishnan, V. / Babitzke, P. / Anand, G. / Gilmour, D.S. / Armache, J.-P. / Murakami, K.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM131860 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM047477 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM098399 United States
CitationJournal: To Be Published
Title: Structural Characterization of Native RNA Polymerase II Transcription Complexes in Drosophila melanogaster
Authors: Venette-Smith, N.L. / Vishwakarma, R.K. / Dollinger, R. / Schultz, J. / Venkatakrishnan, V. / Babitzke, P. / Anand, G. / Gilmour, D.S. / Armache, J.-P. / Murakami, K.
History
DepositionJan 13, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
R: RNA
T: Template DNA
N: Non-template DNA
g: Histone H2A
c: Histone H2A
h: Histone H2B
d: Histone H2B
e: Histone H3
a: Histone H3
f: Histone H4
b: Histone H4
A: DNA-directed RNA polymerase II subunit RPB1
B: DNA-directed RNA polymerase II subunit RPB2
C: DNA-directed RNA polymerase II subunit RPB3
F: DNA-directed RNA polymerases I, II, and III subunit RPABC2
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 polymerase II subunit RPB12
E: DNA-directed RNA polymerase II subunit RPB5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)615,73129
Polymers615,20821
Non-polymers5238
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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DNA chain , 2 types, 2 molecules TN

#2: DNA chain Template DNA


Mass: 53243.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly)
#3: DNA chain Non-template DNA


Mass: 50692.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly)

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Protein , 4 types, 8 molecules gchdeafb

#4: Protein Histone H2A


Mass: 11552.494 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: P84051
#5: Protein Histone H2B


Mass: 10979.741 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: P02283
#6: Protein Histone H3


Mass: 11746.770 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: P02299
#7: Protein Histone H4


Mass: 9067.586 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: P84040

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

#8: Protein DNA-directed RNA polymerase II subunit RPB1 / RNA polymerase II subunit B1 / DNA-directed RNA polymerase III largest subunit / RNA polymerase II subunit A


Mass: 166420.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: P04052, DNA-directed RNA polymerase
#9: Protein DNA-directed RNA polymerase II subunit RPB2 / RNA polymerase II subunit 2 / RNA polymerase II subunit B2 / DNA-directed RNA polymerase II 140 kDa ...RNA polymerase II subunit 2 / RNA polymerase II subunit B2 / DNA-directed RNA polymerase II 140 kDa polypeptide / RNA polymerase II subunit B


Mass: 132640.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: P08266, DNA-directed RNA polymerase
#10: Protein DNA-directed RNA polymerase II subunit RPB3 / RNA polymerase II p33 subunit / RNA polymerase II subunit C


Mass: 30676.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: O97183, DNA-directed RNA polymerase
#13: Protein DNA-directed RNA polymerase II subunit RPB9 / RNA polymerase II subunit B9 / DNA-directed RNA polymerase II 15.1 kDa polypeptide / RNA polymerase ...RNA polymerase II subunit B9 / DNA-directed RNA polymerase II 15.1 kDa polypeptide / RNA polymerase II subunit I


Mass: 13786.586 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: P36958
#15: Protein DNA-directed RNA polymerase II subunit RPB11 / RNA polymerase II subunit B11 / DNA-directed RNA polymerase II 13.3 kDa polypeptide / DNA-directed ...RNA polymerase II subunit B11 / DNA-directed RNA polymerase II 13.3 kDa polypeptide / DNA-directed RNA polymerase II subunit J


Mass: 13288.240 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9VJE4
#16: Protein/peptide DNA-directed RNA polymerase II subunit RPB12 / HDC06513 / IP17848p / Rpb12


Mass: 5647.678 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q6IGE3
#17: Protein DNA-directed RNA polymerase II subunit RPB5


Mass: 24518.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q7JZF5

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DNA-directed RNA polymerases I, II, and III subunit ... , 3 types, 3 molecules FHJ

#11: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC2 / RNA polymerases I / II / and III subunit ABC2 / RNA polymerase II / I and III subunit F / RPB6 homolog


Mass: 9736.510 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q24320
#12: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC3


Mass: 16946.137 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9VNZ3
#14: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC5 / RNA polymerases I / II / and III subunit ABC5 / RNA polymerase II / I and III subunit L / RPB10 homolog


Mass: 7671.124 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9VC49

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RNA chain / Non-polymers , 2 types, 9 molecules R

#18: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#1: RNA chain RNA


Mass: 3247.100 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly)

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Details

Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Native purified Nucleosome Elongation Complex from Drosophila melanogaster
Type: COMPLEX
Details: A composite structure of a native purified Nucleosome Elongation Complex (Pol II EC - nucleosome)
Entity ID: #1-#17 / Source: NATURAL
Molecular weightValue: 0.750 MDa / Experimental value: NO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Buffer solutionpH: 7.5
Details: 10 mM HEPES-HCl (pH = 7.5), 150 mM NaCl, 5% glycerol, 1 mM EDTA, 350 ug/mL 3x FLAG peptide, 1/1000th protease inhibitor
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMSodium chlorideNaCl1
210 mMHEPESHEPES-HCl1
35 percentGlycerolGlycerol1
41 mMEDTAEDTA1
5350 ug/mLFLAG peptideFLAG1
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: double FLAG-tagged Pol II subunit Rpb1 was used for purification of Pol II complexes
Specimen supportGrid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 4 K

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Electron microscopy imaging

MicroscopyModel: TFS TALOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50.65 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 4 / Num. of real images: 31103
Details: Although the data was collected, motion-corrected and CTF estimated using the pixel size of 0.944, all the subsequent data processing was performed using pixel size of 1.1538. This was ...Details: Although the data was collected, motion-corrected and CTF estimated using the pixel size of 0.944, all the subsequent data processing was performed using pixel size of 1.1538. This was achieved by extracting particles in box size 440x440 and Fourier-cropping it to box size 360x360
Image scansSampling size: 0.944 µm / Width: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.3.1particle selection
2EPU3.4image acquisition
4cryoSPARC4.3.1CTF correction
7UCSF ChimeraX1.8model fitting
9cryoSPARC4.3.1initial Euler assignment
10cryoSPARC4.3.1final Euler assignment
12cryoSPARC4.3.13D reconstruction
13Coot0.9.8.7model refinement
14PHENIX1.21.5207model refinement
CTF correctionDetails: 'Patch CTF Estimation' in cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 4197404
Details: Initially, nearly 15 million particles were picked from micrographs. However, the number of particles cited here (4,197,404) is the starting number of particles after initial cleanup and 3D ...Details: Initially, nearly 15 million particles were picked from micrographs. However, the number of particles cited here (4,197,404) is the starting number of particles after initial cleanup and 3D classification of the data representing Pol II and nucleosome subsets, respectively.
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 7.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 36552 / Algorithm: BACK PROJECTION
Details: The Nucleosome EC was refined to an overall resolution of 7.8 A. Then, local refinement was performed with an indvidual focus on the nucleosome and Pol II. This entry represents a composite ...Details: The Nucleosome EC was refined to an overall resolution of 7.8 A. Then, local refinement was performed with an indvidual focus on the nucleosome and Pol II. This entry represents a composite map of the two locally refined entities.
Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 50 / Protocol: AB INITIO MODEL
Details: The model was based on individual models from this study: octameric nucleosome and Pol II. The models were rigid-body fit into the composite structure, connected and fixed in Coot and Phenix.
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00343989
ELECTRON MICROSCOPYf_angle_d0.7260884
ELECTRON MICROSCOPYf_dihedral_angle_d22.998719
ELECTRON MICROSCOPYf_chiral_restr0.0466800
ELECTRON MICROSCOPYf_plane_restr0.0056654

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