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- PDB-5xon: RNA Polymerase II elongation complex bound with Spt4/5 and TFIIS -

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Entry
Database: PDB / ID: 5xon
TitleRNA Polymerase II elongation complex bound with Spt4/5 and TFIIS
Components
  • (DNA (48-MER)) x 2
  • (DNA-directed RNA polymerase ...Polymerase) x 3
  • (RNA polymerase II ...) x 4
  • (RNA polymerase subunit ...) x 4
  • General transcription elongation factor TFIIS
  • Protein that forms a complex with Spt4p
  • RNA (30-MER)
  • RNA polymerase subunit, found in RNA polymerase complexes I, II, and III
  • Transcription elongation factor SPT4
KeywordsTRANSCRIPTION/RNA / transcription / complex / TRANSCRIPTION-RNA complex
Function / homologyRNA polymerase Rpb2, OB-fold / DNA-directed RNA polymerase, subunit RPB6 / Archaeal RpoH /eukaryotic RPB5 RNA polymerase subunit / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerases, subunit N, zinc binding site / Spt5 transcription elongation factor, N-terminal / Spt4/RpoE2 zinc finger / RNA polymerase subunit RPB10 / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / Transcription factor IIS, N-terminal ...RNA polymerase Rpb2, OB-fold / DNA-directed RNA polymerase, subunit RPB6 / Archaeal RpoH /eukaryotic RPB5 RNA polymerase subunit / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerases, subunit N, zinc binding site / Spt5 transcription elongation factor, N-terminal / Spt4/RpoE2 zinc finger / RNA polymerase subunit RPB10 / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / Transcription factor IIS, N-terminal / Pol II subunit B9, C-terminal zinc ribbon / Transcription elongation factor, IIS-type / TFIIS/LEDGF domain superfamily / RPB5-like RNA polymerase subunit / RPB6/omega subunit-like superfamily / Transcription elongation factor S-II, central domain superfamily / RNA polymerase, subunit H/Rpb5, conserved site / Transcription elongation factor Spt5 / DNA-directed RNA polymerase, insert domain superfamily / HRDC-like superfamily / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 5 / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / Translation protein SH3-like domain superfamily / DNA-directed RNA polymerase, RBP11-like dimerisation domain / Transcription initiation Spt4 / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, subunit 2 / 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 / DNA-directed RNA polymerase RPB5 subunit, eukaryote/virus / Ribosomal protein L2, domain 2 / RNA polymerase Rpb1, domain 4 / RNA polymerase, RBP11-like subunit / RNA polymerase Rpb5, N-terminal domain superfamily / RNA polymerase, beta subunit, protrusion / RNA polymerase Rpb2, domain 7 / Early transcription elongation factor of RNA pol II, NGN section / DNA directed RNA polymerase, 7 kDa subunit / 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 2 / RNA polymerases N / 8 kDa subunit / RNA polymerase beta subunit / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 6 / RNA polymerases M/15 Kd subunit / RNA polymerase Rpb3/Rpb11 dimerisation domain / NusG, N-terminal domain superfamily / Spt4 superfamily / RNA polymerase Rpb7-like, N-terminal domain superfamily / 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 / RNA polymerase Rpb6 / KOW motif / RNA polymerase Rpb2, domain 6 / S1 RNA binding domain / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb3/RpoA insert domain / Transcription factor S-II (TFIIS) / RNA polymerase Rpb5, C-terminal domain / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase, subunit H/Rpb5 C-terminal / RNA polymerase, alpha subunit / RNA polymerase II, heptapeptide repeat, eukaryotic / DNA-directed RNA polymerase, subunit N/Rpb10 / RNA polymerase Rpb1 C-terminal repeat / Spt4/RpoE2 zinc finger / RNA polymerase Rpb2, domain 7 / Transcription factor S-II (TFIIS), central domain / TFIIS helical bundle-like domain / Spt5 transcription elongation factor, acidic N-terminal / Eukaryotic RNA polymerase II heptapeptide repeat. / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / RNA polymerases D / 30 to 40 Kd subunits signature. / RNA polymerases H / 23 Kd subunits signature. / RNA polymerases K / 14 to 18 Kd subunits signature. / RNA polymerases N / 8 Kd subunits signature. / RNA polymerases L / 13 to 16 Kd subunits signature. / RNA polymerases beta chain signature. / S1 domain profile. / Zinc finger TFIIS-type profile. / TFIIS N-terminal domain profile. / TFIIS central domain profile. / Zinc finger, TFIIS-type
Function and homology information
Specimen sourceKomagataella phaffii (fungus)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.83 Å resolution
AuthorsEhara, H. / Yokoyama, T. / Shigematsu, H. / Shirouzu, M. / Sekine, S.
CitationJournal: Science / Year: 2017
Title: Structure of the complete elongation complex of RNA polymerase II with basal factors.
Authors: Haruhiko Ehara / Takeshi Yokoyama / Hideki Shigematsu / Shigeyuki Yokoyama / Mikako Shirouzu / Shun-Ichi Sekine
Abstract: In the early stage of transcription, eukaryotic RNA polymerase II (Pol II) exchanges initiation factors with elongation factors to form an elongation complex for processive transcription. Here we ...In the early stage of transcription, eukaryotic RNA polymerase II (Pol II) exchanges initiation factors with elongation factors to form an elongation complex for processive transcription. Here we report the structure of the Pol II elongation complex bound with the basal elongation factors Spt4/5, Elf1, and TFIIS. Spt4/5 (the Spt4/Spt5 complex) and Elf1 modify a wide area of the Pol II surface. Elf1 bridges the Pol II central cleft, completing a "DNA entry tunnel" for downstream DNA. Spt4 and the Spt5 NGN and KOW1 domains encircle the upstream DNA, constituting a "DNA exit tunnel." The Spt5 KOW4 and KOW5 domains augment the "RNA exit tunnel," directing the exiting nascent RNA. Thus, the elongation complex establishes a completely different transcription and regulation platform from that of the initiation complexes.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 29, 2017 / Release: Aug 16, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Aug 16, 2017Structure modelrepositoryInitial release
1.1Sep 13, 2017Structure modelDatabase referencescitation / citation_author_citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name

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Structure visualization

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Assembly

Deposited unit
A: DNA-directed RNA polymerase subunit
B: DNA-directed RNA polymerase subunit beta
C: RNA polymerase II third largest subunit B44, part of central core
D: RNA polymerase II subunit B32
E: RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III
F: RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III
G: RNA polymerase II subunit
H: RNA polymerase subunit ABC14.5, common to RNA polymerases I, II, and III
I: DNA-directed RNA polymerase subunit
J: RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III
K: RNA polymerase II subunit B12.5
L: RNA polymerase subunit, found in RNA polymerase complexes I, II, and III
P: RNA (30-MER)
T: DNA (48-MER)
N: DNA (48-MER)
U: General transcription elongation factor TFIIS
V: Transcription elongation factor SPT4
W: Protein that forms a complex with Spt4p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)652,13829
Polyers651,46018
Non-polymers67811
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)85560
ΔGint (kcal/M)-497
Surface area (Å2)220860

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Components

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DNA-directed RNA polymerase ... , 3 types, 3 molecules ABI

#1: Protein/peptide DNA-directed RNA polymerase subunit / Polymerase / RNA polymerase II subunit Rpb1


Mass: 194107.422 Da / Num. of mol.: 1
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4R4Y0, DNA-directed RNA polymerase
#2: Protein/peptide DNA-directed RNA polymerase subunit beta / Polymerase / RNA polymerase II subunit Rpb2


Mass: 139746.094 Da / Num. of mol.: 1
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4QZQ7, DNA-directed RNA polymerase
#9: Protein/peptide DNA-directed RNA polymerase subunit / Polymerase / RNA polymerase II subunit Rpb9


Mass: 13612.320 Da / Num. of mol.: 1
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4QY79

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RNA polymerase II ... , 4 types, 4 molecules CDGK

#3: Protein/peptide RNA polymerase II third largest subunit B44, part of central core / RNA polymerase II subunit Rpb3


Mass: 34216.293 Da / Num. of mol.: 1
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4R7L2
#4: Protein/peptide RNA polymerase II subunit B32 / / RNA polymerase II subunit Rpb4


Mass: 20622.980 Da / Num. of mol.: 1
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4R2U9
#7: Protein/peptide RNA polymerase II subunit / / RNA polymerase II subunit Rpb7


Mass: 18802.625 Da / Num. of mol.: 1
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4R9A1
#11: Protein/peptide RNA polymerase II subunit B12.5 / / RNA polymerase II subunit Rpb11


Mass: 13832.896 Da / Num. of mol.: 1
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4R3Z5

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RNA polymerase subunit ... , 4 types, 4 molecules EFHJ

#5: Protein/peptide RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III / / RNA polymerase II subunit Rpb5


Mass: 24962.680 Da / Num. of mol.: 1
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4R3P8
#6: Protein/peptide RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III / / RNA polymerase II subunit Rpb6


Mass: 17803.588 Da / Num. of mol.: 1
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4R1V1
#8: Protein/peptide RNA polymerase subunit ABC14.5, common to RNA polymerases I, II, and III / / RNA polymerase II subunit Rpb8


Mass: 16249.220 Da / Num. of mol.: 1
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4R273
#10: Protein/peptide RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III / / RNA polymerase II subunit Rpb10


Mass: 8554.064 Da / Num. of mol.: 1
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4R009

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Protein/peptide , 4 types, 4 molecules LUVW

#12: Protein/peptide RNA polymerase subunit, found in RNA polymerase complexes I, II, and III / / RNA polymerase II subunit Rpb12


Mass: 7862.048 Da / Num. of mol.: 1
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4QWA8
#16: Protein/peptide General transcription elongation factor TFIIS


Mass: 21694.734 Da / Num. of mol.: 1 / Fragment: UNP residues 99-285
Source: (gene. exp.) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / Gene: PAS_chr2-2_0135 / Production host: Escherichia coli (E. coli) / References: UniProt: C4R2R6
#17: Protein/peptide Transcription elongation factor SPT4


Mass: 12039.614 Da / Num. of mol.: 1 / Fragment: UNP residues 8-114
Source: (gene. exp.) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / Gene: PAS_chr2-1_0350 / Production host: Escherichia coli (E. coli) / References: UniProt: C4R0E6
#18: Protein/peptide Protein that forms a complex with Spt4p / Spt5


Mass: 68283.984 Da / Num. of mol.: 1 / Fragment: UNP residues 206-815
Source: (gene. exp.) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / Gene: PAS_chr3_1136 / Production host: Escherichia coli (E. coli) / References: UniProt: C4R370

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RNA chain , 1 types, 1 molecules P

#13: RNA chain RNA (30-MER)


Mass: 9492.561 Da / Num. of mol.: 1 / Source: (synth.) synthetic construct (others)

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DNA chain , 2 types, 2 molecules TN

#14: DNA chain DNA (48-MER)


Mass: 14659.406 Da / Num. of mol.: 1 / Source: (synth.) synthetic construct (others)
#15: DNA chain DNA (48-MER)


Mass: 14917.541 Da / Num. of mol.: 1 / Source: (synth.) synthetic construct (others)

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Non-polymers , 2 types, 11 molecules

#19: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Formula: Zn / Zinc
#20: Chemical ChemComp-MG / MAGNESIUM ION


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

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Details

Sequence detailsFOR ENTITY 9 AND 12, THE SEQUENCE REFERENCE IN UNIPROT (C4QY79 AND C4QWA8) CONTAIN ERRORS. AND ...FOR ENTITY 9 AND 12, THE SEQUENCE REFERENCE IN UNIPROT (C4QY79 AND C4QWA8) CONTAIN ERRORS. AND AUTHOR CONFIRMED THE SEQUENCES IN THIS ENTRY ARE CORRECT.

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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
1RNA polymerase II elongation complex bound with Spt4/5 and TFIISCOMPLEX1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 180MULTIPLE SOURCES
2RNA polymerase IICOMPLEX1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 121NATURAL
3Spt4/5 and TFIISCOMPLEX16, 17, 181RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
214922Komagataella pastoris (fungus)
314922Komagataella pastoris (fungus)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TECNAI ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of real images: 3607

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Processing

EM software
IDNameVersionCategory
1Gautomatchparticle selection
2SerialEMimage acquisition
4GctfCTF correction
7Chimeramodel fitting
8Cootmodel fitting
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
12RELIONclassification
13RELION2.0.23D reconstruction
20Phenixmodel refinement
CTF correctionType: NONE
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.83 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 682749 / Symmetry type: POINT
Atomic model buildingDetails: Model fitting was done with Chimera and Coot. Well-ordered regions were also refined with phenix.real_space_refine.

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