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

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Basic information

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 ...) 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 / homology
Function and homology information


regulation of septum digestion after cytokinesis / RNA polymerase II complex recruiting activity / regulation of mRNA 3'-end processing / siRNA-mediated pericentric heterochromatin formation / DSIF complex / RPB4-RPB7 complex / chromatin-protein adaptor activity / transcription elongation factor activity / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / termination of RNA polymerase II transcription ...regulation of septum digestion after cytokinesis / RNA polymerase II complex recruiting activity / regulation of mRNA 3'-end processing / siRNA-mediated pericentric heterochromatin formation / DSIF complex / RPB4-RPB7 complex / chromatin-protein adaptor activity / transcription elongation factor activity / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / termination of RNA polymerase II transcription / termination of RNA polymerase III transcription / transcription elongation-coupled chromatin remodeling / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / transcription initiation at RNA polymerase III promoter / termination of RNA polymerase I transcription / transcription initiation at RNA polymerase I promoter / RNA polymerase II complex binding / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / positive regulation of translational initiation / chromosome, centromeric region / translation elongation factor activity / RNA polymerase I complex / transcription elongation by RNA polymerase I / RNA polymerase III complex / pericentric heterochromatin / transcription-coupled nucleotide-excision repair / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / : / translation initiation factor binding / DNA-directed RNA polymerase activity / regulation of DNA-templated transcription elongation / transcription antitermination / RNA polymerase II transcription regulatory region sequence-specific DNA binding / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / P-body / ribonucleoside binding / : / : / : / : / : / : / DNA-directed RNA polymerase / peroxisome / single-stranded DNA binding / nucleic acid binding / single-stranded RNA binding / protein dimerization activity / RNA-directed RNA polymerase activity / nucleotide binding / mRNA binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / nucleolus / mitochondrion / DNA binding / RNA binding / zinc ion binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Herpes Virus-1 - #210 / NusG, N-terminal domain / Spt5 C-terminal nonapeptide repeat binding Spt4 / RNA Polymerase II, Rpb4 subunit / Transcription elongation factor, TFIIS / Transcription elongation factor, IIS-type / Transcription factor S-II (TFIIS), central domain / Domain in the central regions of transcription elongation factor S-II (and elsewhere) / Transcription elongation factor S-II, central domain / Transcription elongation factor S-II, central domain superfamily ...Herpes Virus-1 - #210 / NusG, N-terminal domain / Spt5 C-terminal nonapeptide repeat binding Spt4 / RNA Polymerase II, Rpb4 subunit / Transcription elongation factor, TFIIS / Transcription elongation factor, IIS-type / Transcription factor S-II (TFIIS), central domain / Domain in the central regions of transcription elongation factor S-II (and elsewhere) / Transcription elongation factor S-II, central domain / Transcription elongation factor S-II, central domain superfamily / TFIIS central domain profile. / Transcription elongation factor, TFIIS/CRSP70, N-terminal, sub-type / Domain in the N-terminus of transcription elongation factor S-II (and elsewhere) / RNA polymerase Rpb7-like, N-terminal domain / Transcription initiation Spt4 / Spt4 superfamily / TFIIS N-terminal domain profile. / Spt4/RpoE2 zinc finger / Spt4/RpoE2 zinc finger / Spt4/RpoE2 zinc finger / Transcription factor IIS, N-terminal / TFIIS helical bundle-like domain / Transcription elongation factor SPT5, KOWx domain / Transcription elongation factor SPT5, KOW1 domain / Transcription elongation factor SPT5, second KOW domain / Transcription elongation factor SPT5, fifth KOW domain / Transcription elongation factor SPT5, fourth KOW domain / Transcription elongation factor Spt5, eukaryote / Spt5 transcription elongation factor, N-terminal / Spt5, KOW domain repeat 2 / Spt5, KOW domain repeat 3 / Spt5, KOW domain repeat 5 / Spt5 transcription elongation factor, acidic N-terminal / NGN domain, eukaryotic / Spt5, KOW domain repeat 1 / Spt5, KOW domain repeat 4 / Dna-directed Rna Polymerases I, Ii, And Iii 27 Kd Polypeptide; Chain: A; domain 1 / RNA polymerase, Rpb5, N-terminal domain / NGN domain / Transcription elongation factor SPT5 / Early transcription elongation factor of RNA pol II, NGN section / RNA polymerase ii, chain L / Gyrase A; domain 2 - #140 / RPB5-like RNA polymerase subunit / N-terminal domain of TfIIb - #10 / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3 / RNA polymerase Rpb2, domain 2 / TFIIS/LEDGF domain superfamily / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / RNA polymerase Rpb1, domain 3 / RNA polymerase, RBP11-like subunit / NusG, N-terminal domain superfamily / Enzyme I; Chain A, domain 2 / N-terminal domain of TfIIb / Rubrerythrin, domain 2 / Growth Hormone; Chain: A; / DNA-directed RNA polymerase, insert domain / RNA Polymerase Alpha Subunit; Chain A, domain 2 / DNA-directed RNA polymerase II subunit Rpb4-like / RNA polymerase Rpb1 C-terminal repeat / RNA polymerase II, heptapeptide repeat, eukaryotic / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / Herpes Virus-1 / 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 / Gyrase A; domain 2 / Rpb4/RPC9 superfamily / S1 domain profile. / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / Homeodomain-like / HRDC-like superfamily / RNA polymerase Rpb7-like , N-terminal / RNA polymerase Rpb7-like, N-terminal domain superfamily / RNA polymerase subunit Rpb7-like / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / 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 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
Similarity search - Domain/homology
DNA / DNA (> 10) / RNA / RNA (> 10) / RNA polymerase subunit, found in RNA polymerase complexes I, II, and III / DNA-directed RNA polymerase subunit / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / Transcription elongation factor SPT4 / RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III ...DNA / DNA (> 10) / RNA / RNA (> 10) / RNA polymerase subunit, found in RNA polymerase complexes I, II, and III / DNA-directed RNA polymerase subunit / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / Transcription elongation factor SPT4 / RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / Transcription elongation factor / RNA polymerase II subunit B32 / Transcription elongation factor SPT5 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / RNA polymerase II subunit B12.5 / DNA-directed RNA polymerase subunit / RNA polymerase II third largest subunit B44, part of central core / DNA-directed RNA polymerase subunit
Similarity search - Component
Biological speciesKomagataella phaffii (fungus)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.83 Å
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.
History
DepositionMay 29, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.2Nov 6, 2019Group: Data collection / Other / Category: cell / em_software / Item: _cell.Z_PDB / _em_software.name
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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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
Polymers651,46018
Non-polymers67811
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area85560 Å2
ΔGint-497 kcal/mol
Surface area220860 Å2

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Components

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

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


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


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


Mass: 13612.320 Da / Num. of mol.: 1 / Source method: isolated from a natural source
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 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 method: isolated from a natural source
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4R7L2
#4: Protein RNA polymerase II subunit B32 / RNA polymerase II subunit Rpb4


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


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


Mass: 13832.896 Da / Num. of mol.: 1 / Source method: isolated from a natural source
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 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 method: isolated from a natural source
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4R3P8
#6: Protein 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 method: isolated from a natural source
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4R1V1
#8: Protein 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 method: isolated from a natural source
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4R273
#10: Protein 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 method: isolated from a natural source
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4R009

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Protein , 4 types, 4 molecules LUVW

#12: Protein 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 method: isolated from a natural source
Source: (natural) Komagataella phaffii (strain GS115 / ATCC 20864) (fungus)
Strain: GS115 / ATCC 20864 / References: UniProt: C4QWA8
#16: Protein General transcription elongation factor TFIIS


Mass: 21694.734 Da / Num. of mol.: 1 / Fragment: UNP residues 99-285
Source method: isolated from a genetically manipulated source
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 Transcription elongation factor SPT4


Mass: 12039.614 Da / Num. of mol.: 1 / Fragment: UNP residues 8-114
Source method: isolated from a genetically manipulated source
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 Protein that forms a complex with Spt4p / Spt5


Mass: 68283.984 Da / Num. of mol.: 1 / Fragment: UNP residues 206-815
Source method: isolated from a genetically manipulated source
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 method: obtained synthetically / 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 method: obtained synthetically / Source: (synth.) synthetic construct (others)
#15: DNA chain DNA (48-MER)


Mass: 14917.541 Da / Num. of mol.: 1 / Source method: obtained synthetically / 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 / Source method: obtained synthetically / Formula: Zn
#20: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

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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 / 3D 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 TFIISCOMPLEX#1-#180MULTIPLE SOURCES
2RNA polymerase IICOMPLEX#1-#121NATURAL
3Spt4/5 and TFIISCOMPLEX#16-#181RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Komagataella pastoris (fungus)4922
31Komagataella pastoris (fungus)4922
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
MicroscopyModel: FEI TECNAI ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. 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 (asymmetric)
3D reconstructionResolution: 3.83 Å / Resolution method: FSC 0.143 CUT-OFF / Num. 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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