- EMDB-16840: Structure of the mammalian Pol II-SPT6-Elongin complex, Structure... -
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Basic information
Entry
Database: EMDB / ID: EMD-16840
Title
Structure of the mammalian Pol II-SPT6-Elongin complex, Structure 1 (local resolution filtered map)
Map data
Local resolution filtered map for structure 1, Pol II-SPT6-Elongin model with ELOA latch
Sample
Complex: The Pol II-SPT6-Elongin transcription elongation complex
Protein or peptide: x 16 types
DNA: x 2 types
RNA: x 1 types
Ligand: x 2 types
Keywords
Transcription elongation / Elongin / RNA polymerase II / TRANSCRIPTION
Function / homology
Function and homology information
regulation of isotype switching / regulation of mRNA export from nucleus / regulation of muscle cell differentiation / nucleosome organization / regulation of mRNA processing / B-WICH complex positively regulates rRNA expression / RNA Polymerase I Transcription Initiation / RNA Polymerase I Promoter Escape / RNA Polymerase I Transcription Termination / RNA Polymerase III Transcription Initiation From Type 1 Promoter ...regulation of isotype switching / regulation of mRNA export from nucleus / regulation of muscle cell differentiation / nucleosome organization / regulation of mRNA processing / B-WICH complex positively regulates rRNA expression / RNA Polymerase I Transcription Initiation / RNA Polymerase I Promoter Escape / RNA Polymerase I Transcription Termination / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Transcription Initiation From Type 3 Promoter / Formation of RNA Pol II elongation complex / Formation of the Early Elongation Complex / Transcriptional regulation by small RNAs / RNA Polymerase II Pre-transcription Events / TP53 Regulates Transcription of DNA Repair Genes / FGFR2 alternative splicing / RNA polymerase II transcribes snRNA genes / mRNA Capping / mRNA Splicing - Major Pathway / mRNA Splicing - Minor Pathway / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Elongation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Pol II CTD phosphorylation and interaction with CE / Estrogen-dependent gene expression / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / target-directed miRNA degradation / blastocyst formation / elongin complex / VCB complex / Cul5-RING ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / transcription elongation-coupled chromatin remodeling / : / : / site of DNA damage / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / organelle membrane / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / transcription by RNA polymerase I / transcription by RNA polymerase III / Tat-mediated elongation of the HIV-1 transcript / mRNA transport / positive regulation of translational initiation / Formation of HIV-1 elongation complex containing HIV-1 Tat / RNA polymerase I complex / RNA polymerase III complex / transcription-coupled nucleotide-excision repair / RNA polymerase II activity / Formation of HIV elongation complex in the absence of HIV Tat / RNA polymerase II, core complex / nucleosome binding / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / DNA-directed RNA polymerase complex / translation initiation factor binding / RNA Polymerase II Pre-transcription Events / RNA splicing / positive regulation of RNA splicing / transcription corepressor binding / transcription elongation factor complex / Evasion by RSV of host interferon responses / transcription elongation by RNA polymerase II / promoter-specific chromatin binding / transcription initiation at RNA polymerase II promoter / TP53 Regulates Transcription of DNA Repair Genes / positive regulation of transcription elongation by RNA polymerase II / Vif-mediated degradation of APOBEC3G / P-body / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Inactivation of CSF3 (G-CSF) signaling / ribonucleoside binding / fibrillar center / mRNA processing / Regulation of expression of SLITs and ROBOs / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / protein-macromolecule adaptor activity / chromosome / Neddylation / single-stranded DNA binding / histone binding / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / ubiquitin-dependent protein catabolic process / protein-containing complex assembly / transcription by RNA polymerase II / nucleic acid binding Similarity search - Function
RNA polymerase II subunit D / DNA-directed RNA polymerase subunit / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase II subunit RPB11-a / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase subunit beta / RNA polymerase II, I and III subunit K / DNA-directed RNA polymerase II subunit E ...RNA polymerase II subunit D / DNA-directed RNA polymerase subunit / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase II subunit RPB11-a / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase subunit beta / RNA polymerase II, I and III subunit K / DNA-directed RNA polymerase II subunit E / DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB9 / Elongin-A / Elongin-C / Elongin-B / Transcription elongation factor SPT6 Similarity search - Component
Biological species
Homo sapiens (human) / Sus scrofa (pig) / synthetic construct (others)
Method
single particle reconstruction / cryo EM / Resolution: 3.05 Å
Journal: Nat Struct Mol Biol / Year: 2023 Title: Structure of the transcribing RNA polymerase II-Elongin complex. Authors: Ying Chen / Goran Kokic / Christian Dienemann / Olexandr Dybkov / Henning Urlaub / Patrick Cramer / Abstract: Elongin is a heterotrimeric elongation factor for RNA polymerase (Pol) II transcription that is conserved among metazoa. Here, we report three cryo-EM structures of human Elongin bound to ...Elongin is a heterotrimeric elongation factor for RNA polymerase (Pol) II transcription that is conserved among metazoa. Here, we report three cryo-EM structures of human Elongin bound to transcribing Pol II. The structures show that Elongin subunit ELOA binds the RPB2 side of Pol II and anchors the ELOB-ELOC subunit heterodimer. ELOA contains a 'latch' that binds between the end of the Pol II bridge helix and funnel helices, thereby inducing a conformational change near the polymerase active center. The latch is required for the elongation-stimulatory activity of Elongin, but not for Pol II binding, indicating that Elongin functions by allosterically regulating the conformational mobility of the polymerase active center. Elongin binding to Pol II is incompatible with association of the super elongation complex, PAF1 complex and RTF1, which also contain an elongation-stimulatory latch element.
Entire : The Pol II-SPT6-Elongin transcription elongation complex
Entire
Name: The Pol II-SPT6-Elongin transcription elongation complex
Components
Complex: The Pol II-SPT6-Elongin transcription elongation complex
Protein or peptide: DNA-directed RNA polymerase II subunit RPB1Polymerase
Protein or peptide: DNA-directed RNA polymerase subunit betaPolymerase
Protein or peptide: DNA-directed RNA polymerase II subunit RPB3Polymerase
Protein or peptide: RNA polymerase II subunit D
Protein or peptide: DNA-directed RNA polymerase II subunit EPolymerase
Protein or peptide: DNA-directed RNA polymerase II subunit FPolymerase
Protein or peptide: DNA-directed RNA polymerase II subunit RPB7Polymerase
Protein or peptide: DNA-directed RNA polymerases I, II, and III subunit RPABC3RNA polymerase
Protein or peptide: DNA-directed RNA polymerase II subunit RPB9Polymerase
Protein or peptide: DNA-directed RNA polymerases I, II, and III subunit RPABC5RNA polymerase
Protein or peptide: DNA-directed RNA polymerase II subunit RPB11-aPolymerase
Protein or peptide: RNA polymerase II subunit K
DNA: Non-template DNA
RNA: RNA
DNA: Template DNA
Protein or peptide: Elongin-B
Protein or peptide: Elongin-A
Protein or peptide: Elongin-C
Protein or peptide: Transcription elongation factor SPT6
Ligand: MAGNESIUM ION
Ligand: ZINC ION
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Supramolecule #1: The Pol II-SPT6-Elongin transcription elongation complex
Supramolecule
Name: The Pol II-SPT6-Elongin transcription elongation complex type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#19 Details: The map is generated from a sub-class of a Cryo-EM dataset for the Pol II-SPT6-Elongin complex.
Source (natural)
Organism: Homo sapiens (human)
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Macromolecule #1: DNA-directed RNA polymerase II subunit RPB1
Macromolecule
Name: DNA-directed RNA polymerase II subunit RPB1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Name: MAGNESIUM ION / type: ligand / ID: 20 / Number of copies: 1 / Formula: MG
Molecular weight
Theoretical: 24.305 Da
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Macromolecule #21: ZINC ION
Macromolecule
Name: ZINC ION / type: ligand / ID: 21 / Number of copies: 8 / Formula: ZN
Molecular weight
Theoretical: 65.409 Da
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Experimental details
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Structure determination
Method
cryo EM
Processing
single particle reconstruction
Aggregation state
particle
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Sample preparation
Buffer
pH: 7.5
Grid
Model: Quantifoil R3.5/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2.1
Vitrification
Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV
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Electron microscopy
Microscope
FEI TITAN KRIOS
Electron beam
Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
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