6GME

Structure of H. sapiens SPT6 tandem SH2 domain

• PDB DOI: https://doi.org/10.2210/pdb6GME/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2018-05-25 Released: 2018-08-22 
• Deposition Author(s): Vos, S.M., Farnung, L., Cramer, P.
• Funding Organization(s): Volkswagen Foundation, European Molecular Biology Organization, European Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.223 
• R-Value Work: 0.191 
• R-Value Observed: 0.192 

Starting Model: experimental

Literature

Structure of activated transcription complex Pol II-DSIF-PAF-SPT6.

Vos, S.M., Farnung, L., Boehning, M., Wigge, C., Linden, A., Urlaub, H., Cramer, P.

(2018) Nature 560: 607-612

• PubMed: 30135578 
• DOI: https://doi.org/10.1038/s41586-018-0440-4
• Primary Citation of Related Structures:  
  6GME, 6GMH


• PubMed Abstract: 
  

  Gene regulation involves activation of RNA polymerase II (Pol II) that is paused and bound by the protein complexes DRB sensitivity-inducing factor (DSIF) and negative elongation factor (NELF). Here we show that formation of an activated Pol II elongation complex in vitro requires the kinase function of the positive transcription elongation factor b (P-TEFb) and the elongation factors PAF1 complex (PAF) and SPT6. The cryo-EM structure of an activated elongation complex of Sus scrofa Pol II and Homo sapiens DSIF, PAF and SPT6 was determined at 3.1 Å resolution and compared to the structure of the paused elongation complex formed by Pol II, DSIF and NELF. PAF displaces NELF from the Pol II funnel for pause release. P-TEFb phosphorylates the Pol II linker to the C-terminal domain. SPT6 binds to the phosphorylated C-terminal-domain linker and opens the RNA clamp formed by DSIF. These results provide the molecular basis for Pol II pause release and elongation activation.

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Organizational Affiliation: 

Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Göttingen, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 45.79 kDa 
• Atom Count: 3,254 
• Modelled Residue Count: 379 
• Deposited Residue Count: 402 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SPT6 tandem SH2 domain,Transcription elongation factor SPT6	A, B	201	Homo sapiens	Mutation(s): 0  Gene Names: SUPT6H, KIAA0162, SPT6H
UniProt & NIH Common Fund Data Resources
Find proteins for Q7KZ85 (Homo sapiens) Explore Q7KZ85  Go to UniProtKB:  Q7KZ85
PHAROS:  Q7KZ85 GTEx:  ENSG00000109111

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.223 
• R-Value Work: 0.191 
• R-Value Observed: 0.192 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.02	α = 90
b = 81.1	β = 115.08
c = 51.37	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-08-22 
Deposition Author(s): Vos, S.M., Farnung, L., Cramer, P.

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Funding Organization	Location	Grant Number
Volkswagen Foundation	Germany	--
European Molecular Biology Organization	Germany	ALTF 745-2014
European Research Council	Germany	693023

Revision History  

• Version 1.0: 2018-08-22
  Type: Initial release
  
• Version 1.1: 2018-09-05
  Changes: Data collection, Database references
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Refinement description