4WZS | pdb_00004wzs

Crystal structure of the Mot1 N-terminal domain in complex with TBP and NC2 bound to a promoter DNA fragment

• PDB DOI: https://doi.org/10.2210/pdb4WZS/pdb
• NAKB: 4WZS

• Classification: TRANSCRIPTION
• Organism(s): Encephalitozoon cuniculi GB-M1, Encephalitozoon cuniculi, synthetic construct
• Expression System: Escherichia coli, Trichoplusia ni
• Mutation(s): No 


• Deposited: 2014-11-20 Released: 2015-08-26 
• Deposition Author(s): Butryn, A., Hopfner, K.-P.
• Funding Organization(s): German Research Foundation

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.78 Å
• R-Value Free: 
  0.258 (Depositor), 0.289 (DCC) 
• R-Value Work: 
  0.235 (Depositor), 0.252 (DCC) 
• R-Value Observed: 
  0.236 (Depositor) 

Starting Model: experimental

Literature

Structural basis for recognition and remodeling of the TBP:DNA:NC2 complex by Mot1.

Butryn, A., Schuller, J.M., Stoehr, G., Runge-Wollmann, P., Forster, F., Auble, D.T., Hopfner, K.P.

(2015) Elife 4

• PubMed: 26258880 
• DOI: https://doi.org/10.7554/eLife.07432
• Primary Citation Related Structures: 
  4WZS


• PubMed Abstract: 
  

  Swi2/Snf2 ATPases remodel substrates such as nucleosomes and transcription complexes to control a wide range of DNA-associated processes, but detailed structural information on the ATP-dependent remodeling reactions is largely absent. The single subunit remodeler Mot1 (modifier of transcription 1) dissociates TATA box-binding protein (TBP):DNA complexes, offering a useful system to address the structural mechanisms of Swi2/Snf2 ATPases. Here, we report the crystal structure of the N-terminal domain of Mot1 in complex with TBP, DNA, and the transcription regulator negative cofactor 2 (NC2). Our data show that Mot1 reduces DNA:NC2 interactions and unbends DNA as compared to the TBP:DNA:NC2 state, suggesting that Mot1 primes TBP:NC2 displacement in an ATP-independent manner. Electron microscopy and cross-linking data suggest that the Swi2/Snf2 domain of Mot1 associates with the upstream DNA and the histone fold of NC2, thereby revealing parallels to some nucleosome remodelers. This study provides a structural framework for how a Swi2/Snf2 ATPase interacts with its substrate DNA:protein complex.

---

Organizational Affiliation: 
• Gene Center, Department of Biochemistry, Ludwig Maximilian University, Munich, Germany.
Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, , Germany.
Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 156.81 kDa 
• Atom Count: 9,037 
• Modeled Residue Count: 1,118 
• Deposited Residue Count: 1,272 
• Unique protein chains: 4
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ECU11_1470 protein	A	95	Encephalitozoon cuniculi GB-M1	Mutation(s): 0  Gene Names: ECU11_1470
UniProt
Find proteins for Q8SQT6 (Encephalitozoon cuniculi (strain GB-M1)) Explore Q8SQT6  Go to UniProtKB:  Q8SQT6

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
TATA-binding protein-associated phosphoprotein	B	149	Encephalitozoon cuniculi	Mutation(s): 0  Gene Names: ECU11_0730
UniProt
Find proteins for M1K2J7 (Encephalitozoon cuniculi) Explore M1K2J7  Go to UniProtKB:  M1K2J7

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Similarity to HELICASE MOT1	C	780	Encephalitozoon cuniculi GB-M1	Mutation(s): 0  Gene Names: ECU03_1530
UniProt
Find proteins for Q8SVZ5 (Encephalitozoon cuniculi (strain GB-M1)) Explore Q8SVZ5  Go to UniProtKB:  Q8SVZ5

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
ECU04_1440 protein	D	200	Encephalitozoon cuniculi GB-M1	Mutation(s): 0  Gene Names: ECU04_1440
UniProt
Find proteins for Q8ST28 (Encephalitozoon cuniculi (strain GB-M1)) Explore Q8ST28  Go to UniProtKB:  Q8ST28

Entity ID: 5
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*CP*CP*AP*CP*CP*CP*CP*CP*TP*TP*TP*TP*AP*TP*AP*GP*CP*CP*CP*T)-3')	E	24	synthetic construct

Entity ID: 6
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*GP*GP*GP*CP*TP*AP*TP*AP*AP*AP*AP*GP*GP*GP*GP*GP*TP*GP*G)-3')	F	24	synthetic construct

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.78 Å
• R-Value Free:  0.258 (Depositor), 0.289 (DCC) 
• R-Value Work:  0.235 (Depositor), 0.252 (DCC) 
• R-Value Observed: 0.236 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 150.629	α = 90
b = 140.274	β = 113.7
c = 90.778	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
PHASER	phasing
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2015-08-26 
Deposition Author(s): Butryn, A., Hopfner, K.-P.

---

Funding Organization	Location	Grant Number
German Research Foundation	Germany	SFB 646

Revision History  

• Version 1.0: 2015-08-26
  Type: Initial release
  
• Version 1.1: 2017-09-06
  Changes: Author supporting evidence, Data collection, Derived calculations
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-11-06
  Changes: Structure summary