1MNM | pdb_00001mnm

YEAST MATALPHA2/MCM1/DNA TERNARY TRANSCRIPTION COMPLEX CRYSTAL STRUCTURE

• PDB DOI: https://doi.org/10.2210/pdb1MNM/pdb
• NAKB: 1MNM

• Classification: TRANSCRIPTION/DNA
• Organism(s): synthetic construct, Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1997-11-03 Released: 1998-03-18 
• Deposition Author(s): Tan, S., Richmond, T.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.285 (Depositor) 
• R-Value Work: 
  0.240 (Depositor) 
• R-Value Observed: 
  0.240 (Depositor) 

Starting Models: experimental

Literature

Crystal structure of the yeast MATalpha2/MCM1/DNA ternary complex.

Tan, S., Richmond, T.J.

(1998) Nature 391: 660-666

• PubMed: 9490409 
• DOI: https://doi.org/10.1038/35563
• Primary Citation Related Structures: 
  1MNM


• PubMed Abstract: 
  

  The structure of a complex containing the homeodomain repressor protein MATalpha2 and the MADS-box transcription factor MCM1 bound to DNA has been determined by X-ray crystallography at 2.25 A resolution. It reveals the protein-protein interactions responsible for cooperative binding of MATalpha2 and MCM1 to DNA. The otherwise flexible amino-terminal extension of the MATalpha2 homeodomain forms a beta-hairpin that grips the MCM1 surface through parallel beta-strand hydrogen bonds and close-packed, predominantly hydrophobic, side chains. DNA bending induced by MCM1 brings the two proteins closer together, facilitating their interaction. An unusual feature of the complex is that an eight-amino-acid sequence adopts an alpha-helical conformation in one of two copies of the MATalpha2 monomer and a beta-strand conformation in the other. This 'chameleon' sequence of MATalpha2 may be important for recognizing natural operator sites.

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Organizational Affiliation: 
• ETH-Zurich, Institut für Molekularbiologie und Biophysik, Switzerland.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 59.45 kDa 
• Atom Count: 3,657 
• Modeled Residue Count: 372 
• Deposited Residue Count: 426 
• Unique protein chains: 2
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (MCM1 TRANSCRIPTIONAL REGULATOR)	C [auth A], D [auth B]	100	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P11746 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P11746  Go to UniProtKB:  P11746

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (MAT ALPHA-2 TRANSCRIPTIONAL REPRESSOR)	E [auth C], F [auth D]	87	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P0CY08 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0CY08  Go to UniProtKB:  P0CY08

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (STE6 OPERATOR DNA)	A [auth E]	26	synthetic construct

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (STE6 OPERATOR DNA)	B [auth F]	26	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.285 (Depositor) 
• R-Value Work:  0.240 (Depositor) 
• R-Value Observed: 0.240 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.62	α = 90
b = 72.55	β = 90
c = 150.7	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-03-18 
Deposition Author(s): Tan, S., Richmond, T.J.

Revision History  

• Version 1.0: 1998-03-18
  Type: Initial release
  
• Version 1.1: 2008-05-22
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-02-15
  Changes: Source and taxonomy, Structure summary
• Version 1.4: 2023-08-02
  Changes: Database references, Refinement description