3UAL | pdb_00003ual

Crystal Structure of 14-3-3 epsilon with Mlf1 peptide

• PDB DOI: https://doi.org/10.2210/pdb3UAL/pdb

• Classification: SIGNALING PROTEIN/PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-10-21 Released: 2012-01-25 
• Deposition Author(s): Weyand, M., Ottmann, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.222 (Depositor), 0.222 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.171 (DCC) 
• R-Value Observed: 
  0.174 (Depositor) 

Starting Model: experimental

Literature

Structural insights of the MLF1/14-3-3 interaction.

Molzan, M., Weyand, M., Rose, R., Ottmann, C.

(2012) FEBS J 279: 563-571

• PubMed: 22151054 
• DOI: https://doi.org/10.1111/j.1742-4658.2011.08445.x
• Primary Citation Related Structures: 
  3UAL, 3UBW


• PubMed Abstract: 
  

  Myeloid leukaemia factor 1 (MLF1) binds to 14-3-3 adapter proteins by a sequence surrounding Ser34 with the functional consequences of this interaction largely unknown. We present here the high-resolution crystal structure of this binding motif [MLF1(29-42)pSer34] in complex with 14-3-3ε and analyse the interaction with isothermal titration calorimetry. Fragment-based ligand discovery employing crystals of the binary 14-3-3ε/MLF1(29-42)pSer34 complex was used to identify a molecule that binds to the interface rim of the two proteins, potentially representing the starting point for the development of a small molecule that stabilizes the MLF1/14-3-3 protein-protein interaction. Such a compound might be used as a chemical biology tool to further analyse the 14-3-3/MLF1 interaction without the use of genetic methods. Database Structural data are available in the Protein Data Bank under the accession number(s) 3UAL [14-3-3ε/MLF1(29-42)pSer34 complex] and 3UBW [14-3-3ε/MLF1(29-42)pSer34/3-pyrrolidinol complex] Structured digital abstract •  14-3-3 epsilon and MLF1 bind by x-ray crystallography (View interaction) •  14-3-3 epsilon and MLF1 bind by isothermal titration calorimetry (View Interaction: 1, 2).

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Organizational Affiliation: 
• Chemical Genomics Centre of the Max-Planck-Society, Dortmund, Germany.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 28.59 kDa 
• Atom Count: 2,175 
• Modeled Residue Count: 238 
• Deposited Residue Count: 246 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
14-3-3 protein epsilon	A	232	Homo sapiens	Mutation(s): 0  Gene Names: YWHAE
UniProt & NIH Common Fund Data Resources
Find proteins for P62258 (Homo sapiens) Explore P62258  Go to UniProtKB:  P62258
PHAROS:  P62258 GTEx:  ENSG00000108953

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Myeloid leukemia factor 1	B [auth P]	14	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P58340 (Homo sapiens) Explore P58340  Go to UniProtKB:  P58340
PHAROS:  P58340 GTEx:  ENSG00000178053

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TBU	C [auth A], D [auth A], E [auth A]	TERTIARY-BUTYL ALCOHOL C4 H10 O DKGAVHZHDRPRBM-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	B [auth P]	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.222 (Depositor), 0.222 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.171 (DCC) 
• R-Value Observed: 0.174 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.98	α = 90
b = 81.46	β = 90
c = 82.84	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-01-25 
Deposition Author(s): Weyand, M., Ottmann, C.

Revision History  

• Version 1.0: 2012-01-25
  Type: Initial release
  
• Version 1.1: 2012-02-08
  Changes: Database references
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-11-27
  Changes: Structure summary