Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 21.24 kDa 
• Atom Count: 1633 
• Modelled Residue Count: 181 
• Deposited Residue Count: 185 
• Unique protein chains: 2

3KJ0

Mcl-1 in complex with Bim BH3 mutant I2dY

• PDB DOI: 10.2210/pdb3KJ0/pdb

• Classification: APOPTOSIS
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2009-11-02 Released: 2010-02-16 
• Deposition Author(s): Fire, E., Grant, R.A., Keating, A.E.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.224 
• R-Value Work: 0.185 
• R-Value Observed: 0.187 

Literature

Mcl-1-Bim complexes accommodate surprising point mutations via minor structural changes.

Fire, E., Gulla, S.V., Grant, R.A., Keating, A.E.

(2010) Protein Sci 19: 507-519

• PubMed: 20066663 
• DOI: 10.1002/pro.329
• Primary Citation of Related Structures:  
  2PQK, 3KJ0, 3KJ1, 3KJ2


• PubMed Abstract: 
  

Mcl-1 is an antiapoptotic Bcl-2-family protein that protects cells against death. Structures of Mcl-1, and of other anti-apoptotic Bcl-2 proteins, reveal a surface groove into which the alpha-helical BH3 regions of certain proapoptotic proteins can bind. Despite high overall structural conservation, differences in this groove afford binding specificity that is important for the mechanism of Bcl-2 family function. We report the crystal structure of human Mcl-1 bound to a BH3 peptide derived from human Bim and the structures for three complexes that accommodate large physicochemical changes at conserved Bim sites. The mutations had surprisingly modest effects on complex stability, and the structures show that Mcl-1 can undergo small changes to accommodate the mutant ligands. For example, a shift in a leucine side chain fills a hole left by an isoleucine-to-alanine mutation at the first hydrophobic buried position of Bim BH3. Larger changes are also observed, with shifting of helix alpha3 accommodating an isoleucine-to-tyrosine mutation at this same position. We surveyed the variation in available Mcl-1 and Bcl-x(L) structures and observed moderate flexibility that is likely critical for facilitating interactions of diverse BH3-only proteins with Mcl-1. With the antiapoptotic Bcl-2 family members attracting significant attention as therapeutic targets, these structures contribute to our growing understanding of how specificity is achieved and can help to guide the design of novel inhibitors that target Mcl-1.

---

Organizational Affiliation: 

Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Induced myeloid leukemia cell differentiation protein Mcl-1	A	158	Homo sapiens	Mutation(s): 0  Gene Names: BCL2L3, mcl-1, MCL1
UniProt & NIH Common Fund Data Resources
Find proteins for Q07820 (Homo sapiens) Explore Q07820  Go to UniProtKB:  Q07820
PHAROS:  Q07820

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Bcl-2-like protein 11	B	27	Homo sapiens	Mutation(s): 1  Gene Names: BCL2L11, BIM
UniProt & NIH Common Fund Data Resources
Find proteins for O43521 (Homo sapiens) Explore O43521  Go to UniProtKB:  O43521
PHAROS:  O43521

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	C [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.224 
• R-Value Work: 0.185 
• R-Value Observed: 0.187 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.381	α = 90
b = 52.943	β = 90
c = 69.373	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-11-02 
• Released Date: 2010-02-16 
Deposition Author(s): Fire, E., Grant, R.A., Keating, A.E.

Revision History  

• Version 1.0: 2010-02-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-10-13
  Changes: Database references, Derived calculations