2NLA | pdb_00002nla

Crystal structure of the Mcl-1:mNoxaB BH3 complex

• PDB DOI: https://doi.org/10.2210/pdb2NLA/pdb

• Classification: APOPTOSIS
• Organism(s): Mus musculus, Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-10-19 Released: 2007-03-27 
• Deposition Author(s): Czabotar, P.E., Colman, P.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.291 (Depositor), 0.308 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.261 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Literature

Structural insights into the degradation of Mcl-1 induced by BH3 domains.

Czabotar, P.E., Lee, E.F., van Delft, M.F., Day, C.L., Smith, B.J., Huang, D.C., Fairlie, W.D., Hinds, M.G., Colman, P.M.

(2007) Proc Natl Acad Sci U S A 104: 6217-6222

• PubMed: 17389404 
• DOI: https://doi.org/10.1073/pnas.0701297104
• Primary Citation Related Structures: 
  2JM6, 2NL9, 2NLA


• PubMed Abstract: 
  

  Apoptosis is held in check by prosurvival proteins of the Bcl-2 family. The distantly related BH3-only proteins bind to and antagonize them, thereby promoting apoptosis. Whereas binding of the BH3-only protein Noxa to prosurvival Mcl-1 induces Mcl-1 degradation by the proteasome, binding of another BH3-only ligand, Bim, elevates Mcl-1 protein levels. We compared the three-dimensional structures of the complexes formed between BH3 peptides of both Bim and Noxa, and we show that a discrete C-terminal sequence of the Noxa BH3 is necessary to instigate Mcl-1 degradation.

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Organizational Affiliation: 
• The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3050, Australia.

Biological Assembly 1  

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: 20.83 kDa 
• Atom Count: 1,406 
• Modeled Residue Count: 171 
• Deposited Residue Count: 183 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FUSION PROTEIN CONSISTING OF Induced myeloid leukemia cell differentiation protein Mcl-1 homolog	A	157	Mus musculus, Homo sapiens This entity is chimeric	Mutation(s): 0  Gene Names: Mcl1
UniProt & NIH Common Fund Data Resources
Find proteins for P97287 (Mus musculus) Explore P97287  Go to UniProtKB:  P97287
IMPC:  MGI:101769
Find proteins for Q07820 (Homo sapiens) Explore Q07820  Go to UniProtKB:  Q07820
PHAROS:  Q07820 GTEx:  ENSG00000143384
UniProt Groups	P97287Q07820

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Phorbol-12-myristate-13-acetate-induced protein 1	B	26	Mus musculus	Mutation(s): 0
UniProt
Find proteins for Q9JM54 (Mus musculus) Explore Q9JM54  Go to UniProtKB:  Q9JM54

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.291 (Depositor), 0.308 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.261 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.381	α = 90
b = 85.381	β = 90
c = 46.916	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-03-27 
Deposition Author(s): Czabotar, P.E., Colman, P.M.

Revision History  

• Version 1.0: 2007-03-27
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-06-14
  Changes: Source and taxonomy, Structure summary
• Version 1.4: 2017-10-18
  Changes: Refinement description
• Version 1.5: 2023-12-27
  Changes: Advisory, Data collection, Database references
• Version 1.6: 2024-11-20
  Changes: Structure summary