2VM6 | pdb_00002vm6

Human Bcl2-A1 in complex with Bim-BH3 peptide

• PDB DOI: https://doi.org/10.2210/pdb2VM6/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2008-01-23 Released: 2008-02-05 
• Deposition Author(s): Herman, M.D., Lehtio, L., Arrowsmith, C.H., Berglund, H., Busam, R.D., Collins, R., Dahlgren, L.G., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Johansson, I., Kallas, A., Karlberg, T., Kotenyova, T., Moche, M., Nilsson, M.E., Nyman, T., Persson, C., Sagemark, J., Svensson, L., Thorsell, A.G., Tresaugues, L., van den Berg, S., Weigelt, J., Welin, M., Nordlund, P., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.250 (Depositor), 0.247 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Literature

Completing the Family Portrait of the Anti- Apoptotic Bcl-2 Proteins: Crystal Structure of Human Bfl-1 in Complex with Bim.

Herman, M.D., Nyman, T., Welin, M., Lehtio, L., Flodin, S., Tresaugues, L., Kotenyova, T., Flores, A., Nordlund, P.

(2008) FEBS Lett 582: 3590

• PubMed: 18812174 
• DOI: https://doi.org/10.1016/j.febslet.2008.09.028
• Primary Citation Related Structures: 
  2VM6


• PubMed Abstract: 
  

  Evasion of apoptosis is recognized as a characteristic of malignant growth. Anti-apoptotic B-cell lymphoma-2 (Bcl-2) family members have therefore emerged as potential therapeutic targets due to their critical role in proliferating cancer cells. Here, we present the crystal structure of Bfl-1, the last anti-apoptotic Bcl-2 family member to be structurally characterized, in complex with a peptide corresponding to the BH3 region of the pro-apoptotic protein Bim. The structure reveals distinct features at the peptide-binding site, likely to define the binding specificity for pro-apoptotic proteins. Superposition of the Bfl-1:Bim complex with that of Mcl-1:Bim reveals a significant local plasticity of hydrophobic interactions contributed by the Bim peptide, likely to be the basis for the multi specificity of Bim for anti-apoptotic proteins.

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Organizational Affiliation: 
• Department of Medical Biochemistry and Biophysics, Karolinska Institute, Pär Nordlund, 17177 Stockholm, Sweden.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 20.46 kDa 
• Atom Count: 1,436 
• Modeled Residue Count: 169 
• Deposited Residue Count: 175 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BCL-2-RELATED PROTEIN A1	A	150	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q16548 (Homo sapiens) Explore Q16548  Go to UniProtKB:  Q16548
PHAROS:  Q16548 GTEx:  ENSG00000140379

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
BCL-2-LIKE PROTEIN 11	B	25	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for O43521 (Homo sapiens) Explore O43521  Go to UniProtKB:  O43521
PHAROS:  O43521 GTEx:  ENSG00000153094

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.250 (Depositor), 0.247 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.8	α = 90
b = 70.8	β = 90
c = 208.8	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-02-05 
Deposition Author(s): Herman, M.D., Lehtio, L., Arrowsmith, C.H., Berglund, H., Busam, R.D., Collins, R., Dahlgren, L.G., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Johansson, I., Kallas, A., Karlberg, T., Kotenyova, T., Moche, M., Nilsson, M.E., Nyman, T., Persson, C., Sagemark, J., Svensson, L., Thorsell, A.G., Tresaugues, L., van den Berg, S., Weigelt, J., Welin, M., Nordlund, P., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2008-02-05
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2019-09-25
  Changes: Data collection, Experimental preparation, Other
• Version 1.3: 2024-05-08
  Changes: Data collection, Database references