5VAY

Bcl-2 complex with Beclin 1 T108D BH3 domain

• PDB DOI: https://doi.org/10.2210/pdb5VAY/pdb

• Classification: APOPTOSIS
• Organism(s): Homo sapiens
• Expression System: Escherichia coli K-12
• Mutation(s): Yes 


• Deposited: 2017-03-28 Released: 2018-04-04 
• Deposition Author(s): Lee, E.F., Smith, B.J., Yao, S., Fairlie, W.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.228 
• R-Value Work: 0.184 
• R-Value Observed: 0.186 

Starting Model: experimental

Literature

Bcl-2 complex with Beclin 1 pT108 BH3 domain

Lee, E.F., Smith, B.J., Yao, S., Fairlie, W.D.

To be published.

Biological Assembly 1  

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

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 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 89.44 kDa 
• Atom Count: 5,762 
• Modelled Residue Count: 654 
• Deposited Residue Count: 776 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Apoptosis regulator Bcl-2 -- Bcl-2-like protein 1 Chimera	A, B, C, D	168	Homo sapiens	Mutation(s): 0  Gene Names: BCL2, BCL2L1, BCL2L, BCLX
UniProt & NIH Common Fund Data Resources
Find proteins for Q07817 (Homo sapiens) Explore Q07817  Go to UniProtKB:  Q07817
PHAROS:  Q07817 GTEx:  ENSG00000171552
Find proteins for P10415 (Homo sapiens) Explore P10415  Go to UniProtKB:  P10415
PHAROS:  P10415 GTEx:  ENSG00000171791
UniProt Groups	Q07817P10415

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beclin-1	E, F [auth G], G [auth F], H	26	Homo sapiens	Mutation(s): 1
UniProt & NIH Common Fund Data Resources
Find proteins for Q14457 (Homo sapiens) Explore Q14457  Go to UniProtKB:  Q14457
PHAROS:  Q14457 GTEx:  ENSG00000126581

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.228 
• R-Value Work: 0.184 
• R-Value Observed: 0.186 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.205	α = 90
b = 53.192	β = 108.39
c = 91.413	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-04-04 
Deposition Author(s): Lee, E.F., Smith, B.J., Yao, S., Fairlie, W.D.

Revision History  

• Version 1.0: 2018-04-04
  Type: Initial release
  
• Version 1.1: 2023-10-04
  Changes: Data collection, Database references, Refinement description