5VAY: Bcl-2 complex with Beclin 1 T108D BH3 domain

Bcl-2 complex with Beclin 1 T108D BH3 domain. Determined by X-ray diffraction at 1.8 Å resolution. Released 4 Apr 2018.

Method: X-ray diffraction
Resolution: 1.8 Å
Organism: Homo sapiens
Chains: 8
Atoms: 5,762
Mol. weight: 89.44 kDa
Released: 4 Apr 2018

Explore 5VAY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5VAY contains 39 α-helices and 0 β-strands across 8 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 9 helices, 0 β-strands

Element	Residues	Length
α-helix	8-24	17
α-helix	91-111	21
α-helix	115-118	4
α-helix	126-137	12
α-helix	144-163	20
α-helix	169-180	12
α-helix	181-185	5
α-helix	186-191	6
α-helix	194-202	9

Chain B: 8 helices, 0 β-strands

Element	Residues	Length
α-helix	7-24	18
α-helix	91-112	22
α-helix	123-137	15
α-helix	144-163	20
α-helix	169-180	12
α-helix	181-185	5
α-helix	186-191	6
α-helix	194-202	9

Chains C and D: 9 helices, 0 β-strands

Element	Residues	Length
α-helix	11-24	14
α-helix	91-111	21
α-helix	115-118	4
α-helix	126-138	13
α-helix	144-163	20
α-helix	169-180	12
α-helix	181-185	5
α-helix	186-191	6
α-helix	194-202	9

Chain E: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	109-127	19

Chain F: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	110-127	18

Chain G: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	108-126	19

Chain H: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	109-125	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Apoptosis regulator Bcl-2 -- Bcl-2-like protein 1 Chimera	A, B, C, D	protein	168	Homo sapiens	P10415 (AlphaFold model), Q07817 (AlphaFold model)
Beclin-1	E, F, G, H	protein	26	Homo sapiens	Q14457 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>5VAY_1 Apoptosis regulator Bcl-2 -- Bcl-2-like protein 1 Chimera (chains A, B, C, D)
GSMAHAGRTGYDNREIVMKYIHYKLSQRGYEWDAGDDVEENRTEAPEGTESEVVHLTLRQ
AGDDFSRRYRRDFAEMSSQLHLTPFTARGRFATVVEELFRDGVNWGRIVAFFEFGGVMCV
ESVNREMSPLVDNIALWMTEYLNRHLHTWIQDNGGWDAFVELYGPSMR

Sequence of entity 2 (E, F, G, H), FASTA

>5VAY_2 Beclin-1 (chains E, F, G, H)
DGGDMENLSRRLKVTGDLFDIMSGQT

Primary citation

Bcl-2 complex with Beclin 1 pT108 BH3 domain. Lee, E.F., Smith, B.J., Yao, S. et al. To be published.

Other PDB entries of the same protein (UniProt P10415 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8HTS 1.25 Å, Crystal structure of Bcl2 in complex with S-10r
6GL8 1.4 Å, Crystal structure of Bcl-2 in complex with the novel orally active inhibitor S55746
6QGG 1.5 Å, Structure of human Bcl-2 in complex with analogue of ABT-737
9IGG 1.5 Å, Structure of human Bcl-xL in complex with small molecule inhibitor
8HTR 1.6 Å, Crystal structure of Bcl2 in complex with S-9c
6O0K 1.62 Å, crystal structure of BCL-2 with venetoclax
9I9E 1.7 Å, Structure of human Bcl-xL in complex with small molecule inhibitor
9O14 1.73 Å, Crystal Structure of BCL-2 in complex with a stapled BAD BH3 peptide BAD SAHB 4.2
9O16 1.73 Å, Crystal Structure of human BCL-2 (R129L) mutant in complex with a stapled BAD BH3…
6O0M 1.75 Å, crystal structure of BCL-2 F104L mutation with venetoclax
5VAU 1.75 Å, Bcl-2 complex with Beclin 1 BH3 domain
8VWX 1.77 Å, Human Bcl-2 (G101V Mutant)/Bcl-xL Chimera Fused to Maltose-Binding Protein

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