8SPF: Apoptosis regulator BAX

Name: PDB 8SPF: Crystal structure of Bax core domain BH3-groove dimer - hexameric fraction with 2-stearoyl lysoPC
Published: 2023-12-27
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: apoptosis

Crystal structure of Bax core domain BH3-groove dimer - hexameric fraction with 2-stearoyl lysoPC. Determined by X-ray diffraction at 2.2 Å resolution. Released 27 Dec 2023.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: Homo sapiens
Chains: 6
Atoms: 3,285
Mol. weight: 54.73 kDa
Ligands: 1GP, D12, DD9, OCT
Released: 27 Dec 2023

Explore 8SPF in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8SPF contains 23 α-helices and 0 β-strands across 6 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: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	60-72	13
α-helix	74-80	7
α-helix	88-99	12
α-helix	107-123	17

Chain B: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	55-73	19
α-helix	88-99	12
α-helix	107-120	14

Chain C: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	55-71	17
α-helix	74-81	8
α-helix	89-99	11
α-helix	107-123	17

Chain D: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	56-72	17
α-helix	74-81	8
α-helix	88-99	12
α-helix	107-123	17

Chain E: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	54-72	19
α-helix	74-81	8
α-helix	88-99	12
α-helix	107-123	17

Chain F: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	54-72	19
α-helix	74-81	8
α-helix	88-99	12
α-helix	107-125	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Apoptosis regulator BAX	A, B, C, D, E, F	protein	81	Homo sapiens	Q07812 (AlphaFold model)

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

>8SPF_1 Apoptosis regulator BAX (chains A, B, C, D, E, F)
GPLGSDASTKKLSESLKRIGDELDSNMELQRMIAAVDTDSPREVFFRVAADMFSDGNFNW
GRVVALFYFASKLVLKALSTK

Ligands and cofactors

ID	Name	Formula	Copies
1GP	Sn-glycerol-1-phosphate	C3 H9 O6 P	1
D12	Dodecane	C12 H26	1
DD9	nonane	C9 H20	1
OCT	N-octane	C8 H18	1

Water and common crystallization additives (EDO) are not listed.

Primary citation

Sequence differences between BAX and BAK core domains manifest as differences in their interactions with lipids. Miller, M.S., Cowan, A.D., Brouwer, J.M. et al. FEBS J (2024) 291:2335-2353. DOI 10.1111/febs.17031 · PubMed

Other PDB entries of the same protein (UniProt Q07812 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4ZIE 1.8 Å, Crystal Structure of core/latch dimer of Bax in complex with BimBH3
5W60 1.8 Å, Crystal structure of BAXP168G monomer cryo-protected with ethylene glycol
4S0O 1.9 Å, Crystal Structure of the Autoinhibited Dimer of Pro-apoptotic BAX (I)
5W5Z 2.0 Å, Crystal structure of BAXP168G in complex with an activating antibody at high resolution
6EB6 2.02 Å, Crystal structure of BAX W139A monomer
8SRX 2.09 Å, Crystal structure of BAK-BAX heterodimer with lysoPC
8G1T 2.09 Å, Crystal structure of Bax core domain BH3-groove dimer - tetrameric fraction P21
6TRR 2.12 Å, Structural insight into tanapoxvirus mediated inhibition of apoptosis
4ZII 2.19 Å, Crystal Structure of core/latch dimer of BaxI66A in complex with BidBH3
4ZIG 2.2 Å, Crystal Structure of core/latch dimer of Bax in complex with BidBH3mini
4BD2 2.21 Å, Bax domain swapped dimer in complex with BidBH3
7ADT 2.21 Å, Orf virus Apoptosis inhibitor ORFV125

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