7M5B: Human BAK

Name: PDB 7M5B: Crystal Structure of human BAK in complex with M3W5_BID
Published: 2022-01-12
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: apoptosis

Crystal Structure of human BAK in complex with M3W5_BID. Determined by X-ray diffraction at 1.85 Å resolution. Released 12 Jan 2022.

Method: X-ray diffraction
Resolution: 1.85 Å
Organism: Homo sapiens
Chains: 4
Atoms: 3,205
Mol. weight: 43.13 kDa
Ligands: CU
Released: 12 Jan 2022

Explore 7M5B in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7M5B contains 20 α-helices and 4 β-strands across 4 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, 1 β-strand

Element	Residues	Length	Sheet
α-helix	22-47	26
α-helix	70-81	12
α-helix	83-88	6
α-helix	90-100	11
α-helix	107-119	13
α-helix	125-144	20
α-helix	151-164	14
α-helix	167-173	7
α-helix	177-182	6
β-strand	183-184	2	1

Chain B: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
α-helix	81-100	20
β-strand	102-103	2	1

Chain C: 9 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	24-47	24
α-helix	58-61	4
α-helix	70-81	12
α-helix	83-100	18
α-helix	107-119	13
α-helix	125-144	20
α-helix	151-164	14
α-helix	167-173	7
α-helix	177-182	6
β-strand	184	1	2

Chain D: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
α-helix	82-100	19
β-strand	102	1	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Bcl-2 homologous antagonist/killer	A, C	protein	166	Homo sapiens	Q16611 (AlphaFold model)
BH3-interacting domain death agonist p15	B, D	protein	25	Homo sapiens	P55957 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>7M5B_1 Bcl-2 homologous antagonist/killer (chains A, C)
SASEEQVAQDTEEVFRSYVFYRHQQEQEAEGVAAPADPEMVTLPLQPSSTMGQVGRQLAI
IGDDINRRYDSEFQTMLQHLQPTAENAYEYFTKIATSLFESGINWGRVVALLGFGYRLAL
HVYQHGLTGFLGQVTRFVVDFMLHHSIARWIAQRGGWVAALNLCNG

Sequence of entity 2 (B, D), FASTA

>7M5B_2 BH3-interacting domain death agonist p15 (chains B, D)
EDIIRNIARHLAQMGDSMDRSWGGC

Ligands and cofactors

ID	Name	Formula	Copies
CU	Copper (II) ion	Cu	1

Primary citation

Structural basis of BAK activation in mitochondrial apoptosis initiation. Singh, G., Guibao, C.D., Seetharaman, J. et al. Nat Commun (2022) 13:250-250. DOI 10.1038/s41467-021-27851-y · PubMed

Other PDB entries of the same protein (UniProt Q16611 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5VX1 1.22 Å, Bak L100A
8CZF 1.3 Å, Human BAK in complex with the dF2 peptide
8CZH 1.3 Å, Human BAK in complex with the dM2 peptide
2IMS 1.48 Å, The X-ray Structure of a Bak Homodimer Reveals an Inhibitory Zinc Binding Site
2IMT 1.49 Å, The X-ray Structure of a Bak Homodimer Reveals an Inhibitory Zinc Binding Site
9CPE 1.49 Å, Structural basis of BAK sequestration by MCL-1 and consequences for apoptosis initiation
5FMI 1.49 Å, Human Bak Q77L
7M5A 1.5 Å, Crystal Structure of human BAK in complex with W3W5_BID
5VWY 1.55 Å, Bak core latch dimer in complex with Bim-h3Pc-RT
5VX0 1.6 Å, Bak in complex with Bim-h3Glg
5VWZ 1.62 Å, Bak in complex with Bim-h3Pc
6UXQ 1.7 Å, Crystal structure of BAK core domain BH3-groove-dimer in complex with POPC and C8E4

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