7Y13: Apo-state MrgD-Gi complex

Cryo-EM structure of apo-state MrgD-Gi complex (local). Determined by electron microscopy at 3.1 Å resolution. Released 20 Jul 2022.

Method: Electron microscopy
Resolution: 3.1 Å
Organisms: Escherichia coli, Homo sapiens
Chains: 1
Atoms: 2,199
Mol. weight: 51.94 kDa
Ligands: PLM
Released: 20 Jul 2022

Explore 7Y13 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7Y13 contains 14 α-helices and 0 β-strands across 1 chain. 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 R: 14 helices, 0 β-strands

Element	Residues	Length
α-helix	23-52	30
α-helix	62-85	24
α-helix	97-128	32
α-helix	130-135	6
α-helix	141-164	24
α-helix	173-185	13
α-helix	186-190	5
α-helix	191-204	14
α-helix	205-209	5
α-helix	217-229	13
α-helix	230-234	5
α-helix	235-244	10
α-helix	254-273	20
α-helix	274-278	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Soluble cytochrome b562,Mas-related G-protein coupled receptor member D	R	protein	446	Escherichia coli, Homo sapiens	P0ABE7 (AlphaFold model), Q8TDS7 (AlphaFold model)

Sequence of entity 1 (R), FASTA

>7Y13_1 Soluble cytochrome b562,Mas-related G-protein coupled receptor member D (chains R)
MKTIIALSYIFCLVFADYKDDDDKADLEDNWETLNDNLKVIEKADNAAQVKDALTKMRAA
ALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKT
TRNAYIQKYLNSSGTVESALNYSRGSTVHTAYLVLSSLAMFTCLCGMAGNSMVIWLLGFR
MHRNPFCIYILNLAAADLLFLFSMASTLSLETQPLVNTTDKVHELMKRLMYFAYTVGLSL
LTAISTQRCLSVLFPIWFKCHRPRHLSAWVCGLLWTLCLLMNGLTSSFCSKFLKFNEDRC
FRVDMVQAALIMGVLTPVMTLSSLTLFVWVRRSSQQWRRQPTRLFVVVLASVLVFLICSL
PLSIYWFVLYWLSLPPEMQVLCFSLSRLSSSVSSSANPVIYFLVGSRRSHRLPTRSLGTV
LQQALREEPELEGGETPTVGTNEMGA

Ligands and cofactors

ID	Name	Formula	Copies
PLM	Palmitic acid	C16 H32 O2	7

Primary citation

Structural insight into the activation mechanism of MrgD with heterotrimeric Gi-protein revealed by cryo-EM. Suzuki, S., Iida, M., Hiroaki, Y. et al. Commun Biol (2022) 5:707-707. DOI 10.1038/s42003-022-03668-3 · PubMed

Other PDB entries of the same protein (UniProt P0ABE7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6DYF 1.1 Å, Cu(II)-bound structure of the engineered cyt cb562 variant, CH3Y
5YO6 1.2 Å, Crystal Structure of B562RIL with engineered disulfide bond T9C-A36C
4JEA 1.22 Å, Crystal structure of an engineered Zn-RIDC1 construct with four interfacial disulfide…
7LSJ 1.26 Å, Cu-bound crystal structure of the engineered cyt cb562 variant, DiCyt2 - H63A,…
7MK4 1.27 Å, Co-bound crystal structure of the engineered cyt cb562 variant, DiCyt2
6DYC 1.33 Å, Co(II)-bound structure of the engineered cyt cb562 variant, CH3
5YO4 1.37 Å, Crystal Structure of B562RIL with engineered disulfide bond K27C-A79C
256B 1.4 Å, Improvement of the 2.5 Å resolution model of cytochrome B562 by redetermining the…
6OT4 1.4 Å, Bimetallic dodecameric cage design 2 (BMC2) from cytochrome cb562
7LRV 1.4 Å, Ni-bound crystal structure of the engineered cyt cb562 variant, DiCyt2, crystallized in…
9PQ4 1.48 Å, Bi-bound structure of the H77C variant of TriCyt2
6DYG 1.49 Å, Fe(II)-bound structure of the engineered cyt cb562 variant, CH3Y

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