8GF4: Domain Related to Iron

Crystal structure of Domain Related to Iron (DRI) in complex with heme. Determined by X-ray diffraction at 3.0 Å resolution. Released 13 Mar 2024.

Method: X-ray diffraction
Resolution: 3.0 Å
Organism: Synechocystis sp. PCC 6803
Chains: 4
Atoms: 2,817
Mol. weight: 46.72 kDa
Ligands: ZN, HEM
Released: 13 Mar 2024

Explore 8GF4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8GF4 contains 14 α-helices and 12 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: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	7-20	14
α-helix	22-32	11
β-strand	40-47	8	1
β-strand	50-56	7	1
β-strand	62-67	6	1
α-helix	68	1
α-helix	76-92	17

Chain B: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	7-20	14
α-helix	22-31	10
β-strand	41-47	7	2
β-strand	50-57	8	2
β-strand	60-67	8	2
α-helix	75-91	17

Chain C: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	7-20	14
α-helix	22-31	10
β-strand	40-47	8	3
β-strand	50-56	7	3
β-strand	62-67	6	3
α-helix	76-91	16

Chain D: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	7-19	13
α-helix	22-31	10
β-strand	40-46	7	4
β-strand	50-56	7	4
β-strand	61-67	7	4
α-helix	68	1
α-helix	76-92	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ssr1698 protein	A, B, C, D	protein	103	Synechocystis sp. PCC 6803	P73129 (AlphaFold model)

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

>8GF4_1 Ssr1698 protein (chains A, B, C, D)
MADPLTPAISDRICKHMNEDHASAIALYAQVFGQQTDVTMAQMQAIDPTGMDLVVESEGG
SKTIRIEFEQPLKDSEDAHQVLIAMAKQARSVGKNSAENLYFQ

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4
HEM	Protoporphyrin IX containing FE	C34 H32 Fe N4 O4	2

Primary citation

A hemoprotein with a zinc-mirror heme site ties heme availability to carbon metabolism in cyanobacteria. Grosjean, N., Yee, E.F., Kumaran, D. et al. Nat Commun (2024) 15:3167-3167. DOI 10.1038/s41467-024-47486-z · PubMed

Other PDB entries of the same protein (UniProt P73129 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8ZXQ 1.51 Å, Crystal structure of Ssr1698 in complex with heme b
8ZXR 1.6 Å, Crystal structure of Ssr1698 in complex with heme c
8GDW 2.35 Å, Crystal structure of Domain Related to Iron (DRI) from cyanobacteria
8FM6 2.85 Å, Dri1 hemoprotein variant H21A with a zinc-mirror heme site
8GBK 2.9 Å, Dri1 hemoprotein variant H79A-R90A with a zinc-mirror heme site

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