6Z2B: Toprim domain of RNase M5

Toprim domain of RNase M5 bound with two Mg2+ ions. Determined by X-ray diffraction at 2.14 Å resolution. Released 17 Mar 2021.

Method: X-ray diffraction
Resolution: 2.14 Å
Organism: Geobacillus stearothermophilus
Chains: 4
Atoms: 3,340
Mol. weight: 50.16 kDa
Ligands: MG
Released: 17 Mar 2021

Explore 6Z2B in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6Z2B contains 21 α-helices and 24 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: 5 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	6-9	4	1
α-helix	12-19	8
β-strand	26-28	3	1
α-helix	36-48	13
β-strand	51-53	3	1
α-helix	59-71	13
β-strand	76-77	2	1
α-helix	95-97	3
α-helix	100-108	9

Chain B: 6 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	2
β-strand	6-9	4	3
α-helix	12-21	10
β-strand	23	1	2
β-strand	26-28	3	3
α-helix	36-49	14
β-strand	51-53	3	3
α-helix	59-71	13
β-strand	76-77	2	3
α-helix	82-85	4
β-strand	86	1	4
β-strand	93	1	4
α-helix	95-97	3
α-helix	100-107	8
β-strand	111	1	3

Chain C: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	6-9	4	5
α-helix	12-19	8
β-strand	26-28	3	5
α-helix	36-48	13
β-strand	51-54	4	5
α-helix	59-71	13
β-strand	76-78	3	5
α-helix	95-97	3
α-helix	100-108	9
β-strand	111	1	5

Chain D: 5 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	6
β-strand	6-9	4	7
α-helix	12-21	10
β-strand	23	1	6
β-strand	26-28	3	7
α-helix	36-48	13
β-strand	51-53	3	7
α-helix	59-71	13
β-strand	76-77	2	7
α-helix	95-97	3
α-helix	100-109	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ribonuclease M5	A, B, C, D	protein	116	Geobacillus stearothermophilus	A0A087LGV4 (AlphaFold model)

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

>6Z2B_1 Ribonuclease M5 (chains A, B, C, D)
GGSMKIKEVIVVEGKDDTAAIRRAVDADTIETNGAAVGAEVIERIKLAKERRGVIIFTDP
DFPGEKIRRTIAEQVPGCKHAFLPREAAKARSGKGIGVEHASPDDIRQALANVYEE

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2

Primary citation

Structural studies of RNase M5 reveal two-metal-ion supported two-step dsRNA cleavage for 5S rRNA maturation. Oerum, S., Catala, M., Bourguet, M. et al. RNA Biol (2021) 18:1996-2006. DOI 10.1080/15476286.2021.1885896 · PubMed

Other PDB entries of the same protein (UniProt A0A087LGV4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6TG6 1.3 Å, Toprim domain of RNase M5
6TGJ 1.5 Å, RNA-binding domain of RNase M5
6TPQ 3.07 Å, RNase M5 bound to 50S ribosome with precursor 5S rRNA

Browse structure collections

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