8OI3: NopD with AtSUMO2

Structure of NopD with AtSUMO2. Determined by X-ray diffraction at 1.5 Å resolution. Released 3 Apr 2024.

Method: X-ray diffraction
Resolution: 1.5 Å
Organisms: Bradyrhizobium, Arabidopsis thaliana
Chains: 4
Atoms: 4,523
Mol. weight: 67.97 kDa
Ligands: AYE
Released: 3 Apr 2024

Explore 8OI3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8OI3 contains 26 α-helices and 28 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: 10 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	835-837	3
β-strand	838	1	1
α-helix	839-856	18
α-helix	858-862	5
β-strand	864-866	3	2
α-helix	869-875	7
α-helix	880-890	11
α-helix	892-894	3
β-strand	897-903	7	2
β-strand	917-923	7	2
β-strand	931-935	5	2
α-helix	943-952	10
β-strand	956-960	5	2
β-strand	962	1	3
α-helix	963-965	3
α-helix	971-987	17
β-strand	995	1	3
α-helix	1002-1010	9

Chain B: 10 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	835-837	3
β-strand	838	1	4
α-helix	839-856	18
α-helix	858-862	5
β-strand	864-866	3	5
α-helix	869-875	7
α-helix	880-890	11
α-helix	892-894	3
β-strand	897-903	7	5
β-strand	917-923	7	5
β-strand	931-935	5	5
α-helix	943-952	10
β-strand	956-959	4	5
β-strand	962	1	6
α-helix	963-965	3
α-helix	971-987	17
β-strand	995	1	6
α-helix	1002-1009	8

Chain C: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	16-23	8	7
β-strand	28-34	7	7
α-helix	40-50	11
α-helix	54-56	3
β-strand	57-61	5	7
β-strand	64-65	2	7
α-helix	72-75	4
β-strand	82-87	6	7
β-strand	90	1	4

Chain D: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	16-23	8	8
β-strand	28-34	7	8
α-helix	40-50	11
α-helix	54-56	3
β-strand	57-61	5	8
β-strand	64-65	2	8
α-helix	66-67	2
β-strand	81-87	7	8
β-strand	90	1	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Type III effector	A, B	protein	208	Bradyrhizobium	A0ABV4GMV7
Small ubiquitin-related modifier 2	C, D	protein	91	Arabidopsis thaliana	Q9FLP6 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8OI3_1 Type III effector (chains A, B)
MGSSHHHHHHSSGLVPRGSHPVLGPTQWLGDEHIQRDYELLAQELQQNNPDLAARTRFVD
PLIAQMLRSPSKEVAERALGWVRPGTADFLFLPVSDASDTDRHQRGSHWSLLLVDRRDRG
RRVAYHYDSTQGYNDGLAAELAGRLDANLQQAPIRQQQNSYDCGVFVLDGTRELVRRLAA
RRPDLNLNNLVISRQELRDRLGAGVGFN

Sequence of entity 2 (C, D), FASTA

>8OI3_2 Small ubiquitin-related modifier 2 (chains C, D)
MSATPEEDKKPDQGAHINLKVKGQDGNEVFFRIKRSTQLKKLMNAYCDRQSVDFNSIAFL
FDGRRLRAEQTPDELEMEDGDEIDAMLHQTG

Ligands and cofactors

ID	Name	Formula	Copies
AYE	prop-2-en-1-amine	C3 H7 N	2

Primary citation

Broad-spectrum ubiquitin/ubiquitin-like deconjugation activity of the rhizobial effector NopD from Bradyrhizobium (sp. XS1150). Li, Y., Perez-Gil, J., Lois, L.M. et al. Commun Biol (2024) 7:644-644. DOI 10.1038/s42003-024-06344-w · PubMed

Other PDB entries of the same protein (UniProt A0ABV4GMV7), best resolution first:

8RQI 1.94 Å, Structure of Rhizobium NopD with ubiquitin

Browse structure collections

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