8YUM: Ubiquitin

Ubiquitin(late folding intermediate, F') from Oryza sativa subsp. japonica (Rice). Determined by solution NMR. Released 9 Oct 2024.

Method: Solution NMR
Organism: Oryza sativa Japonica Group
Chains: 1
Atoms: 607
Mol. weight: 8.67 kDa
Released: 9 Oct 2024

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

Secondary structure: helices and β-sheets

8YUM contains 3 α-helices and 7 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 A: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	1
β-strand	13-18	6	1
β-strand	23	1	2
α-helix	24-35	12
β-strand	42-46	5	1
β-strand	49-50	2	1
α-helix	51	1
β-strand	56	1	2
α-helix	58-60	3
β-strand	66-72	7	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin	A	protein	77	Oryza sativa Japonica Group	P69326 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8YUM_1 Ubiquitin (chains A)
MMQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADY
NIQKESTLHLVLRLRGG

Primary citation

Slow Conformational Exchange between Partially Folded and Near-Native States of Ubiquitin: Evidence for a Multistate Folding Model. Adhada, S.T., Sarma, S.P. Biochemistry (2024) 63:2565-2579. DOI 10.1021/acs.biochem.4c00321 · PubMed

Other PDB entries of the same protein (UniProt P69326 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6NYA 2.06 Å, Crystal Structure of ubiquitin E1 (Uba1) in complex with Ubc3 (Cdc34) and ubiquitin
7SOL 2.25 Å, Crystal Structures of the bispecific ubiquitin/FAT10 activating enzyme, Uba6
7K5J 3.42 Å, Structure of an E1-E2-ubiquitin thioester mimetic
5TTE 3.5 Å, Crystal Structure of an RBR E3 ubiquitin ligase in complex with an E2-Ub thioester…
8YSY Ubiquitin(native) from Oryza sativa subsp. japonica (Rice)

Browse structure collections

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