5LN1: Ubiquitylated-RPN10 from yeast

Structure of ubiquitylated-RPN10 from yeast;. Determined by X-ray diffraction at 3.14 Å resolution. Released 19 Oct 2016.

Method: X-ray diffraction
Resolution: 3.14 Å
Organisms: Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Homo sapiens
Chains: 2
Atoms: 2,069
Mol. weight: 30.6 kDa
Released: 19 Oct 2016

Explore 5LN1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5LN1 contains 10 α-helices and 19 β-strands across 2 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: 7 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	1
α-helix	14-16	3
α-helix	25-43	19
β-strand	48-53	6	1
β-strand	55	1	2
β-strand	60-66	7	1
α-helix	69-76	8
β-strand	77	1	3
β-strand	79	1	3
β-strand	85	1	2
α-helix	87-99	13
β-strand	107-114	8	1
α-helix	122-134	13
β-strand	137-143	7	1
α-helix	154-161	8
β-strand	171-173	3	1
α-helix	181-187	7

Chain U: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	4
β-strand	12-16	5	4
β-strand	22	1	5
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	4
β-strand	48-49	2	4
α-helix	50-51	2
β-strand	52	1	6
β-strand	54	1	6
β-strand	55	1	5
β-strand	66-71	6	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
26S proteasome regulatory subunit RPN10	A	protein	195	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P38886 (AlphaFold model)
Polyubiquitin-B	U	protein	81	Homo sapiens	P0CG47 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5LN1_1 26S proteasome regulatory subunit RPN10 (chains A)
GPPRMVLEATVLVIDNSEYSRNGDFPRTRFEAQIDSVEFIFQAKRNSNPENTVGLISGAG
ANPRVLSTFTAEFGKILAGLHDTQIEGKLHMATALQIAQLTLKHRQNKVQHQRIVAFVCS
PISDSRDELIRLAKTLKKNNVAVDIINFGEIEQNTELLDEFIAAVNNPQEETSHLLTVTP
GPRLLYENIASSPII

Sequence of entity 2 (U), FASTA

>5LN1_2 Polyubiquitin-B (chains U)
GAMGSMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRT
LSDYNIQKESTLHLVLRLRGG

Primary citation

Structure of ubiquitylated-Rpn10 provides insight into its autoregulation mechanism. Keren-Kaplan, T., Zeev Peters, L., Levin-Kravets, O. et al. Nat Commun (2016) 7:12960-12960. DOI 10.1038/ncomms12960 · PubMed

Other PDB entries of the same protein (UniProt P38886 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9CGC 3.61 Å, Yeast 26S proteasome non-substrate-engaged (S1 state)
6J2Q 3.8 Å, Yeast proteasome in Ub-accepted state (C1-b)
6J2X 3.8 Å, Yeast proteasome in resting state (C1-a)
5MPD 4.1 Å, 26S proteasome in presence of ATP (s1)
6FVT 4.1 Å, 26S proteasome, s1 state
5WVK 4.2 Å, Yeast proteasome-ADP-AlFx
5MPE 4.5 Å, 26S proteasome in presence of ATP (s2)
6FVU 4.5 Å, 26S proteasome, s2 state
6FVW 4.5 Å, 26S proteasome, s4 state
6J30 4.5 Å, yeast proteasome in Ub-engaged state (C2)
3JCP 4.6 Å, Structure of yeast 26S proteasome in M2 state derived from Titan dataset
3JCO 4.8 Å, Structure of yeast 26S proteasome in M1 state derived from Titan dataset

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