5W83: Rpn8/Rpn11 dimer complex

Rpn8/Rpn11 dimer complex. Determined by X-ray diffraction at 1.55 Å resolution. Released 6 Sept 2017.

Method: X-ray diffraction
Resolution: 1.55 Å
Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains: 2
Atoms: 2,871
Mol. weight: 63.31 kDa
Ligands: ZN
Released: 6 Sept 2017

Explore 5W83 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5W83 contains 11 α-helices and 17 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: 5 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	7-10	4	1
α-helix	12-24	13
β-strand	34-40	7	1
β-strand	45-53	9	1
β-strand	56-58	3	2
β-strand	66-68	3	2
α-helix	70-83	14
β-strand	88-94	7	1
α-helix	103-110	8
α-helix	118	1
β-strand	119-123	5	1
β-strand	134-142	9	1
β-strand	151-157	7	1
β-strand	159-161	3	1
α-helix	165-175	11

Chain B: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	26-30	5	3
α-helix	31-44	14
β-strand	50-59	10	3
β-strand	62-70	9	3
α-helix	85-97	13
α-helix	102	1
β-strand	103-110	8	3
α-helix	120-132	13
β-strand	137-142	6	3
α-helix	145-148	4
β-strand	152-158	7	3
β-strand	196-204	9	3
α-helix	207-221	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
26S proteasome regulatory subunit RPN8	A	protein	338	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Q08723 (AlphaFold model)
Ubiquitin carboxyl-terminal hydrolase RPN11	B	protein	222	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P43588 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5W83_1 26S proteasome regulatory subunit RPN8 (chains A)
MSLQHEKVTIAPLVLLSALDHYERTQTKENKRCVGVILGDANSSTIRVTNSFALPFEEDE
KNSDVWFLDHNYIENMNEMCKKINAKEKLIGWYHSGPKLRASDLKINELFKKYTQNNPLL
LIVDVKQQGVGLPTDAYVAIEQVKDDGTSTEKTFLHLPCTIEAEEAEEIGVEHLLRDVRD
QAAGGLSIRLTNQLKSLKGLQSKLKDVVEYLDKVINKELPINHTILGKLQDVFNLLPNLG
TPDDDEIDVENHDRINISNNLQKALTVKTNDELMVIYISNLVRSIIAFDDLIENKIQNKK
IQEQRVKDKQSKVSDDSESESGDKEATAPLIQRKNKKN

Sequence of entity 2 (B), FASTA

>5W83_2 Ubiquitin carboxyl-terminal hydrolase RPN11 (chains B)
MERLQRLMMNSKVGSADTGRDDTKETVYISSIALLKMLKHGRAGVPMEVMGLMLGEFVDD
YTVNVVDVFAMPQSGTGVSVEAVDDVFQAKMMDMLKQTGRDQMVVGWYHSHPGFGCWLSS
VDVNTQKSFEQLNSRAVAVVVDPIQSVKGKVVIDAFRLIDTGALINNLEPRQTTSNTGLL
NKANIQALIHGLNRHYYSLNIDYHKTAKETKMLMNLHKEQWQ

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1

Primary citation

An AAA Motor-Driven Mechanical Switch in Rpn11 Controls Deubiquitination at the 26S Proteasome. Worden, E.J., Dong, K.C., Martin, A. Mol Cell (2017) 67:799-811.e8. DOI 10.1016/j.molcel.2017.07.023 · PubMed

Other PDB entries of the same protein (UniProt Q08723 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4O8Y 1.95 Å, Zinc-free Rpn11 in complex with Rpn8
4OCM 1.99 Å, Crystal Structure of the Rpn8-Rpn11 MPN domain heterodimer, crystal form Ib
4O8X 1.99 Å, Zinc-bound Rpn11 in complex with Rpn8
4OCN 2.25 Å, Crystal Structure of the Rpn8-Rpn11 MPN domain heterodimer, crystal form II
4OWP 2.35 Å, Crystal structure of rpn11 in a heterodimer complex with rpn8, representing the active…
4OCL 2.4 Å, Crystal Structure of the Rpn8-Rpn11 MPN domain heterodimer, crystal form Ia
5U4P 2.5 Å, Protein-protein complex between 26S proteasome regulatory subunit RPN8, RPN11, and…
3JCK 3.5 Å, Structure of the yeast 26S proteasome lid sub-complex
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)

Browse structure collections

About this viewer

MolViewer shows 5W83 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.