4O8X: Zinc-bound Rpn11

Zinc-bound Rpn11 in complex with Rpn8. Determined by X-ray diffraction at 1.99 Å resolution. Released 22 Jan 2014.

Method: X-ray diffraction
Resolution: 1.99 Å
Organism: Saccharomyces cerevisiae
Chains: 2
Atoms: 3,082
Mol. weight: 49.92 kDa
Ligands: ZN
Released: 22 Jan 2014

Explore 4O8X in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4O8X contains 12 α-helices and 20 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: 6 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	56-59	4	2
β-strand	62-68	7	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	134-141	8	1
β-strand	152-157	6	1
β-strand	159-161	3	1
α-helix	165-174	10
α-helix	176-181	6

Chain B: 6 helices, 10 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	71-73	3
α-helix	80-82	3
α-helix	85-96	12
β-strand	103-110	8	3
α-helix	120-132	13
β-strand	137-141	5	3
β-strand	147	1	4
β-strand	150	1	4
β-strand	153-158	6	3
β-strand	196-198	3	3
β-strand	200-204	5	3
α-helix	207-213	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
26S proteasome regulatory subunit RPN8	A	protein	185	Saccharomyces cerevisiae	Q08723 (AlphaFold model)
26S proteasome regulatory subunit RPN11	B	protein	240	Saccharomyces cerevisiae	P43588 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4O8X_1 26S proteasome regulatory subunit RPN8 (chains A)
MGSLQHEKVTIAPLVLLSALDHYERTQTKENKRCVGVILGDANSSTIRVTNSFALPFEED
EKNSDVWFLDHNYIENMNEMCKKINAKEKLIGWYHSGPKLRASDLKINELFKKYTQNNPL
LLIVDVKQQGVGLPTDAYVAIEQVKDDGTSTEKTFLHLPCTIEAEEAEEIGVEHLLRDVL
EVLFQ

Sequence of entity 2 (B), FASTA

>4O8X_2 26S proteasome regulatory subunit RPN11 (chains B)
GPERLQRLMMNSKVGSADTGRDDTKETVYISSIALLKMLKHGRAGVPMEVMGLMLGEFVD
DYTVNVVDVFAMPQSGTGVSVEAVDDVFQAKMMDMLKQTGRDQMVVGWYHSHPGFGCWLS
SVDVNTQKSFEQLNSRAVAVVVDPIQSVKGKVVIDAFRLIDTGALINNLEPRQTTSNTGL
LNKANIQALIHGLNRHYYSLNIDYHKTAKETKMLMNLHKEQWQSGLKMYDYEEKEESNLA

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1

Water and common crystallization additives (EDO) are not listed.

Primary citation

Structure of the Rpn11-Rpn8 dimer reveals mechanisms of substrate deubiquitination during proteasomal degradation. Worden, E.J., Padovani, C., Martin, A. Nat Struct Mol Biol (2014) 21:220-227. DOI 10.1038/nsmb.2771 · PubMed

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

5W83 1.55 Å, Rpn8/Rpn11 dimer complex
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
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)

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