4OCM: 26S proteasome regulatory subunit RPN8

Crystal Structure of the Rpn8-Rpn11 MPN domain heterodimer, crystal form Ib. Determined by X-ray diffraction at 1.99 Å resolution. Released 29 Jan 2014.

Method: X-ray diffraction
Resolution: 1.99 Å
Organisms: Saccharomyces cerevisiae, Lama glama
Chains: 6
Atoms: 7,521
Mol. weight: 120.69 kDa
Ligands: ZN
Released: 29 Jan 2014

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

Secondary structure: helices and β-sheets

4OCM contains 36 α-helices and 59 β-strands across 6 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
α-helix	27-28	2
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
β-strand	119-123	5	1
β-strand	134-140	7	1
β-strand	153-157	5	1
β-strand	159-161	3	1
α-helix	165-176	12

Chain B: 9 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	26-30	5	3
α-helix	31-44	14
β-strand	50-57	8	3
β-strand	62-70	9	3
α-helix	71-73	3
α-helix	80-82	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	179-180	2	4
α-helix	182-194	13
β-strand	196-204	9	3
α-helix	207-214	8

Chain C: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	5
β-strand	12-15	4	6
β-strand	19-25	7	5
β-strand	34-40	7	7
β-strand	47-53	7	7
β-strand	59-61	3	7
α-helix	63-65	3
β-strand	69-74	6	5
β-strand	79-84	6	5
α-helix	89-91	3
β-strand	93-100	8	7
α-helix	107-109	3
β-strand	112-113	2	7
β-strand	117-119	3	7
β-strand	120-126	7	6

Chain D: 7 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	7-10	4	8
α-helix	12-24	13
α-helix	27-28	2
β-strand	34-40	7	8
β-strand	45-53	9	8
β-strand	56-59	4	9
β-strand	62-68	7	9
α-helix	70-83	14
β-strand	88-94	7	8
α-helix	103-110	8
α-helix	111-113	3
α-helix	118	1
β-strand	119-123	5	8
β-strand	134-142	9	8
β-strand	151-157	7	8
β-strand	159-161	3	8
α-helix	165-175	11

Chain E: 9 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	26-30	5	4
α-helix	31-44	14
β-strand	50-58	9	4
β-strand	62-70	9	4
α-helix	71-73	3
α-helix	80-82	3
α-helix	85-97	13
α-helix	102	1
β-strand	103-110	8	4
α-helix	120-132	13
β-strand	137-141	5	4
β-strand	153-158	6	4
α-helix	161-166	6
α-helix	185-190	6
β-strand	196-204	9	4
α-helix	207-214	8

Chain F: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	10
β-strand	12-15	4	11
β-strand	19-25	7	10
β-strand	34-40	7	12
β-strand	47-53	7	12
β-strand	59-61	3	12
β-strand	69-74	6	10
α-helix	75-77	3
β-strand	79-84	6	10
α-helix	89-91	3
β-strand	93-100	8	12
α-helix	107-109	3
β-strand	112-113	2	12
β-strand	117-119	3	12
β-strand	120-126	7	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
26S proteasome regulatory subunit RPN8	A, D	protein	187	Saccharomyces cerevisiae	Q08723 (AlphaFold model)
26S proteasome regulatory subunit RPN11	B, E	protein	220	Saccharomyces cerevisiae	P43588 (AlphaFold model)
Nb1	C, F	protein	133	Lama glama

Sequence of entity 1 (A, D), FASTA

>4OCM_1 26S proteasome regulatory subunit RPN8 (chains A, D)
GHMSLQHEKVTIAPLVLLSALDHYERTQTKENKRCVGVILGDANSSTIRVTNSFALPFEE
DEKNSDVWFLDHNYIENMNEMCKKINAKEKLIGWYHSGPKLRASDLKINELFKKYTQNNP
LLLIVDVKQQGVGLPTDAYVAIEQVKDDGTSTEKTFLHLPCTIEAEEAEEIGVEHLLRGS
GGSGGSG

Sequence of entity 2 (B, E), FASTA

>4OCM_2 26S proteasome regulatory subunit RPN11 (chains B, E)
MERLQRLMMNSKVGSADTGRDDTKETVYISSIALLKMLKHGRAGVPMEVMGLMLGEFVDD
YTVNVVDVFAMPQSGTGVSVEAVDDVFQAKMMDMLKQTGRDQMVVGWYHSHPGFGCWLSS
VDVNTQKSFEQLNSRAVAVVVDPIQSVKGKVVIDAFRLIDTGALINNLEPRQTTSNTGLL
NKANIQALIHGLNRHYYSLNIDYHKTAKETKMLMNLHKEQ

Sequence of entity 3 (C, F), FASTA

>4OCM_3 Nb1 (chains C, F)
MQVQLQESGGGLVPAGGSLRLSCVDSGRTFSSTVMAWFRQAPGKEREFVATIRWSGGNTY
YADSVKGRFTISRDNARNTVYLQMNSLKPEDTAVYYCAGGTYYGTLSYKYDFWGRGTQVT
VSSHHHHHHEPEA

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

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

Primary citation

Crystal structure of the proteasomal deubiquitylation module Rpn8-Rpn11. Pathare, G.R., Nagy, I., Sledz, P. et al. Proc Natl Acad Sci U S A (2014) 111:2984-2989. DOI 10.1073/pnas.1400546111 · 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
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)

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