3JCK: Yeast 26S proteasome lid sub-complex

Structure of the yeast 26S proteasome lid sub-complex. Determined by electron microscopy at 3.5 Å resolution. Released 20 Jan 2016.

Method: Electron microscopy
Resolution: 3.5 Å
Organism: Saccharomyces cerevisiae S288c
Chains: 9
Atoms: 22,457
Mol. weight: 361.33 kDa
Ligands: ZN
Released: 20 Jan 2016

Explore 3JCK in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3JCK contains 160 α-helices and 41 β-strands across 9 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: 24 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	29-36	8
α-helix	44-54	11
α-helix	61-70	10
α-helix	132-149	18
α-helix	153-158	6
α-helix	159-163	5
α-helix	164-172	9
α-helix	175-195	21
α-helix	201-224	24
α-helix	227-243	17
α-helix	248-255	8
α-helix	266-282	17
α-helix	289-298	10
α-helix	307-323	17
α-helix	327-329	3
α-helix	330-333	4
α-helix	337-340	4
α-helix	343-354	12
α-helix	357-372	16
α-helix	376-380	5
α-helix	384-397	14
β-strand	401-403	3	1
α-helix	404-410	7
α-helix	416-428	13
β-strand	434-437	4	1
β-strand	442-445	4	1
α-helix	456-477	22

Chain B: 28 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	32-35	4
α-helix	37-41	5
α-helix	42-44	3
α-helix	49-69	21
α-helix	72-84	13
α-helix	94-106	13
α-helix	111-125	15
α-helix	135-141	7
α-helix	142-146	5
α-helix	147	1
α-helix	153-160	8
α-helix	165-167	3
α-helix	173-190	18
α-helix	194-201	8
α-helix	205-209	5
α-helix	211-231	21
α-helix	235-245	11
α-helix	248-252	5
α-helix	254-270	17
α-helix	272	1
α-helix	275-286	12
α-helix	288-291	4
α-helix	295-304	10
α-helix	311-324	14
α-helix	337-356	20
β-strand	357-361	5	2
α-helix	362-369	8
α-helix	373-385	13
β-strand	392-394	3	2
β-strand	399-401	3	2
α-helix	408-439	32

Chain C: 22 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	55-57	3
α-helix	59-64	6
α-helix	71-83	13
α-helix	94-105	12
α-helix	112-127	16
α-helix	131-144	14
α-helix	152-168	17
α-helix	171-187	17
α-helix	192-207	16
α-helix	212-228	17
α-helix	232-248	17
α-helix	254-272	19
α-helix	276-281	6
α-helix	284-288	5
α-helix	289-291	3
α-helix	294-308	15
α-helix	311-316	6
α-helix	322-325	4
α-helix	329-351	23
β-strand	354-355	2	2
α-helix	359-366	8
α-helix	370-382	13
β-strand	388-391	4	3
β-strand	396-399	4	3
β-strand	405	1	4
α-helix	407-428	22

Chain D: 26 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	25-34	10
α-helix	40-55	16
α-helix	60-71	12
α-helix	96-122	27
α-helix	127-143	17
α-helix	147-157	11
α-helix	164	1
α-helix	165-170	6
α-helix	171-181	11
α-helix	184-200	17
α-helix	204-220	17
α-helix	224-234	11
α-helix	246-260	15
α-helix	263-266	4
α-helix	267-271	5
α-helix	276-279	4
α-helix	280-282	3
α-helix	286-297	12
α-helix	301-311	11
α-helix	312-316	5
α-helix	323-325	3
α-helix	326-342	17
β-strand	345-349	5	3
α-helix	350-357	8
α-helix	361-371	11
α-helix	372-374	3
β-strand	379-382	4	3
β-strand	387-390	4	3
β-strand	395	1	4
α-helix	396-423	28

Chain E: 9 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	8-10	3	5
α-helix	12-25	14
β-strand	34-40	7	5
β-strand	46-53	8	5
β-strand	56-58	3	6
β-strand	66-68	3	6
α-helix	70-81	12
β-strand	88-94	7	5
α-helix	103-110	8
β-strand	120-123	4	5
β-strand	134-140	7	5
β-strand	153-157	5	5
β-strand	161	1	5
α-helix	165-175	11
α-helix	186-215	30
α-helix	219-221	3
α-helix	223-234	12
α-helix	237-238	2
α-helix	261-306	46

Chain F: 26 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	7-16	10
α-helix	20-22	3
α-helix	24-35	12
α-helix	38-51	14
α-helix	52-54	3
α-helix	58-61	4
α-helix	62-66	5
α-helix	67-68	2
α-helix	69-71	3
α-helix	75-88	14
α-helix	92-112	21
α-helix	122-140	19
α-helix	143-159	17
α-helix	165-182	18
α-helix	185-198	14
α-helix	207-223	17
α-helix	231-234	4
α-helix	239-242	4
α-helix	246-248	3
α-helix	249-259	11
α-helix	263-276	14
α-helix	278-281	4
α-helix	284-302	19
β-strand	308-309	2	2
α-helix	310-317	8
α-helix	324-333	10
β-strand	337-338	2	7
β-strand	341-342	2	2
β-strand	347-348	2	2
β-strand	352-353	2	7
α-helix	360-384	25

Chain G: 10 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	26-29	4	8
α-helix	31-44	14
β-strand	50-56	7	8
β-strand	62-71	10	8
α-helix	85-96	12
β-strand	103-108	6	8
β-strand	110	1	8
α-helix	120-128	9
β-strand	137-141	5	8
α-helix	151-152	2
β-strand	153-158	6	8
α-helix	187-190	4
β-strand	196-198	3	8
β-strand	201-202	2	8
α-helix	207-214	8
α-helix	230-260	31
α-helix	263-270	8
α-helix	276-300	25
α-helix	301-305	5

Chain H: 12 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	8-17	10
α-helix	20-40	21
α-helix	52-71	20
α-helix	75-90	16
α-helix	101-115	15
α-helix	119-133	15
α-helix	143-154	12
α-helix	157-166	10
α-helix	175-196	22
β-strand	199-201	3	9
α-helix	202-209	8
α-helix	215-223	9
β-strand	228-229	2	9
β-strand	232-234	3	9
α-helix	259-271	13

1 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
26S proteasome regulatory subunit RPN3	A	protein	438	Saccharomyces cerevisiae S288c	P40016 (AlphaFold model)
26S proteasome regulatory subunit RPN5	B	protein	445	Saccharomyces cerevisiae S288c	Q12250 (AlphaFold model)
26S proteasome regulatory subunit RPN6	C	protein	434	Saccharomyces cerevisiae S288c	Q12377 (AlphaFold model)
26S proteasome regulatory subunit RPN7	D	protein	429	Saccharomyces cerevisiae S288c	Q06103 (AlphaFold model)
26S proteasome regulatory subunit RPN8	E	protein	338	Saccharomyces cerevisiae S288c	Q08723
26S proteasome regulatory subunit RPN9	F	protein	393	Saccharomyces cerevisiae S288c	Q04062
Ubiquitin carboxyl-terminal hydrolase RPN11	G	protein	306	Saccharomyces cerevisiae S288c	P43588
26S proteasome regulatory subunit RPN12	H	protein	274	Saccharomyces cerevisiae S288c	P32496
26S proteasome complex subunit SEM1	I	protein	89	Saccharomyces cerevisiae S288c	O94742

Sequence of entity 1 (A), FASTA

>3JCK_1 26S proteasome regulatory subunit RPN3 (chains A)
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXTAEINCFMHLLVQLF
LWDSKELEQLVEFNRKVVIPNLLCYYNLRSLNLINAKLWFYIYLSHETLARSSEEINSDN
QNIILRSTMMKFLKIASLKHDNETKAMLINLILRDFLNNGEVDSASDFISKLEYPHTDVS
SSLEARYFFYLSKINAIQLDYSTANEYIIAAIRKAPHNSKSLGFLQQSNKLHCCIQLLMG
DIPELSFFHQSNMQKSLLPYYHLTKAVKLGDLKKFTSTITKYKQLLLKDDTYQLCVRLRS
NVIKTGIRIISLTYKKISLRDICLKLNLDSEQTVEYMVSRAIRDGVIEAKINHEDGFIET
TELLNIYDSEDPQQVFDERIKFANQLHDEYLVSMRYPEDKKTQQNEKSENGENDDDTLDG
DLMDDMSDISDLDDLGFL

Sequence of entity 2 (B), FASTA

>3JCK_2 26S proteasome regulatory subunit RPN5 (chains B)
MSRDAPIKADKDYSQILKEEFPKIDSLAQNDCNSALDQLLVLEKKTRQASDLASSKEVLA
KIVDLLASRNKWDDLNEQLTLLSKKHGQLKLSIQYMIQKVMEYLKSSKSLDLNTRISVIE
TIRVVTENKIFVEVERARVTKDLVEIKKEEGKIDEAADILCELQVETYGSMEMSEKIQFI
LEQMELSILKGDYSQATVLSRKILKKTFKNPKYESLKLEYYNLLVKISLHKREYLEVAQY
LQEIYQTDAIKSDEAKWKPVLSHIVYFLVLSPYGNLQNDLIHKIQNDNNLKKLESQESLV
KLFTTNELMRWPIVQKTYEPVLNEDDLAFGGEANKHHWEDLQKRVIEHNLRVISEYYSRI
TLLRLNELLDLTESQTETYISDLVNQGIIYAKVNRPAKIVNFEKPKNSSQLLNEWSHNVD
ELLEHIETIGHLITKEEIMHGLQAK

Sequence of entity 3 (C), FASTA

>3JCK_3 26S proteasome regulatory subunit RPN6 (chains C)
MSLPGSKLEEARRLVNEKQYNEAEQVYLSLLDKDSSQSSAAAGASVDDKRRNEQETSILE
LGQLYVTMGAKDKLREFIPHSTEYMMQFAKSKTVKVLKTLIEKFEQVPDSLDDQIFVCEK
SIEFAKREKRVFLKHSLSIKLATLHYQKKQYKDSLALINDLLREFKKLDDKPSLVDVHLL
ESKVYHKLRNLAKSKASLTAARTAANSIYCPTQTVAELDLMSGILHCEDKDYKTAFSYFF
ESFESYHNLTTHNSYEKACQVLKYMLLSKIMLNLIDDVKNILNAKYTKETYQSRGIDAMK
AVAEAYNNRSLLDFNTALKQYEKELMGDELTRSHFNALYDTLLESNLCKIIEPFECVEIS
HISKIIGLDTQQVEGKLSQMILDKIFYGVLDQGNGWLYVYETPNQDATYDSALELVGQLN
KVVDQLFEKASVLY

Sequence of entity 4 (D), FASTA

>3JCK_4 26S proteasome regulatory subunit RPN7 (chains D)
MVDVEEKSQEVEYVDPTVNRVPNYEVSEKAFLLTQSKVSIEQRKEAAEFVLAKIKEEEMA
PYYKYLCEEYLVNNGQSDLEHDEKSDSLNEWIKFDQELYNELCKKNESKIKELNEKIQKL
EEDDEGELEQAQAWINLGEYYAQIGDKDNAEKTLGKSLSKAISTGAKIDVMLTIARLGFF
YNDQLYVKEKLEAVNSMIEKGGDWERRNRYKTYYGIHCLAVRNFKEAAKLLVDSLATFTS
IELTSYESIATYASVTGLFTLERTDLKSKVIDSPELLSLISTTAALQSISSLTISLYASD
YASYFPYLLETYANVLIPCKYLNRHADFFVREMRRKVYAQLLESYKTLSLKSMASAFGVS
VAFLDNDLGKFIPNKQLNCVIDRVNGIVETNRPDNKNAQYHLLVKQGDGLLTKLQKYGAA
VRLTGSDRV

Sequence of entity 5 (E), FASTA

>3JCK_5 26S proteasome regulatory subunit RPN8 (chains E)
MSLQHEKVTIAPLVLLSALDHYERTQTKENKRCVGVILGDANSSTIRVTNSFALPFEEDE
KNSDVWFLDHNYIENMNEMCKKINAKEKLIGWYHSGPKLRASDLKINELFKKYTQNNPLL
LIVDVKQQGVGLPTDAYVAIEQVKDDGTSTEKTFLHLPCTIEAEEAEEIGVEHLLRDVRD
QAAGGLSIRLTNQLKSLKGLQSKLKDVVEYLDKVINKELPINHTILGKLQDVFNLLPNLG
TPDDDEIDVENHDRINISNNLQKALTVKTNDELMVIYISNLVRSIIAFDDLIENKIQNKK
IQEQRVKDKQSKVSDDSESESGDKEATAPLIQRKNKKN

Sequence of entity 6 (F), FASTA

>3JCK_6 26S proteasome regulatory subunit RPN9 (chains F)
MFNNHEIDTILSTLRMEADPSLHPLFEQFEKFYEEKLWFQLSESLTKFFDDAKSTPLRLR
LYDNFVSKFYDKINQLSVVKYLLASLKDSKDFDESLKYLDDLKAQFQELDSKKQRNNGSK
DHGDGILLIDSEIARTYLLKNDLVKARDLLDDLEKTLDKKDSIPLRITNSFYSTNSQYFK
FKNDFNSFYYTSLLYLSTLEPSTSITLAERQQLAYDLSISALLGDKIYNFGELLHHPIME
TIVNDSNYDWLFQLLNALTVGDFDKFDSLIKVQISKIPILAQHESFLRQKICLMTLIETV
FVKNIRMLSFEDISKATHLPKDNVEHLVMRAISLGLLKGSIDQVNELVTISWVQPRIISG
DQITKMKDRLVEWNDQVEKLGKKMEARGQSIWV

Sequence of entity 7 (G), FASTA

>3JCK_7 Ubiquitin carboxyl-terminal hydrolase RPN11 (chains G)
MERLQRLMMNSKVGSADTGRDDTKETVYISSIALLKMLKHGRAGVPMEVMGLMLGEFVDD
YTVNVVDVFAMPQSGTGVSVEAVDDVFQAKMMDMLKQTGRDQMVVGWYHSHPGFGCWLSS
VDVNTQKSFEQLNSRAVAVVVDPIQSVKGKVVIDAFRLIDTGALINNLEPRQTTSNTGLL
NKANIQALIHGLNRHYYSLNIDYHKTAKETKMLMNLHKEQWQSGLKMYDYEEKEESNLAA
TKSMVKIAEQYSKRIEEEKELTEEELKTRYVGRQDPKKHLSETADETLENNIVSVLTAGV
NSVAIK

Sequence of entity 8 (H), FASTA

>3JCK_8 26S proteasome regulatory subunit RPN12 (chains H)
MPSLAELTKSLSIAFENGDYAACEKLLPPIKIELIKNNLLIPDLSIQNDIYLNDLMITKR
ILEVGALASIQTFNFDSFENYFNQLKPYYFSNNHKLSESDKKSKLISLYLLNLLSQNNTT
KFHSELQYLDKHIKNLEDDSLLSYPIKLDRWLMEGSYQKAWDLLQSGSQNISEFDSFTDI
LKSAIRDEIAKNTELSYDFLPLSNIKALLFFNNEKETEKFALERNWPIVNSKVYFNNQSK
EKADYEDEMMHEEDQKTNIIEKAMDYAISIENIV

Sequence of entity 9 (I), FASTA

>3JCK_9 26S proteasome complex subunit SEM1 (chains I)
MSTDVAAAQAQSKIDLTKKKNEEINKKSLEEDDEFEDFPIDTWANGETIKSNAVTQTNIW
EENWDDVEVDDDFTNELKAELDRYKRENQ

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1

Primary citation

Atomic structure of the 26S proteasome lid reveals the mechanism of deubiquitinase inhibition. Dambacher, C.M., Worden, E.J., Herzik, M.A. et al. Elife (2016) 5:e13027-e13027. DOI 10.7554/eLife.13027 · PubMed

Other PDB entries of the same protein (UniProt P40016 (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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