9E8O: Nub1/Fat10-processing human 26S proteasome

Nub1/Fat10-processing human 26S proteasome bound to Txnl1 with Rpt2 at top of spiral staircase and partially unfolded Eos. Determined by electron microscopy at 3.1 Å resolution. Released 4 Dec 2024.

Method: Electron microscopy
Resolution: 3.1 Å
Organisms: Homo sapiens, Lobophyllia hemprichii
Chains: 34
Atoms: 83,181
Mol. weight: 1375.46 kDa
Ligands: MG, ADP, ZN, ATP
Released: 4 Dec 2024

Explore 9E8O in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9E8O contains 509 α-helices and 382 β-strands across 34 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: 19 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	5-10	6
α-helix	18-30	13
β-strand	33	1	89
α-helix	35-45	11
α-helix	54-68	15
α-helix	73-87	15
α-helix	90-103	14
α-helix	111-123	13
α-helix	131-141	11
α-helix	151-161	11
α-helix	171-182	12
α-helix	190-206	17
α-helix	220-226	7
α-helix	231-241	11
α-helix	247-254	8
α-helix	262-264	3
α-helix	265-283	19
β-strand	291-292	2	90
α-helix	293-299	7
α-helix	307-316	10
β-strand	320	1	91
β-strand	323-325	3	90
β-strand	330-332	3	90
β-strand	335	1	91
α-helix	344-375	32

Chain A: 21 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	22-25	4
α-helix	27-33	7
α-helix	42-62	21
β-strand	72	1	2
α-helix	73-74	2
α-helix	80-89	10
β-strand	93-98	6	1
β-strand	111-114	4	1
β-strand	120-123	4	1
β-strand	125	1	1
α-helix	131-133	3
β-strand	139-142	4	1
β-strand	149-152	4	1
α-helix	174-176	3
α-helix	181-187	7
α-helix	188-192	5
α-helix	193-196	4
α-helix	198-203	6
β-strand	211-215	5	14
α-helix	222-232	11
β-strand	236-241	6	14
α-helix	242-246	5
α-helix	253-266	14
β-strand	270-275	6	14
α-helix	278-281	4
α-helix	293-308	16
β-strand	317-321	5	14
β-strand	339-342	4	14
α-helix	344-346	3
α-helix	348-359	12
β-strand	364	1	15
α-helix	370-376	7
α-helix	382-398	17
β-strand	404	1	15
α-helix	406-416	11
β-strand	432	1	52

Chain b: 7 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	92
β-strand	13	1	93
α-helix	14-16	3
β-strand	18	1	89
α-helix	25-43	19
β-strand	48-52	5	92
β-strand	55	1	94
β-strand	62-65	4	92
α-helix	69-75	7
β-strand	82	1	93
β-strand	84	1	94
α-helix	86-98	13
β-strand	106-113	8	92
α-helix	121-133	13
β-strand	136-142	7	92
α-helix	151-160	10
β-strand	171-172	2	92
α-helix	180-190	11

Chain B: 20 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	60-84	25
α-helix	94-103	10
β-strand	107-115	9	1
β-strand	120-125	6	1
β-strand	130-135	6	1
β-strand	139	1	2
β-strand	149-153	5	1
β-strand	158-163	6	1
α-helix	169-174	6
β-strand	175	1	3
α-helix	179-180	2
α-helix	191-197	7
α-helix	198-202	5
α-helix	209-214	6
α-helix	216-218	3
β-strand	222-225	4	3
α-helix	232-241	10
β-strand	246-250	5	3
α-helix	262-276	15
β-strand	280-285	6	3
α-helix	288-291	4
β-strand	292	1	4
α-helix	293-294	2
α-helix	300-318	19
β-strand	325-331	7	3
α-helix	334-336	3
β-strand	337	1	4
β-strand	349-352	4	3
α-helix	354-356	3
α-helix	358-368	11
α-helix	381-385	5
α-helix	392-408	17
α-helix	416-426	11
α-helix	436-438	3
β-strand	439	1	5

Chain c: 11 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	26	1	16
β-strand	30-34	5	17
α-helix	35-47	13
β-strand	54-63	10	17
β-strand	66-74	9	17
α-helix	89-102	14
β-strand	107-114	8	17
α-helix	124-136	13
β-strand	144-145	2	17
β-strand	157-158	2	17
β-strand	160	1	18
α-helix	165-169	5
β-strand	176	1	16
α-helix	181-183	3
α-helix	186-188	3
α-helix	189-193	5
β-strand	196	1	19
β-strand	200	1	19
β-strand	202	1	18
β-strand	204-208	5	17
α-helix	211-218	8
α-helix	230-232	3
α-helix	234-263	30
α-helix	280-308	29

Chain C: 19 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	22-65	44
α-helix	69-70	2
β-strand	71-78	8	1
β-strand	84-89	6	1
β-strand	93-99	7	1
β-strand	113-116	4	1
β-strand	122-126	5	1
α-helix	133-136	4
β-strand	139	1	8
α-helix	148-150	3
α-helix	155-165	11
α-helix	167-170	4
α-helix	173-178	6
α-helix	180-183	4
β-strand	185-189	5	8
α-helix	196-205	10
β-strand	210-213	4	8
β-strand	223	1	9
α-helix	226-240	15
β-strand	244-248	5	8
α-helix	258-259	2
α-helix	268-280	13
β-strand	291-295	5	8
α-helix	303-306	4
β-strand	314-316	3	8
α-helix	318-320	3
α-helix	322-332	11
α-helix	344-349	6
α-helix	356-372	17
α-helix	380-390	11
α-helix	399-402	4
β-strand	405	1	10

Chain d: 12 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	86-102	17
α-helix	109-125	17
α-helix	138-158	21
α-helix	161-173	13
α-helix	188-201	14
α-helix	205-214	10
α-helix	224-238	15
α-helix	241-247	7
α-helix	257-276	20
β-strand	279	1	95
β-strand	283	1	96
α-helix	284-290	7
α-helix	296-305	10
β-strand	315	1	96
α-helix	343-355	13

Chain D: 19 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	40-82	43
β-strand	87-95	9	1
β-strand	100-105	6	1
β-strand	109-115	7	1
α-helix	121-123	3
β-strand	128-133	6	1
β-strand	139-142	4	1
α-helix	164-166	3
α-helix	171-181	11
α-helix	183-186	4
α-helix	188-194	7
α-helix	197-199	3
β-strand	202-205	4	11
α-helix	212-221	10
β-strand	226-231	6	11
α-helix	232-235	4
β-strand	239	1	12
α-helix	242-256	15
β-strand	260-265	6	11
α-helix	267-269	3
β-strand	272	1	13
α-helix	273-274	2
α-helix	280-297	18
β-strand	305-311	7	11
α-helix	314-316	3
β-strand	317	1	13
β-strand	329-332	4	11
α-helix	334-336	3
α-helix	339-349	11
α-helix	360-365	6
α-helix	372-389	18
α-helix	396-406	11

26 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 4	B	protein	440	Homo sapiens	P62191 (AlphaFold model)
26S protease regulatory subunit 8	C	protein	406	Homo sapiens	P62195 (AlphaFold model)
26S proteasome regulatory subunit 6B	D	protein	418	Homo sapiens	P43686 (AlphaFold model)
26S proteasome non-ATPase regulatory subunit 14	c	protein	424	Homo sapiens	O00487 (AlphaFold model)
Proteasome subunit alpha type-6	G	protein	246	Homo sapiens	P60900
Proteasome subunit alpha type-2	H	protein	234	Homo sapiens	P25787
Proteasome subunit alpha type-4	I	protein	261	Homo sapiens	P25789
Proteasome subunit alpha type-7	J	protein	248	Homo sapiens	O14818
Proteasome subunit alpha type-5	K	protein	241	Homo sapiens	P28066
Proteasome subunit alpha type-1	L	protein	263	Homo sapiens	P25786
Proteasome subunit alpha type-3	M	protein	255	Homo sapiens	P25788
Proteasome subunit beta type-6	N	protein	239	Homo sapiens	P28072

22 more molecules are not listed.

Sequence of entity 1 (B), FASTA

>9E8O_1 26S proteasome regulatory subunit 4 (chains B)
MGQSQSGGHGPGGGKKDDKDKKKKYEPPVPTRVGKKKKKTKGPDAASKLPLVTPHTQCRL
KLLKLERIKDYLLMEEEFIRNQEQMKPLEEKQEEERSKVDDLRGTPMSVGTLEEIIDDNH
AIVSTSVGSEHYVSILSFVDKDLLEPGCSVLLNHKVHAVIGVLMDDTDPLVTVMKVEKAP
QETYADIGGLDNQIQEIKESVELPLTHPEYYEEMGIKPPKGVILYGPPGTGKTLLAKAVA
NQTSATFLRVVGSELIQKYLGDGPKLVRELFRVAEEHAPSIVFIDEIDAIGTKRYDSNSG
GEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDEKT
KKRIFQIHTSRMTLADDVTLDDLIMAKDDLSGADIKAICTEAGLMALRERRMKVTNEDFK
KSKENVLYKKQEGTPEGLYL

Sequence of entity 2 (C), FASTA

>9E8O_2 26S protease regulatory subunit 8 (chains C)
MALDGPEQMELEEGKAGSGLRQYYLSKIEELQLIVNDKSQNLRRLQAQRNELNAKVRLLR
EELQLLQEQGSYVGEVVRAMDKKKVLVKVHPEGKFVVDVDKNIDINDVTPNCRVALRNDS
YTLHKILPNKVDPLVSLMMVEKVPDSTYEMIGGLDKQIKEIKEVIELPVKHPELFEALGI
AQPKGVLLYGPPGTGKTLLARAVAHHTDCTFIRVSGSELVQKFIGEGARMVRELFVMARE
HAPSIIFMDEIDSIGSSRLEGGSGGDSEVQRTMLELLNQLDGFEATKNIKVIMATNRIDI
LDSALLRPGRIDRKIEFPPPNEEARLDILKIHSRKMNLTRGINLRKIAELMPGASGAEVK
GVCTEAGMYALRERRVHVTQEDFEMAVAKVMQKDSEKNMSIKKLWK

Sequence of entity 3 (D), FASTA

>9E8O_3 26S proteasome regulatory subunit 6B (chains D)
MEEIGILVEKAQDEIPALSVSRPQTGLSFLGPEPEDLEDLYSRYKKLQQELEFLEVQEEY
IKDEQKNLKKEFLHAQEEVKRIQSIPLVIGQFLEAVDQNTAIVGSTTGSNYYVRILSTID
RELLKPNASVALHKHSNALVDVLPPEADSSIMMLTSDQKPDVMYADIGGMDIQKQEVREA
VELPLTHFELYKQIGIDPPRGVLMYGPPGCGKTMLAKAVAHHTTAAFIRVVGSEFVQKYL
GEGPRMVRDVFRLAKENAPAIIFIDEIDAIATKRFDAQTGADREVQRILLELLNQMDGFD
QNVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLIFSTITSKMNLSEEVDL
EDYVARPDKISGADINSICQESGMLAVRENRYIVLAKDFEKAYKTVIKKDEQEHEFYK

Sequence of entity 4 (c), FASTA

>9E8O_4 26S proteasome non-ATPase regulatory subunit 14 (chains c)
MDRLLRLGGGMPGLGQGPPTDAPAVDTAEQVYISSLALLKMLKHGRAGVPMEVMGLMLGE
FVDDYTVRVIDVFAMPQSGTGVSVEAVDPVFQAKMLDMLKQTGRPEMVVGWYHSHPGFGC
WLSGVDINTQQSFEALSERAVAVVVDPIQSVKGKVVIDAFRLINANMMVLGHEPRQTTSN
LGHLNKPSIQALIHGLNRHYYSITINYRKNELEQKMLLNLHKKSWMEGLTLQDYSEHCKH
NESVVKEMLELAKNYNKAVEEEDKMTPEQLAIKNVGKQDPKRHLEEHVDVLMTSNIVQCL
AAMLDTVVFKLINHHHHHHDYDIPTTASENLYFQGELGMRGSAGKAGEGEIPAPLAGTVS
KILVKEGDTVKAGQTVLVLEAMKMETEINAPTDGKVEKVLVKERDAVQGGQGLIKIGVHH
HHHH

Sequence of entity 5 (G), FASTA

>9E8O_5 Proteasome subunit alpha type-6 (chains G)
MSRGSSAGFDRHITIFSPEGRLYQVEYAFKAINQGGLTSVAVRGKDCAVIVTQKKVPDKL
LDSSTVTHLFKITENIGCVMTGMTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKRIAD
ISQVYTQNAEMRPLGCCMILIGIDEEQGPQVYKCDPAGYYCGFKATAAGVKQTESTSFLE
KKVKKKFDWTFEQTVETAITCLSTVLSIDFKPSEIEVGVVTVENPKFRILTEAEIDAHLV
ALAERD

Sequence of entity 6 (H), FASTA

>9E8O_6 Proteasome subunit alpha type-2 (chains H)
MAERGYSFSLTTFSPSGKLVQIEYALAAVAGGAPSVGIKAANGVVLATEKKQKSILYDER
SVHKVEPITKHIGLVYSGMGPDYRVLVHRARKLAQQYYLVYQEPIPTAQLVQRVASVMQE
YTQSGGVRPFGVSLLICGWNEGRPYLFQSDPSGAYFAWKATAMGKNYVNGKTFLEKRYNE
DLELEDAIHTAILTLKESFEGQMTEDNIEVGICNEAGFRRLTPTEVKDYLAAIA

Sequence of entity 7 (I), FASTA

>9E8O_7 Proteasome subunit alpha type-4 (chains I)
MSRRYDSRTTIFSPEGRLYQVEYAMEAIGHAGTCLGILANDGVLLAAERRNIHKLLDEVF
FSEKIYKLNEDMACSVAGITSDANVLTNELRLIAQRYLLQYQEPIPCEQLVTALCDIKQA
YTQFGGKRPFGVSLLYIGWDKHYGFQLYQSDPSGNYGGWKATCIGNNSAAAVSMLKQDYK
EGEMTLKSALALAIKVLNKTMDVSKLSAEKVEIATLTRENGKTVIRVLKQKEVEQLIKKH
EEEEAKAEREKKEKEQKEKDK

Sequence of entity 8 (J), FASTA

>9E8O_8 Proteasome subunit alpha type-7 (chains J)
MSYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVEKKSVAKLQDERTVR
KICALDDNVCMAFAGLTADARIVINRARVECQSHRLTVEDPVTVEYITRYIASLKQRYTQ
SNGRRPFGISALIVGFDFDGTPRLYQTDPSGTYHAWKANAIGRGAKSVREFLEKNYTDEA
IETDDLTIKLVIKALLEVVQSGGKNIELAVMRRDQSLKILNPEEIEKYVAEIEKEKEENE
KKKQKKAS

Sequence of entity 9 (K), FASTA

>9E8O_9 Proteasome subunit alpha type-5 (chains K)
MFLTRSEYDRGVNTFSPEGRLFQVEYAIEAIKLGSTAIGIQTSEGVCLAVEKRITSPLME
PSSIEKIVEIDAHIGCAMSGLIADAKTLIDKARVETQNHWFTYNETMTVESVTQAVSNLA
LQFGEEDADPGAMSRPFGVALLFGGVDEKGPQLFHMDPSGTFVQCDARAIGSASEGAQSS
LQEVYHKSMTLKEAIKSSLIILKQVMEEKLNATNIELATVQPGQNFHMFTKEELEEVIKD
I

Sequence of entity 10 (L), FASTA

>9E8O_10 Proteasome subunit alpha type-1 (chains L)
MFRNQYDNDVTVWSPQGRIHQIEYAMEAVKQGSATVGLKSKTHAVLVALKRAQSELAAHQ
KKILHVDNHIGISIAGLTADARLLCNFMRQECLDSRFVFDRPLPVSRLVSLIGSKTQIPT
QRYGRRPYGVGLLIAGYDDMGPHIFQTCPSANYFDCRAMSIGARSQSARTYLERHMSEFM
ECNLNELVKHGLRALRETLPAEQDLTTKNVSIGIVGKDLEFTIYDDDDVSPFLEGLEERP
QRKAQPAQPADEPAEKADEPMEH

Sequence of entity 11 (M), FASTA

>9E8O_11 Proteasome subunit alpha type-3 (chains M)
MSSIGTGYDLSASTFSPDGRVFQVEYAMKAVENSSTAIGIRCKDGVVFGVEKLVLSKLYE
EGSNKRLFNVDRHVGMAVAGLLADARSLADIAREEASNFRSNFGYNIPLKHLADRVAMYV
HAYTLYSAVRPFGCSFMLGSYSVNDGAQLYMIDPSGVSYGYWGCAIGKARQAAKTEIEKL
QMKEMTCRDIVKEVAKIIYIVHDEVKDKAFELELSWVGELTNGRHEIVPKDIREEAEKYA
KESLKEEDESDDDNM

Sequence of entity 12 (N), FASTA

>9E8O_12 Proteasome subunit beta type-6 (chains N)
MAATLLAARGAGPAPAWGPEAFTPDWESREVSTGTTIMAVQFDGGVVLGADSRTTTGSYI
ANRVTDKLTPIHDRIFCCRSGSAADTQAVADAVTYQLGFHSIELNEPPLVHTAASLFKEM
CYRYREDLMAGIIIAGWDPQEGGQVYSVPMGGMMVRQSFAIGGSGSSYIYGYVDATYREG
MTKEECLQFTANALALAMERDGSSGGVIRLAAIAESGVERQVLLGDQIPKFAVATLPPA

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	3
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	4
ZN	Zinc ion	Zn	1
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	2

Primary citation

Structural landscape of the degrading 26S proteasome reveals conformation-specific binding of TXNL1. Arkinson, C., Gee, C.L., Zhang, Z. et al. Nat Struct Mol Biol (2025) 32:2403-2415. DOI 10.1038/s41594-025-01695-2 · PubMed

Other PDB entries of the same protein (UniProt P62191 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9K53 2.5 Å, Structure of substrate-engaged human 26S proteasome RP-CP subcomplex in state ED2.1
8USD 2.7 Å, Rpn1/Nub1UBL-focused alignment of the non-substrate-engaged human 26S proteasome
8USB 2.73 Å, Non-substrate-engaged human 26S proteasome with Nub1/FAT10 bound to Rpn1
9MBP 2.75 Å, Substrate-engaged human 26S proteasome bound to midnolin with RPT1 at top of spiral…
9PDL 2.76 Å, Nub1/Fat10-processing human 26S proteasome with Rpt5 at top of spiral staircase (AAA+…
9NKG 2.8 Å, Structure of substrate engaged MIDN-bound human 26S proteasome, EB-MIDN (Composite map)
9E8I 2.87 Å, Human proteasome in resting state conformation bound to TXNL1 in Forward conformation
9BV3 2.9 Å, M1B Midnolin-Proteasome
9E8H 2.9 Å, Human proteasome in resting state conformation bound to TXNL1 in backward conformation
9K4J 2.9 Å, Structure of substrate-engaged human 26S proteasome RP-CP subcomplex in state EA1.0
9NKF 2.9 Å, Structure of human substrate-free 26S proteasome in the presence of ATPgS and…
9U3L 2.91 Å, Substrate-engaged human 26S proteasome bound to midnolin with RPT2 at top of spiral…

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