9E8J: Nub1/Fat10-processing human 26S proteasome

Nub1/Fat10-processing human 26S proteasome bound to Txnl1 with Rpt1 at top of spiral staircase. Determined by electron microscopy at 3.47 Å resolution. Released 4 Dec 2024.

Method: Electron microscopy
Resolution: 3.47 Å
Organism: Homo sapiens
Chains: 28
Atoms: 70,858
Mol. weight: 1214.76 kDa
Ligands: ATP, MG, ADP, ZN
Released: 4 Dec 2024

Explore 9E8J in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9E8J contains 460 α-helices and 309 β-strands across 28 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, 5 β-strands

Element	Residues	Length	Sheet
α-helix	5-10	6
α-helix	18	1
α-helix	19-23	5
α-helix	24-30	7
α-helix	36-46	11
α-helix	54-66	13
α-helix	73-87	15
α-helix	90-103	14
α-helix	110-122	13
α-helix	131-141	11
α-helix	150-161	12
α-helix	162-164	3
α-helix	170-182	13
α-helix	190-204	15
α-helix	215-218	4
α-helix	220-224	5
α-helix	232-240	9
α-helix	247-255	9
α-helix	262-264	3
α-helix	265-283	19
β-strand	292	1	55
α-helix	293-299	7
α-helix	304-317	14
β-strand	323	1	56
β-strand	324-325	2	48
β-strand	330	1	55
β-strand	332	1	56
α-helix	343-368	26
α-helix	372-375	4

Chain A: 28 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	27-35	9
α-helix	42-64	23
β-strand	72	1	75
α-helix	73-74	2
α-helix	75-77	3
α-helix	80-89	10
β-strand	93-101	9	76
β-strand	111-114	4	76
β-strand	120-123	4	76
β-strand	139-143	5	76
β-strand	151-152	2	76
α-helix	154-156	3
α-helix	159-164	6
β-strand	165	1	77
α-helix	174-176	3
α-helix	181-187	7
α-helix	188-192	5
α-helix	193-196	4
α-helix	200-203	4
α-helix	206-209	4
β-strand	211-215	5	77
α-helix	224-231	8
β-strand	236-240	5	77
α-helix	252-266	15
β-strand	270-275	6	77
α-helix	277-280	4
β-strand	282	1	78
α-helix	283-284	2
α-helix	292-306	15
β-strand	315-321	7	77
α-helix	324-326	3
β-strand	327	1	78
α-helix	329-332	4
β-strand	339	1	77
β-strand	342	1	77
α-helix	344-346	3
α-helix	348-359	12
β-strand	364	1	79
α-helix	370-375	6
α-helix	384-398	15
β-strand	404	1	79
α-helix	406-413	8
α-helix	414-418	5
α-helix	419-421	3
α-helix	426-429	4
β-strand	432	1	80

Chain b: 8 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	57
β-strand	13	1	58
α-helix	14-17	4
α-helix	25-43	19
β-strand	48-53	6	57
β-strand	55	1	59
β-strand	62-65	4	57
α-helix	68-75	8
β-strand	82	1	58
β-strand	84	1	59
α-helix	86-97	12
β-strand	106-113	8	57
α-helix	121-134	14
β-strand	137-142	6	57
α-helix	151-160	10
β-strand	172	1	57
α-helix	181-183	3
α-helix	184-188	5

Chain B: 16 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	59-85	27
α-helix	96-103	8
β-strand	107-117	11	2
β-strand	120-124	5	2
β-strand	134-135	2	2
β-strand	139	1	75
β-strand	149-153	5	2
β-strand	158-162	5	2
β-strand	175	1	81
α-helix	191-198	8
α-helix	203-206	4
α-helix	208-212	5
β-strand	222-225	4	81
α-helix	232-240	9
β-strand	246-250	5	81
α-helix	262-276	15
β-strand	280-284	5	81
α-helix	287-289	3
β-strand	292	1	82
α-helix	293-294	2
α-helix	300-312	13
β-strand	325-331	7	81
β-strand	337	1	82
β-strand	349	1	81
β-strand	352	1	81
α-helix	354	1
α-helix	356-357	2
α-helix	358-368	11
β-strand	374	1	83
α-helix	381-384	4
α-helix	392-408	17
β-strand	414	1	83
α-helix	417-426	10
β-strand	439	1	35

Chain c: 12 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	30-33	4	60
α-helix	35-47	13
β-strand	54-63	10	60
β-strand	66-75	10	60
α-helix	76-77	2
α-helix	84-86	3
α-helix	89-102	14
β-strand	107-113	7	60
α-helix	124-136	13
β-strand	141-143	3	60
β-strand	159-162	4	60
α-helix	165-168	4
α-helix	189-192	4
β-strand	196	1	60
β-strand	200-207	8	60
α-helix	214-217	4
α-helix	218-221	4
α-helix	234-261	28
α-helix	267-273	7
α-helix	286-308	23

Chain C: 19 helices, 26 β-strands

Element	Residues	Length	Sheet
α-helix	22-65	44
α-helix	69-70	2
β-strand	71-73	3	1
β-strand	74-79	6	2
β-strand	85-89	5	2
β-strand	94-97	4	2
β-strand	99	1	1
α-helix	105-107	3
β-strand	112	1	2
β-strand	115-116	2	1
β-strand	123	1	1
α-helix	128-130	3
β-strand	139	1	3
α-helix	148-150	3
α-helix	155-162	8
α-helix	167-170	4
α-helix	173-178	6
α-helix	181-183	3
β-strand	185	1	3
β-strand	186	1	4
β-strand	188	1	5
β-strand	189	1	6
α-helix	198-205	8
β-strand	210-213	4	3
β-strand	223	1	7
α-helix	227-237	11
β-strand	244-247	4	3
β-strand	249	1	5
β-strand	256	1	8
α-helix	258-261	4
α-helix	268-280	13
β-strand	289-291	3	3
β-strand	294	1	5
β-strand	301	1	8
β-strand	313	1	4
β-strand	316	1	6
α-helix	318-320	3
α-helix	322-331	10
β-strand	338	1	9
α-helix	344-349	6
α-helix	358-371	14
β-strand	378	1	9
α-helix	380-384	5
α-helix	399-402	4
β-strand	405	1	10

Chain d: 15 helices, 0 β-strands

Element	Residues	Length
α-helix	83-103	21
α-helix	109-126	18
α-helix	138-158	21
α-helix	161-176	16
α-helix	187-201	15
α-helix	205-214	10
α-helix	217-222	6
α-helix	224-238	15
α-helix	241-247	7
α-helix	248-250	3
α-helix	254-277	24
α-helix	284-290	7
α-helix	296-304	9
α-helix	319-322	4
α-helix	333-345	13

Chain D: 18 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	40-82	43
β-strand	87-91	5	16
β-strand	101	1	17
β-strand	104-105	2	16
β-strand	110	1	16
β-strand	111-112	2	1
β-strand	113	1	17
β-strand	115	1	16
β-strand	129-133	5	16
β-strand	139-141	3	16
α-helix	143-145	3
β-strand	153	1	18
α-helix	171-177	7
α-helix	178-182	5
α-helix	183-186	4
α-helix	188-192	5
α-helix	197-199	3
β-strand	201-205	5	18
α-helix	212-221	10
β-strand	226-231	6	18
α-helix	232-235	4
α-helix	243-256	14
β-strand	260-265	6	18
α-helix	267-269	3
β-strand	272	1	19
α-helix	282-296	15
β-strand	305-311	7	18
β-strand	317	1	19
α-helix	319-321	3
β-strand	329	1	18
β-strand	332	1	18
α-helix	334-336	3
α-helix	340-349	10
β-strand	354	1	20
α-helix	360-362	3
α-helix	372-388	17
β-strand	394	1	20
α-helix	396-403	8

20 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 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)
Proteasome subunit alpha type-6	G	protein	246	Homo sapiens	P60900 (AlphaFold model)
Proteasome subunit alpha type-2	H	protein	234	Homo sapiens	P25787 (AlphaFold model)
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-1	L	protein	263	Homo sapiens	P25786
Proteasome subunit alpha type-3	M	protein	255	Homo sapiens	P25788
26S proteasome non-ATPase regulatory subunit 3	V	protein	534	Homo sapiens	O43242
26S proteasome non-ATPase regulatory subunit 12	W	protein	456	Homo sapiens	O00232
26S proteasome non-ATPase regulatory subunit 11	X	protein	422	Homo sapiens	O00231
26S proteasome non-ATPase regulatory subunit 6	Y	protein	389	Homo sapiens	Q15008

16 more molecules are not listed.

Sequence of entity 1 (C), FASTA

>9E8J_1 26S protease regulatory subunit 8 (chains C)
MALDGPEQMELEEGKAGSGLRQYYLSKIEELQLIVNDKSQNLRRLQAQRNELNAKVRLLR
EELQLLQEQGSYVGEVVRAMDKKKVLVKVHPEGKFVVDVDKNIDINDVTPNCRVALRNDS
YTLHKILPNKVDPLVSLMMVEKVPDSTYEMIGGLDKQIKEIKEVIELPVKHPELFEALGI
AQPKGVLLYGPPGTGKTLLARAVAHHTDCTFIRVSGSELVQKFIGEGARMVRELFVMARE
HAPSIIFMDEIDSIGSSRLEGGSGGDSEVQRTMLELLNQLDGFEATKNIKVIMATNRIDI
LDSALLRPGRIDRKIEFPPPNEEARLDILKIHSRKMNLTRGINLRKIAELMPGASGAEVK
GVCTEAGMYALRERRVHVTQEDFEMAVAKVMQKDSEKNMSIKKLWK

Sequence of entity 2 (D), FASTA

>9E8J_2 26S proteasome regulatory subunit 6B (chains D)
MEEIGILVEKAQDEIPALSVSRPQTGLSFLGPEPEDLEDLYSRYKKLQQELEFLEVQEEY
IKDEQKNLKKEFLHAQEEVKRIQSIPLVIGQFLEAVDQNTAIVGSTTGSNYYVRILSTID
RELLKPNASVALHKHSNALVDVLPPEADSSIMMLTSDQKPDVMYADIGGMDIQKQEVREA
VELPLTHFELYKQIGIDPPRGVLMYGPPGCGKTMLAKAVAHHTTAAFIRVVGSEFVQKYL
GEGPRMVRDVFRLAKENAPAIIFIDEIDAIATKRFDAQTGADREVQRILLELLNQMDGFD
QNVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLIFSTITSKMNLSEEVDL
EDYVARPDKISGADINSICQESGMLAVRENRYIVLAKDFEKAYKTVIKKDEQEHEFYK

Sequence of entity 3 (G), FASTA

>9E8J_3 Proteasome subunit alpha type-6 (chains G)
MSRGSSAGFDRHITIFSPEGRLYQVEYAFKAINQGGLTSVAVRGKDCAVIVTQKKVPDKL
LDSSTVTHLFKITENIGCVMTGMTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKRIAD
ISQVYTQNAEMRPLGCCMILIGIDEEQGPQVYKCDPAGYYCGFKATAAGVKQTESTSFLE
KKVKKKFDWTFEQTVETAITCLSTVLSIDFKPSEIEVGVVTVENPKFRILTEAEIDAHLV
ALAERD

Sequence of entity 4 (H), FASTA

>9E8J_4 Proteasome subunit alpha type-2 (chains H)
MAERGYSFSLTTFSPSGKLVQIEYALAAVAGGAPSVGIKAANGVVLATEKKQKSILYDER
SVHKVEPITKHIGLVYSGMGPDYRVLVHRARKLAQQYYLVYQEPIPTAQLVQRVASVMQE
YTQSGGVRPFGVSLLICGWNEGRPYLFQSDPSGAYFAWKATAMGKNYVNGKTFLEKRYNE
DLELEDAIHTAILTLKESFEGQMTEDNIEVGICNEAGFRRLTPTEVKDYLAAIA

Sequence of entity 5 (I), FASTA

>9E8J_5 Proteasome subunit alpha type-4 (chains I)
MSRRYDSRTTIFSPEGRLYQVEYAMEAIGHAGTCLGILANDGVLLAAERRNIHKLLDEVF
FSEKIYKLNEDMACSVAGITSDANVLTNELRLIAQRYLLQYQEPIPCEQLVTALCDIKQA
YTQFGGKRPFGVSLLYIGWDKHYGFQLYQSDPSGNYGGWKATCIGNNSAAAVSMLKQDYK
EGEMTLKSALALAIKVLNKTMDVSKLSAEKVEIATLTRENGKTVIRVLKQKEVEQLIKKH
EEEEAKAEREKKEKEQKEKDK

Sequence of entity 6 (J), FASTA

>9E8J_6 Proteasome subunit alpha type-7 (chains J)
MSYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVEKKSVAKLQDERTVR
KICALDDNVCMAFAGLTADARIVINRARVECQSHRLTVEDPVTVEYITRYIASLKQRYTQ
SNGRRPFGISALIVGFDFDGTPRLYQTDPSGTYHAWKANAIGRGAKSVREFLEKNYTDEA
IETDDLTIKLVIKALLEVVQSGGKNIELAVMRRDQSLKILNPEEIEKYVAEIEKEKEENE
KKKQKKAS

Sequence of entity 7 (L), FASTA

>9E8J_7 Proteasome subunit alpha type-1 (chains L)
MFRNQYDNDVTVWSPQGRIHQIEYAMEAVKQGSATVGLKSKTHAVLVALKRAQSELAAHQ
KKILHVDNHIGISIAGLTADARLLCNFMRQECLDSRFVFDRPLPVSRLVSLIGSKTQIPT
QRYGRRPYGVGLLIAGYDDMGPHIFQTCPSANYFDCRAMSIGARSQSARTYLERHMSEFM
ECNLNELVKHGLRALRETLPAEQDLTTKNVSIGIVGKDLEFTIYDDDDVSPFLEGLEERP
QRKAQPAQPADEPAEKADEPMEH

Sequence of entity 8 (M), FASTA

>9E8J_8 Proteasome subunit alpha type-3 (chains M)
MSSIGTGYDLSASTFSPDGRVFQVEYAMKAVENSSTAIGIRCKDGVVFGVEKLVLSKLYE
EGSNKRLFNVDRHVGMAVAGLLADARSLADIAREEASNFRSNFGYNIPLKHLADRVAMYV
HAYTLYSAVRPFGCSFMLGSYSVNDGAQLYMIDPSGVSYGYWGCAIGKARQAAKTEIEKL
QMKEMTCRDIVKEVAKIIYIVHDEVKDKAFELELSWVGELTNGRHEIVPKDIREEAEKYA
KESLKEEDESDDDNM

Sequence of entity 9 (V), FASTA

>9E8J_9 26S proteasome non-ATPase regulatory subunit 3 (chains V)
MKQEGSARRRGADKAKPPPGGGEQEPPPPPAPQDVEMKEEAATGGGSTGEADGKTAAAAA
EHSQRELDTVTLEDIKEHVKQLEKAVSGKEPRFVLRALRMLPSTSRRLNHYVLYKAVQGF
FTSNNATRDFLLPFLEEPMDTEADLQFRPRTGKAASTPLLPEVEAYLQLLVVIFMMNSKR
YKEAQKISDDLMQKISTQNRRALDLVAAKCYYYHARVYEFLDKLDVVRSFLHARLRTATL
RHDADGQATLLNLLLRNYLHYSLYDQAEKLVSKSVFPEQANNNEWARYLYYTGRIKAIQL
EYSEARRTMTNALRKAPQHTAVGFKQTVHKLLIVVELLLGEIPDRLQFRQPSLKRSLMPY
FLLTQAVRTGNLAKFNQVLDQFGEKFQADGTYTLIIRLRHNVIKTGVRMISLSYSRISLA
DIAQKLQLDSPEDAEFIVAKAIRDGVIEASINHEKGYVQSKEMIDIYSTREPQLAFHQRI
SFCLDIHNMSVKAMRFPPKSYNKDLESAEERREREQQDLEFAKEMAEDDDDSFP

Sequence of entity 10 (W), FASTA

>9E8J_10 26S proteasome non-ATPase regulatory subunit 12 (chains W)
MADGGSERADGRIVKMEVDYSATVDQRLPECAKLAKEGRLQEVIETLLSLEKQTRTASDM
VSTSRILVAVVKMCYEAKEWDLLNENIMLLSKRRSQLKQAVAKMVQQCCTYVEEITDLPI
KLRLIDTLRMVTEGKIYVEIERARLTKTLATIKEQNGDVKEAASILQELQVETYGSMEKK
ERVEFILEQMRLCLAVKDYIRTQIISKKINTKFFQEENTEKLKLKYYNLMIQLDQHEGSY
LSICKHYRAIYDTPCIQAESEKWQQALKSVVLYVILAPFDNEQSDLVHRISGDKKLEEIP
KYKDLLKLFTTMELMRWSTLVEDYGMELRKGSLESPATDVFGSTEEGEKRWKDLKNRVVE
HNIRIMAKYYTRITMKRMAQLLDLSVDESEAFLSNLVVNKTIFAKVDRLAGIINFQRPKD
PNNLLNDWSQKLNSLMSLVNKTTHLIAKEEMIHNLQ

Sequence of entity 11 (X), FASTA

>9E8J_11 26S proteasome non-ATPase regulatory subunit 11 (chains X)
MAAAAVVEFQRAQSLLSTDREASIDILHSIVKRDIQENDEEAVQVKEQSILELGSLLAKT
GQAAELGGLLKYVRPFLNSISKAKAARLVRSLLDLFLDMEAATGQEVELCLECIEWAKSE
KRTFLRQALEARLVSLYFDTKRYQEALHLGSQLLRELKKMDDKALLVEVQLLESKTYHAL
SNLPKARAALTSARTTANAIYCPPKLQATLDMQSGIIHAAEEKDWKTAYSYFYEAFEGYD
SIDSPKAITSLKYMLLCKIMLNTPEDVQALVSGKLALRYAGRQTEALKCVAQASKNRSLA
DFEKALTDYRAELRDDPIISTHLAKLYDNLLEQNLIRVIEPFSRVQIEHISSLIKLSKAD
VERKLSQMILDKKFHGILDQGEGVLIIFDEPPVDKTYEAALETIQNMSKVVDSLYNKAKK
LT

Sequence of entity 12 (Y), FASTA

>9E8J_12 26S proteasome non-ATPase regulatory subunit 6 (chains Y)
MPLENLEEEGLPKNPDLRIAQLRFLLSLPEHRGDAAVRDELMAAVRDNNMAPYYEALCKS
LDWQIDVDLLNKMKKANEDELKRLDEELEDAEKNLGESEIRDAMMAKAEYLCRIGDKEGA
LTAFRKTYDKTVALGHRLDIVFYLLRIGLFYMDNDLITRNTEKAKSLIEEGGDWDRRNRL
KVYQGLYCVAIRDFKQAAELFLDTVSTFTSYELMDYKTFVTYTVYVSMIALERPDLREKV
IKGAEILEVLHSLPAVRQYLFSLYECRYSVFFQSLAVVEQEMKKDWLFAPHYRYYVREMR
IHAYSQLLESYRSLTLGYMAEAFGVGVEFIDQELSRFIAAGRLHCKIDKVNEIVETNRPD
SKNWQYQETIKKGDLLLNRVQKLSRVINM

Ligands and cofactors

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

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 P62195 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3KW6 2.1 Å, Crystal Structure of a domain of 26S proteasome regulatory subunit 8 from homo sapiens.…
9K53 2.5 Å, Structure of substrate-engaged human 26S proteasome RP-CP subcomplex in state ED2.1
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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