9E8N: Nub1/Fat10-processing human 26S proteasome

Nub1/Fat10-processing human 26S proteasome bound to Txnl1 with Rpt3 at top of spiral staircase (locally refined on the AAA+ motor). Determined by electron microscopy at 3.62 Å resolution. Released 4 Dec 2024.

Method: Electron microscopy
Resolution: 3.62 Å
Organism: Homo sapiens
Chains: 15
Atoms: 32,785
Mol. weight: 530.83 kDa
Ligands: ZN, MG, ATP, ADP
Released: 4 Dec 2024

Explore 9E8N in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9E8N contains 193 α-helices and 187 β-strands across 15 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: 22 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	27-35	9
α-helix	42-63	22
α-helix	75-77	3
α-helix	80-89	10
β-strand	93-95	3	1
β-strand	97-99	3	2
β-strand	111-115	5	2
β-strand	119-123	5	2
β-strand	125	1	1
α-helix	131-133	3
β-strand	140-142	3	1
β-strand	149-152	4	1
α-helix	159-162	4
β-strand	165	1	3
α-helix	181-187	7
α-helix	188-192	5
α-helix	193-196	4
α-helix	198-204	7
β-strand	211-215	5	3
α-helix	222-232	11
β-strand	236-241	6	3
β-strand	249	1	4
α-helix	252-266	15
β-strand	270-275	6	3
α-helix	277-279	3
β-strand	282	1	5
α-helix	283-284	2
α-helix	293-306	14
β-strand	315-321	7	3
β-strand	327	1	5
α-helix	329-332	4
β-strand	339-342	4	3
α-helix	348-361	14
α-helix	370-376	7
α-helix	382-398	17
α-helix	406-413	8
α-helix	414-418	5
α-helix	419-421	3

Chain B: 20 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	59-75	17
α-helix	94-102	9
α-helix	104	1
β-strand	107-112	6	1
β-strand	117	1	1
β-strand	120-124	5	1
β-strand	130-135	6	1
α-helix	136	1
β-strand	148-153	6	1
β-strand	159-162	4	1
α-helix	169-174	6
β-strand	175	1	35
α-helix	184-186	3
α-helix	191-197	7
α-helix	198-202	5
α-helix	209-214	6
α-helix	216-219	4
β-strand	221-225	5	35
α-helix	232-242	11
β-strand	246-251	6	35
α-helix	252-255	4
α-helix	262-277	16
β-strand	280-285	6	35
α-helix	287-289	3
α-helix	301-315	15
β-strand	326-331	6	35
α-helix	339-342	4
β-strand	349-352	4	35
α-helix	354-356	3
α-helix	358-368	11
β-strand	374	1	36
α-helix	392-408	17
β-strand	414	1	36
α-helix	416-428	13

Chain c: 13 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	31-33	3	42
α-helix	35-47	13
β-strand	54-63	10	42
β-strand	66-74	9	42
α-helix	89-100	12
β-strand	107-114	8	42
α-helix	124-135	12
β-strand	141-145	5	42
β-strand	151	1	43
β-strand	154	1	43
β-strand	157-162	6	42
α-helix	163-164	2
α-helix	165-169	5
α-helix	189-194	6
β-strand	196	1	42
β-strand	200-203	4	42
α-helix	204	1
β-strand	205-207	3	42
α-helix	211-217	7
α-helix	218-220	3
α-helix	222-224	3
α-helix	225-228	4
α-helix	234-260	27
α-helix	280-308	29

Chain C: 20 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	22-66	45
β-strand	74-78	5	1
β-strand	84-89	6	1
β-strand	94-98	5	1
β-strand	99	1	6
α-helix	105-107	3
β-strand	114	1	1
β-strand	115-116	2	6
β-strand	123-125	3	6
β-strand	140-141	2	7
α-helix	148-150	3
α-helix	156-161	6
α-helix	162-166	5
α-helix	167-170	4
α-helix	172-177	6
α-helix	181-183	3
β-strand	185-189	5	7
α-helix	196-207	12
α-helix	209	1
β-strand	210-214	5	7
α-helix	216-219	4
α-helix	227-240	14
β-strand	244-248	5	7
α-helix	270-282	13
β-strand	290-294	5	7
α-helix	300-305	6
β-strand	315-316	2	7
α-helix	318-320	3
α-helix	322-333	12
α-helix	344-348	5
α-helix	356-371	16
α-helix	380-393	14
α-helix	397-405	9

Chain D: 18 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	40-82	43
β-strand	88-95	8	8
β-strand	100-105	6	8
β-strand	110-115	6	8
α-helix	121-123	3
β-strand	128-132	5	8
β-strand	139	1	8
α-helix	171-177	7
α-helix	178-182	5
α-helix	183-186	4
α-helix	190-193	4
α-helix	196-199	4
β-strand	201-204	4	34
α-helix	212-222	11
β-strand	228-229	2	34
α-helix	232-235	4
α-helix	243-256	14
β-strand	261-263	3	34
α-helix	281-297	17
β-strand	306-310	5	34
α-helix	319-322	4
β-strand	330-331	2	34
α-helix	334-336	3
α-helix	340-351	12
α-helix	360-365	6
α-helix	372-388	17
α-helix	394-395	2
α-helix	396-405	10

Chain E: 20 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	16-50	35
β-strand	55-65	11	8
β-strand	68-72	5	8
β-strand	78-81	4	8
β-strand	83	1	8
α-helix	89-91	3
β-strand	97-101	5	8
β-strand	107-110	4	8
α-helix	117-123	7
α-helix	132-134	3
α-helix	139-149	11
α-helix	151-154	4
α-helix	156-162	7
α-helix	164-167	4
β-strand	169-173	5	9
α-helix	180-190	11
β-strand	194-199	6	9
β-strand	207	1	10
α-helix	210-224	15
β-strand	228-233	6	9
α-helix	236-239	4
β-strand	240	1	11
α-helix	241-243	3
α-helix	248-265	18
β-strand	275-279	5	9
α-helix	282-284	3
β-strand	285	1	11
α-helix	287-290	4
β-strand	295	1	9
β-strand	299-300	2	9
α-helix	302-305	4
α-helix	306-317	12
β-strand	322	1	12
α-helix	328-334	7
α-helix	340-356	17
β-strand	362	1	12
α-helix	364-378	15

Chain F: 18 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	52-83	32
β-strand	90-93	4	8
α-helix	97-99	3
β-strand	122-126	5	8
β-strand	131-134	4	8
β-strand	138	1	37
β-strand	150-152	3	8
β-strand	153	1	37
β-strand	160	1	37
α-helix	170-175	6
β-strand	176	1	38
α-helix	185-187	3
α-helix	192-207	16
α-helix	210-215	6
α-helix	217-220	4
β-strand	222-226	5	38
α-helix	233-244	12
β-strand	247-252	6	38
α-helix	253-256	4
α-helix	263-277	15
β-strand	281-286	6	38
α-helix	289-292	4
α-helix	304-318	15
β-strand	326-332	7	38
α-helix	335-337	3
β-strand	350-353	4	38
α-helix	355-358	4
α-helix	359-370	12
β-strand	375	1	39
α-helix	381-387	7
α-helix	393-410	18
β-strand	415	1	39
α-helix	417-427	11

Chain H: 9 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	15-17	3
α-helix	23-34	12
β-strand	38-43	6	13
β-strand	47-53	7	13
β-strand	61	1	14
α-helix	63-66	4
β-strand	69-73	5	15
β-strand	76-82	7	15
α-helix	84-105	22
α-helix	111-127	17
β-strand	131	1	16
β-strand	136-144	9	15
β-strand	148-154	7	15
β-strand	160-163	4	15
β-strand	165-169	5	13
α-helix	173-183	11
α-helix	191-205	15
α-helix	212-214	3
β-strand	215-221	7	13
β-strand	228-229	2	13
α-helix	232-242	11

7 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 7	A	protein	433	Homo sapiens	P35998 (AlphaFold model)
26S protease regulatory subunit 8	C	protein	406	Homo sapiens	P62195 (AlphaFold model)
26S protease regulatory subunit 10B	E	protein	389	Homo sapiens	P62333 (AlphaFold model)
Proteasome subunit alpha type-6	H	protein	246	Homo sapiens	P25787 (AlphaFold model)
Proteasome subunit alpha type-2	J	protein	234	Homo sapiens	O14818
Proteasome subunit alpha type-4	K	protein	261	Homo sapiens	P28066
Proteasome subunit alpha type-7	L	protein	248	Homo sapiens	P25786
Proteasome subunit alpha type-1	M	protein	263	Homo sapiens	P25788
Proteasome subunit alpha type-3	N	protein	255	Homo sapiens	P25788
substrate	v	protein	14	Homo sapiens
26S proteasome regulatory subunit 6B	D	protein	418	Homo sapiens	P43686
26S proteasome regulatory subunit 4	B	protein	440	Homo sapiens	P62191

3 more molecules are not listed.

Sequence of entity 1 (A), FASTA

>9E8N_1 26S proteasome regulatory subunit 7 (chains A)
MPDYLGADQRKTKEDEKDDKPIRALDEGDIALLKTYGQSTYSRQIKQVEDDIQQLLKKIN
ELTGIKESDTGLAPPALWDLAADKQTLQSEQPLQVARCTKIINADSEDPKYIINVKQFAK
FVVDLSDQVAPTDIEEGMRVGVDRNKYQIHIPLPPIADPTVTMMQVEEKPDVTYSDVGGC
KEQIEKLREVVETPLLHPERFVNLGIEPPKGVLLFGPPGTGKTLCARAVANRTDACFIRV
IGSELVQKYVGEGARMVRELFEMARTKKACLIFFDEIDAIGGARFDDGAGGDNEVQRTML
ELINQLDGFDPRGNIKVLMATNRPDTLDPALMRPGRLDRKIEFSLPDLEGRTHIFKIHAR
SMSVERDIRFELLARLCPNSTGAEIRSVCTEAGMFAIRARRKIATEKDFLEAVNKVIKSY
AKFSATPRYMTYN

Sequence of entity 2 (C), FASTA

>9E8N_2 26S protease regulatory subunit 8 (chains C)
MALDGPEQMELEEGKAGSGLRQYYLSKIEELQLIVNDKSQNLRRLQAQRNELNAKVRLLR
EELQLLQEQGSYVGEVVRAMDKKKVLVKVHPEGKFVVDVDKNIDINDVTPNCRVALRNDS
YTLHKILPNKVDPLVSLMMVEKVPDSTYEMIGGLDKQIKEIKEVIELPVKHPELFEALGI
AQPKGVLLYGPPGTGKTLLARAVAHHTDCTFIRVSGSELVQKFIGEGARMVRELFVMARE
HAPSIIFMDEIDSIGSSRLEGGSGGDSEVQRTMLELLNQLDGFEATKNIKVIMATNRIDI
LDSALLRPGRIDRKIEFPPPNEEARLDILKIHSRKMNLTRGINLRKIAELMPGASGAEVK
GVCTEAGMYALRERRVHVTQEDFEMAVAKVMQKDSEKNMSIKKLWK

Sequence of entity 3 (E), FASTA

>9E8N_3 26S protease regulatory subunit 10B (chains E)
MADPRDKALQDYRKKLLEHKEIDGRLKELREQLKELTKQYEKSENDLKALQSVGQIVGEV
LKQLTEEKFIVKATNGPRYVVGCRRQLDKSKLKPGTRVALDMTTLTIMRYLPREVDPLVY
NMSHEDPGNVSYSEIGGLSEQIRELREVIELPLTNPELFQRVGIIPPKGCLLYGPPGTGK
TLLARAVASQLDCNFLKVVSSSIVDKYIGESARLIREMFNYARDHQPCIIFMDEIDAIGG
RRFSEGTSADREIQRTLMELLNQMDGFDTLHRVKMIMATNRPDTLDPALLRPGRLDRKIH
IDLPNEQARLDILKIHAGPITKHGEIDYEAIVKLSDGFNGADLRNVCTEAGMFAIRADHD
FVVQEDFMKAVRKVADSKKLESKLDYKPV

Sequence of entity 4 (H), FASTA

>9E8N_4 Proteasome subunit alpha type-6 (chains H)
MSRGSSAGFDRHITIFSPEGRLYQVEYAFKAINQGGLTSVAVRGKDCAVIVTQKKVPDKL
LDSSTVTHLFKITENIGCVMTGMTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKRIAD
ISQVYTQNAEMRPLGCCMILIGIDEEQGPQVYKCDPAGYYCGFKATAAGVKQTESTSFLE
KKVKKKFDWTFEQTVETAITCLSTVLSIDFKPSEIEVGVVTVENPKFRILTEAEIDAHLV
ALAERD

Sequence of entity 5 (J), FASTA

>9E8N_5 Proteasome subunit alpha type-2 (chains J)
MAERGYSFSLTTFSPSGKLVQIEYALAAVAGGAPSVGIKAANGVVLATEKKQKSILYDER
SVHKVEPITKHIGLVYSGMGPDYRVLVHRARKLAQQYYLVYQEPIPTAQLVQRVASVMQE
YTQSGGVRPFGVSLLICGWNEGRPYLFQSDPSGAYFAWKATAHGKNYVNGKTFLEHHYNE
DLELEDAIHTAILTLKESFEGQMTEDNIEVGICNEAGFRRLTPTEVKDYLAAIA

Sequence of entity 6 (K), FASTA

>9E8N_6 Proteasome subunit alpha type-4 (chains K)
MSRRYDSRTTIFSPEGRLYQVEYAMEAIGHAGTCLGILANDGVLLAAERRNIHKLLDEVF
FSEKIYKLNEDMACSVAGITSDANVLTNELRLIAQRYLLQYQEPIPCEQLVTALCDIKQA
YTQFGGKRPFGVSLLYIGWDKHYGFQLYQSDPSGNYGGWKATCIGNNSAAAVSMLKQDYK
EGEMTLKSALALAIKVLNKTMDVSKLSAEKVEIATLTRENGKTVIRVLKQKEVEQLIKKH
EEEEAKAEREKKEKEQKEKDK

Sequence of entity 7 (L), FASTA

>9E8N_7 Proteasome subunit alpha type-7 (chains L)
MSYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVEKKSVAKLQDERTVR
KICALDDNVCMAFAGLTADARIVINRARVECQSHRLTVEDPVTVEYITRYIASLKQRYTQ
SNGRRPFGISALIVGFDFDGTPRLYQTDPSGTYHAWKANAIGRGAKSVREFLEKNYTDEA
IETDDLTIKLVIKALLEVVQSGGKNIELAVMRRDQSLKILNPEEIEKYVAEIEKEKEENE
KKKQKKAS

Sequence of entity 8 (M), FASTA

>9E8N_8 Proteasome subunit alpha type-1 (chains M)
MFRNQYDNDVTVWSPQGRIHQIEYAMEAVKQGSATVGLKSKTHAVLVALKRAQSELAAHQ
KKILHVDNHIGISIAGLTADARLLCNFMRQECLDSRFVFDRPLPVSRLVSLIGSKTQIPT
QRYGRRPYGVGLLIAGYDDMGPHIFQTCPSANYFDCRAMSIGARSQSARTYLERHMSEFM
ECNLNELVKHGLRALRETLPAEQDLTTKNVSIGIVGKDLEFTIYDDDDVSPFLEGLEERP
QRKAQPAQPADEPAEKADEPMEH

Sequence of entity 9 (N), FASTA

>9E8N_9 Proteasome subunit alpha type-3 (chains N)
MSSIGTGYDLSASTFSPDGRVFQVEYAMKAVENSSTAIGIRCKDGVVFGVEKLVLSKLYE
EGSNKRLFNVDRHVGMAVAGLLADARSLADIAREEASNFRSNFGYNIPLKHLADRVAMYV
HAYTLYSAVRPFGCSFMLGSYSVNDGAQLYMIDPSGVSYGYWGCAIGKARQAAKTEIEKL
QMKEMTCRDIVKEVAKIIYIVHDEVKDKAFELELSWVGELTNGRHEIVPKDIREEAEKYA
KESLKEEDESDDDNM

Sequence of entity 10 (v), FASTA

>9E8N_10 substrate (chains v)
XXXXXXXXXXXXXX

Sequence of entity 11 (D), FASTA

>9E8N_11 26S proteasome regulatory subunit 6B (chains D)
MEEIGILVEKAQDEIPALSVSRPQTGLSFLGPEPEDLEDLYSRYKKLQQELEFLEVQEEY
IKDEQKNLKKEFLHAQEEVKRIQSIPLVIGQFLEAVDQNTAIVGSTTGSNYYVRILSTID
RELLKPNASVALHKHSNALVDVLPPEADSSIMMLTSDQKPDVMYADIGGMDIQKQEVREA
VELPLTHFELYKQIGIDPPRGVLMYGPPGCGKTMLAKAVAHHTTAAFIRVVGSEFVQKYL
GEGPRMVRDVFRLAKENAPAIIFIDEIDAIATKRFDAQTGADREVQRILLELLNQMDGFD
QNVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLIFSTITSKMNLSEEVDL
EDYVARPDKISGADINSICQESGMLAVRENRYIVLAKDFEKAYKTVIKKDEQEHEFYK

Sequence of entity 12 (B), FASTA

>9E8N_12 26S proteasome regulatory subunit 4 (chains B)
MGQSQSGGHGPGGGKKDDKDKKKKYEPPVPTRVGKKKKKTKGPDAASKLPLVTPHTQCRL
KLLKLERIKDYLLMEEEFIRNQEQMKPLEEKQEEERSKVDDLRGTPMSVGTLEEIIDDNH
AIVSTSVGSEHYVSILSFVDKDLLEPGCSVLLNHKVHAVIGVLMDDTDPLVTVMKVEKAP
QETYADIGGLDNQIQEIKESVELPLTHPEYYEEMGIKPPKGVILYGPPGTGKTLLAKAVA
NQTSATFLRVVGSELIQKYLGDGPKLVRELFRVAEEHAPSIVFIDEIDAIGTKRYDSNSG
GEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDEKT
KKRIFQIHTSRMTLADDVTLDDLIMAKDDLSGADIKAICTEAGLMALRERRMKVTNEDFK
KSKENVLYKKQEGTPEGLYL

Ligands and cofactors

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

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 P35998 (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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