9E8L: Nub1/Fat10-processing human 26S proteasome

Nub1/Fat10-processing human 26S proteasome bound to Txnl1 with Rpt4 at top of spiral staircase. Determined by electron microscopy at 3.59 Å resolution. Released 4 Dec 2024.

Method: Electron microscopy
Resolution: 3.59 Å
Organism: Homo sapiens
Chains: 28
Atoms: 70,522
Mol. weight: 1214.68 kDa
Ligands: ZN, ATP, MG, ADP
Released: 4 Dec 2024

Explore 9E8L in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9E8L contains 494 α-helices and 269 β-strands across 27 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: 26 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	7-10	4
α-helix	18	1
α-helix	19-23	5
α-helix	24-30	7
α-helix	35-43	9
α-helix	44-46	3
α-helix	53-65	13
α-helix	74-87	14
α-helix	90-101	12
α-helix	111-124	14
α-helix	133-139	7
α-helix	140-142	3
α-helix	150-161	12
α-helix	162-164	3
α-helix	170-182	13
α-helix	190-206	17
α-helix	220-226	7
α-helix	231-240	10
α-helix	248-256	9
α-helix	262-264	3
α-helix	265-282	18
β-strand	290-291	2	54
α-helix	293-299	7
α-helix	304-306	3
α-helix	307-317	11
β-strand	323-324	2	54
β-strand	331-332	2	54
α-helix	343-370	28
α-helix	372-375	4

Chain A: 24 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	27-36	10
α-helix	42-63	22
α-helix	66-67	2
α-helix	75-77	3
α-helix	81-89	9
β-strand	93-96	4	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	1	1
α-helix	159-162	4
β-strand	165	1	3
α-helix	174-176	3
α-helix	181-191	11
α-helix	193-196	4
α-helix	198-204	7
α-helix	207-209	3
β-strand	211-215	5	3
α-helix	222-232	11
β-strand	236-241	6	3
α-helix	242-245	4
α-helix	252-266	15
β-strand	270-275	6	3
α-helix	277-279	3
β-strand	282	1	4
α-helix	283-284	2
α-helix	294-306	13
β-strand	315-321	7	3
β-strand	327	1	4
α-helix	329-332	4
β-strand	339-342	4	3
α-helix	344-346	3
α-helix	348-360	13
β-strand	364	1	5
α-helix	370-376	7
α-helix	382-398	17
β-strand	404	1	5
α-helix	406-421	16

Chain b: 9 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	57
β-strand	5-10	6	58
β-strand	13	1	59
α-helix	14-17	4
α-helix	25-43	19
β-strand	48-53	6	58
β-strand	55	1	60
β-strand	62-65	4	58
α-helix	68-74	7
β-strand	82	1	59
β-strand	84	1	60
α-helix	86-97	12
β-strand	106	1	57
α-helix	107	1
β-strand	109-113	5	58
α-helix	121-133	13
β-strand	138-142	5	58
α-helix	151-160	10
β-strand	170-172	3	58
α-helix	173-174	2
α-helix	181-184	4

Chain B: 26 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	59-80	22
α-helix	93-95	3
α-helix	96-100	5
α-helix	101-102	2
α-helix	104	1
α-helix	106	1
β-strand	107-115	9	1
β-strand	120-124	5	1
β-strand	130-135	6	1
α-helix	141-143	3
β-strand	149-153	5	1
β-strand	159-162	4	1
α-helix	163-165	3
α-helix	169-174	6
α-helix	184-186	3
α-helix	191-197	7
α-helix	198-202	5
α-helix	203-206	4
α-helix	208-214	7
α-helix	216-219	4
β-strand	222-225	4	10
α-helix	232-242	11
β-strand	246-251	6	10
α-helix	252-255	4
α-helix	262-277	16
β-strand	280-285	6	10
α-helix	288-291	4
α-helix	304-317	14
β-strand	326-331	6	10
α-helix	334-336	3
β-strand	349-352	4	10
α-helix	354-356	3
α-helix	358-369	12
β-strand	374	1	11
α-helix	380-384	5
α-helix	392-408	17
β-strand	414	1	11
α-helix	416-429	14

Chain c: 10 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	31-33	3	61
α-helix	35-48	14
β-strand	54-63	10	61
β-strand	66-74	9	61
α-helix	89-102	14
α-helix	106-107	2
β-strand	108-114	7	61
α-helix	124-136	13
β-strand	142-145	4	61
β-strand	157-162	6	61
α-helix	189-194	6
β-strand	200-203	4	61
β-strand	205-207	3	61
α-helix	218-220	3
α-helix	222-224	3
α-helix	225-229	5
α-helix	234-260	27
α-helix	280-308	29

Chain C: 20 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	22-65	44
β-strand	74-78	5	1
β-strand	86-89	4	1
β-strand	94-96	3	1
β-strand	99	1	12
α-helix	105-107	3
β-strand	114	1	1
β-strand	115-117	3	13
β-strand	121-125	5	13
α-helix	134-137	4
β-strand	140	1	14
α-helix	148-150	3
α-helix	155-161	7
α-helix	162-166	5
α-helix	167-170	4
α-helix	172-178	7
α-helix	180-183	4
β-strand	185-189	5	14
α-helix	196-206	11
β-strand	210-213	4	14
α-helix	216-219	4
α-helix	227-241	15
β-strand	244-249	6	14
α-helix	251-253	3
α-helix	269-281	13
β-strand	289-295	7	14
α-helix	298-300	3
β-strand	313-316	4	14
α-helix	318-320	3
α-helix	322-333	12
α-helix	344-349	6
α-helix	357-372	16
α-helix	380-390	11

Chain d: 15 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	84-103	20
α-helix	109-125	17
α-helix	138-158	21
α-helix	161-177	17
α-helix	188-201	14
α-helix	205-214	10
α-helix	217-222	6
α-helix	224-237	14
α-helix	241-244	4
α-helix	248-250	3
α-helix	254-278	25
β-strand	279	1	52
β-strand	281-283	3	62
α-helix	284-290	7
α-helix	297-306	10
β-strand	310	1	62
β-strand	315-317	3	62
α-helix	319-322	4
α-helix	333-347	15

Chain D: 19 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	40-82	43
α-helix	84	1
α-helix	86	1
β-strand	87-97	11	15
β-strand	100-105	6	15
β-strand	110-113	4	15
α-helix	114	1
β-strand	115	1	15
α-helix	116	1
α-helix	121-123	3
β-strand	129-133	5	15
β-strand	139-142	4	15
α-helix	171-177	7
α-helix	178-182	5
α-helix	183-193	11
β-strand	201-205	5	16
α-helix	212-222	11
β-strand	227-231	5	16
α-helix	244-256	13
β-strand	261-265	5	16
α-helix	268-271	4
α-helix	280-298	19
α-helix	300	1
β-strand	306-311	6	16
β-strand	329-332	4	16
α-helix	334-336	3
α-helix	340-351	12
α-helix	360-365	6
α-helix	372-388	17
α-helix	396-405	10

19 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 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 protease regulatory subunit 10B	E	protein	389	Homo sapiens	P62333
26S proteasome regulatory subunit 6A	F	protein	439	Homo sapiens	P17980
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

16 more molecules are not listed.

Sequence of entity 1 (A), FASTA

>9E8L_1 26S proteasome regulatory subunit 7 (chains A)
MPDYLGADQRKTKEDEKDDKPIRALDEGDIALLKTYGQSTYSRQIKQVEDDIQQLLKKIN
ELTGIKESDTGLAPPALWDLAADKQTLQSEQPLQVARCTKIINADSEDPKYIINVKQFAK
FVVDLSDQVAPTDIEEGMRVGVDRNKYQIHIPLPPKIDPTVTMMQVEEKPDVTYSDVGGC
KEQIEKLREVVETPLLHPERFVNLGIEPPKGVLLFGPPGTGKTLCARAVANRTDACFIRV
IGSELVQKYVGEGARMVRELFEMARTKKACLIFFDEIDAIGGARFDDGAGGDNEVQRTML
ELINQLDGFDPRGNIKVLMATNRPDTLDPALMRPGRLDRKIEFSLPDLEGRTHIFKIHAR
SMSVERDIRFELLARLCPNSTGAEIRSVCTEAGMFAIRARRKIATEKDFLEAVNKVIKSY
AKFSATPRYMTYN

Sequence of entity 2 (B), FASTA

>9E8L_2 26S proteasome regulatory subunit 4 (chains B)
MGQSQSGGHGPGGGKKDDKDKKKKYEPPVPTRVGKKKKKTKGPDAASKLPLVTPHTQCRL
KLLKLERIKDYLLMEEEFIRNQEQMKPLEEKQEEERSKVDDLRGTPMSVGTLEEIIDDNH
AIVSTSVGSEHYVSILSFVDKDLLEPGCSVLLNHKVHAVIGVLMDDTDPLVTVMKVEKAP
QETYADIGGLDNQIQEIKESVELPLTHPEYYEEMGIKPPKGVILYGPPGTGKTLLAKAVA
NQTSATFLRVVGSELIQKYLGDGPKLVRELFRVAEEHAPSIVFIDEIDAIGTKRYDSNSG
GEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDEKT
KKRIFQIHTSRMTLADDVTLDDLIMAKDDLSGADIKAICTEAGLMALRERRMKVTNEDFK
KSKENVLYKKQEGTPEGLYL

Sequence of entity 3 (C), FASTA

>9E8L_3 26S protease regulatory subunit 8 (chains C)
MALDGPEQMELEEGKAGSGLRQYYLSKIEELQLIVNDKSQNLRRLQAQRNELNAKVRLLR
EELQLLQEQGSYVGEVVRAMDKKKVLVKVHPEGKFVVDVDKNIDINDVTPNCRVALRNDS
YTLHKILPNKVDPLVSLMMVEKVPDSTYEMIGGLDKQIKEIKEVIELPVKHPELFEALGI
AQPKGVLLYGPPGTGKTLLARAVAHHTDCTFIRVSGSELVQKFIGEGARMVRELFVMARE
HAPSIIFMDEIDSIGSSRLEGGSGGDSEVQRTMLELLNQLDGFEATKNIKVIMATNRIDI
LDSALLRPGRIDRKIEFPPPNEEARLDILKIHSRKMNLTRGINLRKIAELMPGASGAEVK
GVCTEAGMYALRERRVHVTQEDFEMAVAKVMQKDSEKNMSIKKLWK

Sequence of entity 4 (D), FASTA

>9E8L_4 26S proteasome regulatory subunit 6B (chains D)
MEEIGILVEKAQDEIPALSVSRPQTGLSFLGPEPEDLEDLYSRYKKLQQELEFLEVQEEY
IKDEQKNLKKEFLHAQEEVKRIQSIPLVIGQFLEAVDQNTAIVGSTTGSNYYVRILSTID
RELLKPNASVALHKHSNALVDVLPPEADSSIMMLTSDQKPDVMYADIGGMDIQKQEVREA
VELPLTHFELYKQIGIDPPRGVLMYGPPGCGKTMLAKAVAHHTTAAFIRVVGSEFVQKYL
GEGPRMVRDVFRLAKENAPAIIFIDEIDAIATKRFDAQTGADREVQRILLELLNQMDGFD
QNVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLIFSTITSKMNLSEEVDL
EDYVARPDKISGADINSICQESGMLAVRENRYIVLAKDFEKAYKTVIKKDEQEHEFYK

Sequence of entity 5 (E), FASTA

>9E8L_5 26S protease regulatory subunit 10B (chains E)
MADPRDKALQDYRKKLLEHKEIDGRLKELREQLKELTKQYEKSENDLKALQSVGQIVGEV
LKQLTEEKFIVKATNGPRYVVGCRRQLDKSKLKPGTRVALDMTTLTIMRYLPREVDPLVY
NMSHEDPGNVSYSEIGGLSEQIRELREVIELPLTNPELFQRVGIIPPKGCLLYGPPGTGK
TLLARAVASQLDCNFLKVVSSSIVDKYIGESARLIREMFNYARDHQPCIIFMDEIDAIGG
RRFSEGTSADREIQRTLMELLNQMDGFDTLHRVKMIMATNRPDTLDPALLRPGRLDRKIH
IDLPNEQARLDILKIHAGPITKHGEIDYEAIVKLSDGFNGADLRNVCTEAGMFAIRADHD
FVVQEDFMKAVRKVADSKKLESKLDYKPV

Sequence of entity 6 (F), FASTA

>9E8L_6 26S proteasome regulatory subunit 6A (chains F)
MNLLPNIESPVTRQEKMATVWDEAEQDGIGEEVLKMSTEEIIQRTRLLDSEIKIMKSEVL
RVTHELQAMKDKIKENSEKIKVNKTLPYLVSNVIELLDVDPNDQEEDGANIDLDSQRKGK
CAVIKTSTRQTYFLPVIGLVDAEKLKPGDLVGVNKDSYLILETLPTEYDSRVKAMEVDER
PTEQYSDIGGLDKQIQELVEAIVLPMNHKEKFENLGIQPPKGVLMYGPPGTGKTLLARAC
AAQTKATFLKLAGPQLVQMFIGDGAKLVRDAFALAKEKAPSIIFIDELDAIGTKRFDSEK
AGDREVQRTMLELLNQLDGFQPNTQVKVIAATNRVDILDPALLRSGRLDRKIEFPMPNEE
ARARIMQIHSRKMNVSPDVNYEELARCTDDFNGAQCKAVCVEAGMIALRRGATELTHEDY
MEGILEVQAKKKANLQYYA

Sequence of entity 7 (G), FASTA

>9E8L_7 Proteasome subunit alpha type-6 (chains G)
MSRGSSAGFDRHITIFSPEGRLYQVEYAFKAINQGGLTSVAVRGKDCAVIVTQKKVPDKL
LDSSTVTHLFKITENIGCVMTGMTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKRIAD
ISQVYTQNAEMRPLGCCMILIGIDEEQGPQVYKCDPAGYYCGFKATAAGVKQTESTSFLE
KKVKKKFDWTFEQTVETAITCLSTVLSIDFKPSEIEVGVVTVENPKFRILTEAEIDAHLV
ALAERD

Sequence of entity 8 (H), FASTA

>9E8L_8 Proteasome subunit alpha type-2 (chains H)
MAERGYSFSLTTFSPSGKLVQIEYALAAVAGGAPSVGIKAANGVVLATEKKQKSILYDER
SVHKVEPITKHIGLVYSGMGPDYRVLVHRARKLAQQYYLVYQEPIPTAQLVQRVASVMQE
YTQSGGVRPFGVSLLICGWNEGRPYLFQSDPSGAYFAWKATAHGKNYVNGKTFLEKRYNE
DLELEDAIHTAILTLKESFEGQMTEDNIEVGICNEAGFRRLTPTEVKDYLAAIA

Sequence of entity 9 (I), FASTA

>9E8L_9 Proteasome subunit alpha type-4 (chains I)
MSRRYDSRTTIFSPEGRLYQVEYAMEAIGHAGTCLGILANDGVLLAAERRNIHKLLDEVF
FSEKIYKLNEDMACSVAGITSDANVLTNELRLIAQRYLLQYQEPIPCEQLVTALCDIKQA
YTQFGGKRPFGVSLLYIGWDKHYGFQLYQSDPSGNYGGWKATCIGNNSAAAVSMLKQDYK
EGEMTLKSALALAIKVLNKTMDVSKLSAEKVEIATLTRENGKTVIRVLKQKEVEQLIKKH
EEEEAKAEREKKEKEQKEKDK

Sequence of entity 10 (J), FASTA

>9E8L_10 Proteasome subunit alpha type-7 (chains J)
MSYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVEKKSVAKLQDERTVR
KICALDDNVCMAFAGLTADARIVINRARVECQSHRLTVEDPVTVEYITRYIASLKQRYTQ
SNGRRPFGISALIVGFDFDGTPRLYQTDPSGTYHAWKANAIGRGAKSVREFLEKNYTDEA
IETDDLTIKLVIKALLEVVQSGGKNIELAVMRRDQSLKILNPEEIEKYVAEIEKEKEENE
KKKQKKAS

Sequence of entity 11 (K), FASTA

>9E8L_11 Proteasome subunit alpha type-5 (chains K)
MFLTRSEYDRGVNTFSPEGRLFQVEYAIEAIKLGSTAIGIQTSEGVCLAVEKRITSPLME
PSSIEKIVEIDAHIGCAMSGLIADAKTLIDKARVETQNHWFTYNETMTVESVTQAVSNLA
LQFGEEDADPGAMSRPFGVALLFGGVDEKGPQLFHMDPSGTFVQCDARAIGSASEGAQSS
LQEVYHKSMTLKEAIKSSLIILKQVMEEKLNATNIELATVQPGQNFHMFTKEELEEVIKD
I

Sequence of entity 12 (L), FASTA

>9E8L_12 Proteasome subunit alpha type-1 (chains L)
MFRNQYDNDVTVWSPQGRIHQIEYAMEAVKQGSATVGLKSKTHAVLVALKRAQSELAAHQ
KKILHVDNHIGISIAGLTADARLLCNFMRQECLDSRFVFDRPLPVSRLVSLIGSKTQIPT
QRYGRRPYGVGLLIAGYDDMGPHIFQTCPSANYFDCRAMSIGARSQSARTYLERHMSEFM
ECNLNELVKHGLRALRETLPAEQDLTTKNVSIGIVGKDLEFTIYDDDDVSPFLEGLEERP
QRKAQPAQPADEPAEKADEPMEH

Ligands and cofactors

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