9PDI: 26S protease regulatory subunit 8

Nub1/Fat10-processing human 26S proteasome with Rpt2 at top of spiral staircase and partially unfolded Eos (AAA+ motor locally refined). Determined by electron microscopy at 2.98 Å resolution. Released 19 Nov 2025.

Method: Electron microscopy
Resolution: 2.98 Å
Organism: Homo sapiens
Chains: 15
Atoms: 33,548
Mol. weight: 531.6 kDa
Ligands: ZN, ADP, MG, ATP
Released: 19 Nov 2025

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

Secondary structure: helices and β-sheets

9PDI contains 207 α-helices and 190 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: 20 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	27-35	9
α-helix	42-63	22
β-strand	72	1	37
α-helix	73-74	2
α-helix	75-77	3
α-helix	80-89	10
β-strand	93-98	6	1
β-strand	111-115	5	1
β-strand	119-123	5	1
β-strand	139-142	4	1
β-strand	149-152	4	1
β-strand	167	1	38
α-helix	181-196	16
α-helix	198-203	6
α-helix	207-209	3
β-strand	211-215	5	38
α-helix	222-233	12
α-helix	235	1
β-strand	236-240	5	38
α-helix	243-246	4
α-helix	253-266	14
β-strand	270-275	6	38
α-helix	278-281	4
α-helix	294-303	10
α-helix	304-308	5
β-strand	317-320	4	38
β-strand	339-342	4	38
α-helix	348-360	13
β-strand	364	1	39
α-helix	370-376	7
α-helix	382-398	17
β-strand	404	1	39
α-helix	406-416	11
α-helix	427-430	4
β-strand	432	1	26

Chain B: 21 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	49-52	4
α-helix	59-84	26
α-helix	95-103	9
β-strand	107-117	11	1
β-strand	120-125	6	1
β-strand	130-135	6	1
β-strand	139	1	37
α-helix	141-143	3
β-strand	149-153	5	1
β-strand	159-162	4	1
α-helix	169-173	5
β-strand	175	1	40
α-helix	184-186	3
α-helix	191-201	11
α-helix	209-213	5
α-helix	216-218	3
β-strand	222-225	4	40
α-helix	232-242	11
β-strand	246-250	5	40
β-strand	259	1	36
α-helix	262-276	15
β-strand	280-285	6	40
α-helix	287-289	3
β-strand	292	1	41
α-helix	293-294	2
α-helix	300-318	19
β-strand	325-331	7	40
α-helix	334-336	3
β-strand	337	1	41
β-strand	349-352	4	40
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	434-435	2

Chain c: 12 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	26	1	43
β-strand	30-34	5	44
α-helix	35-47	13
β-strand	54-63	10	44
β-strand	66-74	9	44
α-helix	89-102	14
α-helix	106	1
β-strand	107-114	8	44
α-helix	124-136	13
β-strand	144-145	2	44
β-strand	157-158	2	44
β-strand	159-160	2	45
α-helix	165-170	6
β-strand	176	1	43
α-helix	181-183	3
α-helix	186-188	3
α-helix	189-193	5
β-strand	196	1	46
β-strand	200	1	46
β-strand	202-203	2	45
β-strand	204-208	5	44
α-helix	211-218	8
α-helix	230-233	4
α-helix	234-263	30
α-helix	280-308	29

Chain C: 22 helices, 15 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
α-helix	105-107	3
β-strand	112-116	5	1
β-strand	122-126	5	1
α-helix	127-130	4
α-helix	133-136	4
β-strand	139	1	2
α-helix	148-150	3
α-helix	155-165	11
α-helix	167-170	4
α-helix	172-178	7
α-helix	180-183	4
β-strand	185-189	5	2
α-helix	196-205	10
β-strand	210-213	4	2
β-strand	223	1	3
α-helix	226-240	15
β-strand	244-248	5	2
α-helix	258-259	2
α-helix	268-280	13
β-strand	291-295	5	2
α-helix	303-306	4
β-strand	314-316	3	2
α-helix	318-320	3
α-helix	322-332	11
β-strand	337-338	2	4
α-helix	339	1
α-helix	344-349	6
α-helix	356-372	17
β-strand	377-378	2	4
α-helix	380-390	11
α-helix	399-402	4
β-strand	405	1	5

Chain D: 20 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	171-181	11
α-helix	183-186	4
α-helix	188-194	7
α-helix	197-199	3
β-strand	202-205	4	6
α-helix	212-221	10
β-strand	226-231	6	6
α-helix	232-235	4
β-strand	239	1	7
α-helix	242-256	15
β-strand	260-265	6	6
α-helix	267-269	3
β-strand	272	1	8
α-helix	273-274	2
α-helix	280-297	18
β-strand	305-311	7	6
α-helix	314-316	3
β-strand	317	1	8
β-strand	329-332	4	6
α-helix	334-336	3
α-helix	338-349	12
α-helix	353-354	2
α-helix	360-365	6
α-helix	372-388	17
α-helix	396-406	11
α-helix	415-417	3

Chain E: 20 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	26-29	4
α-helix	32-34	3
α-helix	35-50	16
β-strand	55-63	9	1
β-strand	69-73	5	1
β-strand	78-81	4	1
β-strand	83	1	1
α-helix	89-91	3
β-strand	97-101	5	1
β-strand	107-110	4	1
α-helix	112-116	5
α-helix	117-123	7
α-helix	139-145	7
α-helix	146-150	5
α-helix	151-154	4
α-helix	156-162	7
α-helix	165-167	3
β-strand	169-173	5	9
α-helix	180-191	12
β-strand	194-199	6	9
β-strand	207	1	10
α-helix	210-224	15
β-strand	228-233	6	9
α-helix	248-264	17
β-strand	273-279	7	9
α-helix	282-284	3
α-helix	287-290	4
β-strand	297-300	4	9
α-helix	306-316	11
β-strand	322	1	11
α-helix	329-334	6
α-helix	341-356	16
β-strand	362	1	11
α-helix	364-378	15

Chain F: 16 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	53-83	31
β-strand	88-98	11	1
β-strand	120-126	7	1
β-strand	130-134	5	1
β-strand	150-153	4	1
β-strand	160-163	4	1
α-helix	171-174	4
α-helix	192-207	16
α-helix	209-215	7
α-helix	218-220	3
β-strand	223-226	4	42
α-helix	233-244	12
β-strand	247-250	4	42
α-helix	268-273	6
α-helix	274-276	3
β-strand	281-285	5	42
α-helix	304-317	14
β-strand	326-330	5	42
α-helix	340-343	4
β-strand	350-353	4	42
α-helix	355-357	3
α-helix	360-369	10
α-helix	381-386	6
α-helix	394-409	16
α-helix	418-426	9
α-helix	427-430	4
β-strand	438	1	31

Chain G: 11 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	15-17	3
α-helix	18-20	3
α-helix	23-33	11
β-strand	38-43	6	12
β-strand	47-53	7	12
β-strand	61	1	13
α-helix	63-65	3
β-strand	69-73	5	14
β-strand	76-82	7	14
α-helix	84-105	22
α-helix	108-110	3
α-helix	111-127	17
β-strand	128	1	15
β-strand	136-144	9	14
β-strand	148-154	7	14
β-strand	160-163	4	14
β-strand	165-169	5	12
α-helix	172-183	12
α-helix	191-206	16
α-helix	212-214	3
β-strand	215-221	7	12
β-strand	228-230	3	12
α-helix	232-244	13

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 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 (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
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
Substrate polypeptide	v	protein	22	Homo sapiens
26S proteasome regulatory subunit 7	A	protein	433	Homo sapiens	P35998

3 more molecules are not listed.

Sequence of entity 1 (C), FASTA

>9PDI_1 26S protease regulatory subunit 8 (chains C)
MALDGPEQMELEEGKAGSGLRQYYLSKIEELQLIVNDKSQNLRRLQAQRNELNAKVRLLR
EELQLLQEQGSYVGEVVRAMDKKKVLVKVHPEGKFVVDVDKNIDINDVTPNCRVALRNDS
YTLHKILPNKVDPLVSLMMVEKVPDSTYEMIGGLDKQIKEIKEVIELPVKHPELFEALGI
AQPKGVLLYGPPGTGKTLLARAVAHHTDCTFIRVSGSELVQKFIGEGARMVRELFVMARE
HAPSIIFMDEIDSIGSSRLEGGSGGDSEVQRTMLELLNQLDGFEATKNIKVIMATNRIDI
LDSALLRPGRIDRKIEFPPPNEEARLDILKIHSRKMNLTRGINLRKIAELMPGASGAEVK
GVCTEAGMYALRERRVHVTQEDFEMAVAKVMQKDSEKNMSIKKLWK

Sequence of entity 2 (D), FASTA

>9PDI_2 26S proteasome regulatory subunit 6B (chains D)
MEEIGILVEKAQDEIPALSVSRPQTGLSFLGPEPEDLEDLYSRYKKLQQELEFLEVQEEY
IKDEQKNLKKEFLHAQEEVKRIQSIPLVIGQFLEAVDQNTAIVGSTTGSNYYVRILSTID
RELLKPNASVALHKHSNALVDVLPPEADSSIMMLTSDQKPDVMYADIGGMDIQKQEVREA
VELPLTHFELYKQIGIDPPRGVLMYGPPGCGKTMLAKAVAHHTTAAFIRVVGSEFVQKYL
GEGPRMVRDVFRLAKENAPAIIFIDEIDAIATKRFDAQTGADREVQRILLELLNQMDGFD
QNVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLIFSTITSKMNLSEEVDL
EDYVARPDKISGADINSICQESGMLAVRENRYIVLAKDFEKAYKTVIKKDEQEHEFYK

Sequence of entity 3 (E), FASTA

>9PDI_3 26S protease regulatory subunit 10B (chains E)
MADPRDKALQDYRKKLLEHKEIDGRLKELREQLKELTKQYEKSENDLKALQSVGQIVGEV
LKQLTEEKFIVKATNGPRYVVGCRRQLDKSKLKPGTRVALDMTTLTIMRYLPREVDPLVY
NMSHEDPGNVSYSEIGGLSEQIRELREVIELPLTNPELFQRVGIIPPKGCLLYGPPGTGK
TLLARAVASQLDCNFLKVVSSSIVDKYIGESARLIREMFNYARDHQPCIIFMDEIDAIGG
RRFSEGTSADREIQRTLMELLNQMDGFDTLHRVKMIMATNRPDTLDPALLRPGRLDRKIH
IDLPNEQARLDILKIHAGPITKHGEIDYEAIVKLSDGFNGADLRNVCTEAGMFAIRADHD
FVVQEDFMKAVRKVADSKKLESKLDYKPV

Sequence of entity 4 (G), FASTA

>9PDI_4 Proteasome subunit alpha type-6 (chains G)
MSRGSSAGFDRHITIFSPEGRLYQVEYAFKAINQGGLTSVAVRGKDCAVIVTQKKVPDKL
LDSSTVTHLFKITENIGCVMTGMTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKRIAD
ISQVYTQNAEMRPLGCCMILIGIDEEQGPQVYKCDPAGYYCGFKATAAGVKQTESTSFLE
KKVKKKFDWTFEQTVETAITCLSTVLSIDFKPSEIEVGVVTVENPKFRILTEAEIDAHLV
ALAERD

Sequence of entity 5 (H), FASTA

>9PDI_5 Proteasome subunit alpha type-2 (chains H)
MAERGYSFSLTTFSPSGKLVQIEYALAAVAGGAPSVGIKAANGVVLATEKKQKSILYDER
SVHKVEPITKHIGLVYSGMGPDYRVLVHRARKLAQQYYLVYQEPIPTAQLVQRVASVMQE
YTQSGGVRPFGVSLLICGWNEGRPYLFQSDPSGAYFAWKATAMGKNYVNGKTFLEKRYNE
DLELEDAIHTAILTLKESFEGQMTEDNIEVGICNEAGFRRLTPTEVKDYLAAIA

Sequence of entity 6 (I), FASTA

>9PDI_6 Proteasome subunit alpha type-4 (chains I)
MSRRYDSRTTIFSPEGRLYQVEYAMEAIGHAGTCLGILANDGVLLAAERRNIHKLLDEVF
FSEKIYKLNEDMACSVAGITSDANVLTNELRLIAQRYLLQYQEPIPCEQLVTALCDIKQA
YTQFGGKRPFGVSLLYIGWDKHYGFQLYQSDPSGNYGGWKATCIGNNSAAAVSMLKQDYK
EGEMTLKSALALAIKVLNKTMDVSKLSAEKVEIATLTRENGKTVIRVLKQKEVEQLIKKH
EEEEAKAEREKKEKEQKEKDK

Sequence of entity 7 (J), FASTA

>9PDI_7 Proteasome subunit alpha type-7 (chains J)
MSYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVEKKSVAKLQDERTVR
KICALDDNVCMAFAGLTADARIVINRARVECQSHRLTVEDPVTVEYITRYIASLKQRYTQ
SNGRRPFGISALIVGFDFDGTPRLYQTDPSGTYHAWKANAIGRGAKSVREFLEKNYTDEA
IETDDLTIKLVIKALLEVVQSGGKNIELAVMRRDQSLKILNPEEIEKYVAEIEKEKEENE
KKKQKKAS

Sequence of entity 8 (K), FASTA

>9PDI_8 Proteasome subunit alpha type-5 (chains K)
MFLTRSEYDRGVNTFSPEGRLFQVEYAIEAIKLGSTAIGIQTSEGVCLAVEKRITSPLME
PSSIEKIVEIDAHIGCAMSGLIADAKTLIDKARVETQNHWFTYNETMTVESVTQAVSNLA
LQFGEEDADPGAMSRPFGVALLFGGVDEKGPQLFHMDPSGTFVQCDARAIGSASEGAQSS
LQEVYHKSMTLKEAIKSSLIILKQVMEEKLNATNIELATVQPGQNFHMFTKEELEEVIKD
I

Sequence of entity 9 (L), FASTA

>9PDI_9 Proteasome subunit alpha type-1 (chains L)
MFRNQYDNDVTVWSPQGRIHQIEYAMEAVKQGSATVGLKSKTHAVLVALKRAQSELAAHQ
KKILHVDNHIGISIAGLTADARLLCNFMRQECLDSRFVFDRPLPVSRLVSLIGSKTQIPT
QRYGRRPYGVGLLIAGYDDMGPHIFQTCPSANYFDCRAMSIGARSQSARTYLERHMSEFM
ECNLNELVKHGLRALRETLPAEQDLTTKNVSIGIVGKDLEFTIYDDDDVSPFLEGLEERP
QRKAQPAQPADEPAEKADEPMEH

Sequence of entity 10 (M), FASTA

>9PDI_10 Proteasome subunit alpha type-3 (chains M)
MSSIGTGYDLSASTFSPDGRVFQVEYAMKAVENSSTAIGIRCKDGVVFGVEKLVLSKLYE
EGSNKRLFNVDRHVGMAVAGLLADARSLADIAREEASNFRSNFGYNIPLKHLADRVAMYV
HAYTLYSAVRPFGCSFMLGSYSVNDGAQLYMIDPSGVSYGYWGCAIGKARQAAKTEIEKL
QMKEMTCRDIVKEVAKIIYIVHDEVKDKAFELELSWVGELTNGRHEIVPKDIREEAEKYA
KESLKEEDESDDDNM

Sequence of entity 11 (v), FASTA

>9PDI_11 Substrate polypeptide (chains v)
XXXXXXXXXXXXXXXXXXXXXX

Sequence of entity 12 (A), FASTA

>9PDI_12 26S proteasome regulatory subunit 7 (chains A)
MPDYLGADQRKTKEDEKDDKPIRALDEGDIALLKTYGQSTYSRQIKQVEDDIQQLLKKIN
ELTGIKESDTGLAPPALWDLAADKQTLQSEQPLQVARCTKIINADSEDPKYIINVKQFAK
FVVDLSDQVAPTDIEEGMRVGVDRNKYQIHIPLPPKIDPTVTMMQVEEKPDVTYSDVGGC
KEQIEKLREVVETPLLHPERFVNLGIEPPKGVLLFGPPGTGKTLCARAVANRTDACFIRV
IGSELVQKYVGEGARMVRELFEMARTKKACLIFFDEIDAIGGARFDDGAGGDNEVQRTML
ELINQLDGFDPRGNIKVLMATNRPDTLDPALMRPGRLDRKIEFSLPDLEGRTHIFKIHAR
SMSVERDIRFELLARLCPNSTGAEIRSVCTEAGMFAIRARRKIATEKDFLEAVNKVIKSY
AKFSATPRYMTYN

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	4
MG	Magnesium ion	Mg	3
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 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…

Browse structure collections

About this viewer

MolViewer shows 9PDI directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.