9PDL: 26S protease regulatory subunit 8

Nub1/Fat10-processing human 26S proteasome with Rpt5 at top of spiral staircase (AAA+ locally refined). Determined by electron microscopy at 2.76 Å resolution. Released 19 Nov 2025.

Method: Electron microscopy
Resolution: 2.76 Å
Organism: Homo sapiens
Chains: 15
Atoms: 33,269
Mol. weight: 530.96 kDa
Ligands: ZN, ATP, MG, ADP
Released: 19 Nov 2025

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

Secondary structure: helices and β-sheets

9PDL contains 211 α-helices and 203 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: 27 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	24-26	3
α-helix	27-35	9
α-helix	42-63	22
β-strand	70	1	34
α-helix	72-74	3
α-helix	75-78	4
α-helix	82-89	8
β-strand	93-102	10	1
β-strand	110-115	6	1
β-strand	119-123	5	1
β-strand	125	1	1
β-strand	139-143	5	1
β-strand	149-152	4	1
α-helix	154-156	3
α-helix	159-163	5
β-strand	165	1	35
α-helix	174-176	3
α-helix	181-191	11
α-helix	193-196	4
α-helix	199-202	4
β-strand	211-215	5	35
α-helix	222-232	11
β-strand	236-240	5	35
α-helix	241	1
α-helix	242-245	4
α-helix	252-266	15
β-strand	270-275	6	35
α-helix	277-279	3
β-strand	282	1	36
α-helix	283-284	2
α-helix	294-306	13
β-strand	315-321	7	35
α-helix	324-326	3
β-strand	327	1	36
β-strand	339-342	4	35
α-helix	344-346	3
α-helix	348-358	11
β-strand	364	1	37
α-helix	370-375	6
α-helix	382-398	17
β-strand	404	1	37
α-helix	406-413	8
α-helix	414-418	5
α-helix	427-430	4
β-strand	432	1	38

Chain B: 23 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	45-46	2
β-strand	47	1	39
α-helix	49-52	4
α-helix	59-85	27
α-helix	92-103	12
β-strand	107-117	11	1
β-strand	120-124	5	1
β-strand	130-135	6	1
α-helix	136	1
β-strand	149-153	5	1
β-strand	159-162	4	1
β-strand	163	1	34
α-helix	169-172	4
β-strand	175	1	40
β-strand	178	1	39
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	217-219	3
β-strand	221-225	5	40
α-helix	232-242	11
β-strand	246-250	5	40
β-strand	259	1	33
α-helix	262-276	15
β-strand	280-284	5	40
α-helix	288-291	4
β-strand	292	1	41
α-helix	293-294	2
α-helix	300-316	17
β-strand	325-331	7	40
β-strand	337	1	41
α-helix	339-342	4
β-strand	349-352	4	40
α-helix	354-356	3
α-helix	358-368	11
β-strand	374	1	42
α-helix	381-385	5
α-helix	392-408	17
β-strand	414	1	42
α-helix	416-426	11
β-strand	439	1	20

Chain c: 11 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	25-26	2	31
β-strand	30-34	5	32
α-helix	35-48	14
β-strand	54-63	10	32
β-strand	66-74	9	32
α-helix	75-77	3
α-helix	84-86	3
α-helix	89-102	14
β-strand	107-114	8	32
α-helix	124-136	13
β-strand	141-145	5	32
β-strand	157-162	6	32
α-helix	167-170	4
β-strand	175-176	2	31
α-helix	189-194	6
β-strand	196	1	32
β-strand	200-208	9	32
α-helix	217-219	3
α-helix	234-261	28
α-helix	267-273	7
α-helix	286-308	23

Chain C: 24 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	22-67	46
α-helix	69-70	2
β-strand	71-79	9	1
β-strand	84-89	6	1
β-strand	93-99	7	1
α-helix	100	1
α-helix	105-107	3
β-strand	113-116	4	1
β-strand	123-125	3	1
α-helix	128-130	3
α-helix	133-136	4
β-strand	139	1	2
α-helix	148-150	3
α-helix	156-165	10
α-helix	167-170	4
α-helix	173-178	6
α-helix	180-183	4
β-strand	185-189	5	2
α-helix	196-206	11
β-strand	210-213	4	2
β-strand	223	1	3
α-helix	226-240	15
β-strand	244-249	6	2
α-helix	252-255	4
β-strand	256	1	4
α-helix	257-260	4
α-helix	267-280	14
α-helix	285-286	2
β-strand	289-295	7	2
β-strand	301	1	4
α-helix	303-306	4
β-strand	313-316	4	2
α-helix	318-320	3
α-helix	322-332	11
β-strand	337-338	2	5
α-helix	344-349	6
α-helix	356-372	17
β-strand	377-378	2	5
α-helix	380-390	11
α-helix	399-402	4
β-strand	405	1	6

Chain D: 18 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	40-82	43
β-strand	87-97	11	1
β-strand	100-105	6	1
β-strand	110-113	4	1
β-strand	115	1	1
α-helix	121-123	3
β-strand	129-132	4	1
β-strand	139-142	4	1
α-helix	156-158	3
α-helix	171-181	11
α-helix	183-186	4
α-helix	188-194	7
β-strand	201-205	5	43
α-helix	212-222	11
β-strand	226-231	6	43
α-helix	232-235	4
α-helix	243-256	14
β-strand	260-265	6	43
α-helix	269-271	3
β-strand	272	1	44
α-helix	273-274	2
α-helix	280-296	17
β-strand	305-311	7	43
β-strand	317	1	44
β-strand	329-332	4	43
α-helix	334-336	3
α-helix	340-350	11
α-helix	360-364	5
α-helix	372-388	17
α-helix	396-407	12
α-helix	413-415	3

Chain E: 15 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	16-50	35
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	97-100	4	1
β-strand	107-111	5	1
α-helix	112-116	5
α-helix	139-154	16
α-helix	156-162	7
β-strand	171	1	45
α-helix	180-186	7
α-helix	187-189	3
α-helix	217-223	7
β-strand	229	1	46
α-helix	235-237	3
α-helix	254-261	8
α-helix	265-268	4
β-strand	274	1	46
β-strand	298	1	45
α-helix	306-316	11
α-helix	331-334	4
α-helix	340-355	16
α-helix	364-377	14

Chain F: 21 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	53-83	31
β-strand	89-97	9	1
β-strand	121-126	6	1
β-strand	131-134	4	1
β-strand	138	1	1
β-strand	150-153	4	1
β-strand	160-163	4	1
α-helix	170-175	6
β-strand	176	1	47
α-helix	185-187	3
α-helix	193-198	6
α-helix	199-203	5
α-helix	204-207	4
α-helix	210-214	5
α-helix	218-220	3
β-strand	222-226	5	47
α-helix	233-242	10
β-strand	247-252	6	47
α-helix	254-256	3
α-helix	263-277	15
β-strand	281-286	6	47
α-helix	288-290	3
β-strand	293	1	48
α-helix	294-295	2
α-helix	302-319	18
α-helix	321	1
β-strand	326-332	7	47
β-strand	338	1	48
α-helix	340-343	4
β-strand	350-353	4	47
α-helix	355-357	3
α-helix	359-369	11
β-strand	375	1	49
α-helix	381-387	7
α-helix	393-409	17
β-strand	415	1	49
α-helix	417-427	11
β-strand	438	1	25

Chain G: 10 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	7-9	3
α-helix	23-31	9
α-helix	32-35	4
β-strand	38-43	6	7
β-strand	47-53	7	7
β-strand	61	1	8
α-helix	63-65	3
β-strand	69-71	3	9
β-strand	76-82	7	9
α-helix	84-105	22
α-helix	108-110	3
α-helix	111-127	17
β-strand	128	1	10
β-strand	136-144	9	9
β-strand	148-154	7	9
β-strand	160-163	4	9
β-strand	165-169	5	7
α-helix	173-182	10
α-helix	191-206	16
β-strand	215-221	7	7
β-strand	228-230	3	7
α-helix	232-243	12

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)
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 (AlphaFold model)
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 14	c	protein	424	Homo sapiens	O00487
Substrate polypeptide	v	protein	12	Homo sapiens
26S proteasome regulatory subunit 7	A	protein	433	Homo sapiens	P35998
26S proteasome regulatory subunit 4	B	protein	440	Homo sapiens	P62191
26S proteasome regulatory subunit 6B	D	protein	418	Homo sapiens	P43686

3 more molecules are not listed.

Sequence of entity 1 (C), FASTA

>9PDL_1 26S protease regulatory subunit 8 (chains C)
MALDGPEQMELEEGKAGSGLRQYYLSKIEELQLIVNDKSQNLRRLQAQRNELNAKVRLLR
EELQLLQEQGSYVGEVVRAMDKKKVLVKVHPEGKFVVDVDKNIDINDVTPNCRVALRNDS
YTLHKILPNKVDPLVSLMMVEKVPDSTYEMIGGLDKQIKEIKEVIELPVKHPELFEALGI
AQPKGVLLYGPPGTGKTLLARAVAHHTDCTFIRVSGSELVQKFIGEGARMVRELFVMARE
HAPSIIFMDEIDSIGSSRLEGGSGGDSEVQRTMLELLNQLDGFEATKNIKVIMATNRIDI
LDSALLRPGRIDRKIEFPPPNEEARLDILKIHSRKMNLTRGINLRKIAELMPGASGAEVK
GVCTEAGMYALRERRVHVTQEDFEMAVAKVMQKDSEKNMSIKKLWK

Sequence of entity 2 (G), FASTA

>9PDL_2 Proteasome subunit alpha type-6 (chains G)
MSRGSSAGFDRHITIFSPEGRLYQVEYAFKAINQGGLTSVAVRGKDCAVIVTQKKVPDKL
LDSSTVTHLFKITENIGCVMTGMTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKRIAD
ISQVYTQNAEMRPLGCCMILIGIDEEQGPQVYKCDPAGYYCGFKATAAGVKQTESTSFLE
KKVKKKFDWTFEQTVETAITCLSTVLSIDFKPSEIEVGVVTVENPKFRILTEAEIDAHLV
ALAERD

Sequence of entity 3 (H), FASTA

>9PDL_3 Proteasome subunit alpha type-2 (chains H)
MAERGYSFSLTTFSPSGKLVQIEYALAAVAGGAPSVGIKAANGVVLATEKKQKSILYDER
SVHKVEPITKHIGLVYSGMGPDYRVLVHRARKLAQQYYLVYQEPIPTAQLVQRVASVMQE
YTQSGGVRPFGVSLLICGWNEGRPYLFQSDPSGAYFAWKATAMGKNYVNGKTFLEKRYNE
DLELEDAIHTAILTLKESFEGQMTEDNIEVGICNEAGFRRLTPTEVKDYLAAIA

Sequence of entity 4 (I), FASTA

>9PDL_4 Proteasome subunit alpha type-4 (chains I)
MSRRYDSRTTIFSPEGRLYQVEYAMEAIGHAGTCLGILANDGVLLAAERRNIHKLLDEVF
FSEKIYKLNEDMACSVAGITSDANVLTNELRLIAQRYLLQYQEPIPCEQLVTALCDIKQA
YTQFGGKRPFGVSLLYIGWDKHYGFQLYQSDPSGNYGGWKATCIGNNSAAAVSMLKQDYK
EGEMTLKSALALAIKVLNKTMDVSKLSAEKVEIATLTRENGKTVIRVLKQKEVEQLIKKH
EEEEAKAEREKKEKEQKEKDK

Sequence of entity 5 (J), FASTA

>9PDL_5 Proteasome subunit alpha type-7 (chains J)
MSYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVEKKSVAKLQDERTVR
KICALDDNVCMAFAGLTADARIVINRARVECQSHRLTVEDPVTVEYITRYIASLKQRYTQ
SNGRRPFGISALIVGFDFDGTPRLYQTDPSGTYHAWKANAIGRGAKSVREFLEKNYTDEA
IETDDLTIKLVIKALLEVVQSGGKNIELAVMRRDQSLKILNPEEIEKYVVEIEKEKEENE
KKKQKKAS

Sequence of entity 6 (L), FASTA

>9PDL_6 Proteasome subunit alpha type-1 (chains L)
MFRNQYDNDVTVWSPQGRIHQIEYAMEAVKQGSATVGLKSKTHAVLVALKRAQSELAAHQ
KKILHVDNHIGISIAGLTADARLLCNFMRQECLDSRFVFDRPLPVSRLVSLIGSKTQIPT
QRYGRRPYGVGLLIAGYDDMGPHIFQTCPSANYFDCRAMSIGARSQSARTYLERHMSEFM
ECNLNELVKHGLRALRETLPAEQDLTTKNVSIGIVGKDLEFTIYDDDDVSPFLEGLEERP
QRKAQPAQPADEPAEKADEPMEH

Sequence of entity 7 (M), FASTA

>9PDL_7 Proteasome subunit alpha type-3 (chains M)
MSSIGTGYDLSASTFSPDGRVFQVEYAMKAVENSSTAIGIRCKDGVVFGVEKLVLSKLYE
EGSNKRLFNVDRHVGMAVAGLLADARSLADIAREEASNFRSNFGYNIPLKHLADRVAMYV
HAYTLYSAVRPFGCSFMLGSYSVNDGAQLYMIDPSGVSYGYWGCAIGKARQAAKTEIEKL
QMKEMTCRDIVKEVAKIIYIVHDEVKDKAFELELSWVGELTNGRHEIVPKDIREEAEKYA
KESLKEEDESDDDNM

Sequence of entity 8 (c), FASTA

>9PDL_8 26S proteasome non-ATPase regulatory subunit 14 (chains c)
MDRLLRLGGGMPGLGQGPPTDAPAVDTAEQVYISSLALLKMLKHGRAGVPMEVMGLMLGE
FVDDYTVRVIDVFAMPQSGTGVSVEAVDPVFQAKMLDMLKQTGRPEMVVGWYHSHPGFGC
WLSGVDINTQQSFEALSERAVAVVVDPIQSVKGKVVIDAFRLINANMMVLGHEPRQTTSN
LGHLNKPSIQALIHGLNRHYYSITINYRKNELEQKMLLNLHKKSWMEGLTLQDYSEHCKH
NESVVKEMLELAKNYNKAVEEEDKMTPEQLAIKNVGKQDPKRHLEEHVDVLMTSNIVQCL
AAMLDTVVFKLINHHHHHHDYDIPTTASENLYFQGELGMRGSAGKAGEGEIPAPLAGTVS
KILVKEGDTVKAGQTVLVLEAMKMETEINAPTDGKVEKVLVKERDAVQGGQGLIKIGVHH
HHHH

Sequence of entity 9 (v), FASTA

>9PDL_9 Substrate polypeptide (chains v)
XXXXXXXXXXXX

Sequence of entity 10 (A), FASTA

>9PDL_10 26S proteasome regulatory subunit 7 (chains A)
MPDYLGADQRKTKEDEKDDKPIRALDEGDIALLKTYGQSTYSRQIKQVEDDIQQLLKKIN
ELTGIKESDTGLAPPALWDLAADKQTLQSEQPLQVARCTKIINADSEDPKYIINVKQFAK
FVVDLSDQVAPTDIEEGMRVGVDRNKYQIHIPLPPKIDPTVTMMQVEEKPDVTYSDVGGC
KEQIEKLREVVETPLLHPERFVNLGIEPPKGVLLFGPPGTGKTLCARAVANRTDACFIRV
IGSELVQKYVGEGARMVRELFEMARTKKACLIFFDEIDAIGGARFDDGAGGDNEVQRTML
ELINQLDGFDPRGNIKVLMATNRPDTLDPALMRPGRLDRKIEFSLPDLEGRTHIFKIHAR
SMSVERDIRFELLARLCPNSTGAEIRSVCTEAGMFAIRARRKIATEKDFLEAVNKVIKSY
AKFSATPRYMTYN

Sequence of entity 11 (B), FASTA

>9PDL_11 26S proteasome regulatory subunit 4 (chains B)
MGQSQSGGHGPGGGKKDDKDKKKKYEPPVPTRVGKKKKKTKGPDAASKLPLVTPHTQCRL
KLLKLERIKDYLLMEEEFIRNQEQMKPLEEKQEEERSKVDDLRGTPMSVGTLEEIIDDNH
AIVSTSVGSEHYVSILSFVDKDLLEPGCSVLLNHKVHAVIGVLMDDTDPLVTVMKVEKAP
QETYADIGGLDNQIQEIKESVELPLTHPEYYEEMGIKPPKGVILYGPPGTGKTLLAKAVA
NQTSATFLRVVGSELIQKYLGDGPKLVRELFRVAEEHAPSIVFIDEIDAIGTKRYDSNSG
GEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDEKT
KKRIFQIHTSRMTLADDVTLDDLIMAKDDLSGADIKAICTEAGLMALRERRMKVTNEDFK
KSKENVLYKKQEGTPEGLYL

Sequence of entity 12 (D), FASTA

>9PDL_12 26S proteasome regulatory subunit 6B (chains D)
MEEIGILVEKAQDEIPALSVSRPQTGLSFLGPEPEDLEDLYSRYKKLQQELEFLEVQEEY
IKDEQKNLKKEFLHAQEEVKRIQSIPLVIGQFLEAVDQNTAIVGSTTGSNYYVRILSTID
RELLKPNASVALHKHSNALVDVLPPEADSSIMMLTSDQKPDVMYADIGGMDIQKQEVREA
VELPLTHFELYKQIGIDPPRGVLMYGPPGCGKTMLAKAVAHHTTAAFIRVVGSEFVQKYL
GEGPRMVRDVFRLAKENAPAIIFIDEIDAIATKRFDAQTGADREVQRILLELLNQMDGFD
QNVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLIFSTITSKMNLSEEVDL
EDYVARPDKISGADINSICQESGMLAVRENRYIVLAKDFEKAYKTVIKKDEQEHEFYK

Ligands and cofactors

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

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…
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…
9NKI 2.94 Å, Structure of substrate engaged MIDN-bound human 26S proteasome, EB MIDN_UBL state…

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