9PDN: 26S protease regulatory subunit 8

Nub1/Fat10-processing human 26S proteasome with Rpt1 at top of spiral staircase (AAA+ locally refined). Determined by electron microscopy at 3.04 Å resolution. Released 19 Nov 2025.

Method: Electron microscopy
Resolution: 3.04 Å
Organism: Homo sapiens
Chains: 15
Atoms: 33,115
Mol. weight: 530.93 kDa
Ligands: ZN, ADP, MG, ATP
Released: 19 Nov 2025

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

Secondary structure: helices and β-sheets

9PDN contains 210 α-helices and 216 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: 28 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	27-35	9
α-helix	42-63	22
β-strand	72	1	39
α-helix	73-74	2
α-helix	75-77	3
α-helix	80-89	10
β-strand	93-100	8	2
β-strand	111-114	4	2
β-strand	120-123	4	2
β-strand	125	1	2
α-helix	131-133	3
β-strand	139-142	4	2
β-strand	149-152	4	2
α-helix	154-156	3
α-helix	159-164	6
β-strand	165	1	40
α-helix	169-170	2
α-helix	174-176	3
α-helix	181-191	11
α-helix	193-196	4
α-helix	200-203	4
α-helix	206-209	4
β-strand	211-215	5	40
α-helix	222-231	10
β-strand	236-240	5	40
α-helix	252-266	15
β-strand	270-275	6	40
α-helix	277-279	3
β-strand	282	1	41
α-helix	283-284	2
α-helix	292-306	15
β-strand	315-321	7	40
α-helix	324-326	3
β-strand	327	1	41
α-helix	329-332	4
β-strand	339	1	40
β-strand	342	1	40
α-helix	344-346	3
α-helix	348-358	11
β-strand	364	1	42
α-helix	370-375	6
α-helix	382-398	17
β-strand	404	1	42
α-helix	406-416	11
α-helix	418-421	4
α-helix	426-429	4
β-strand	432	1	43

Chain B: 21 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	49-52	4
α-helix	59-85	27
α-helix	95-103	9
β-strand	107-114	8	2
β-strand	120-124	5	2
β-strand	131-135	5	2
β-strand	139	1	39
β-strand	149-153	5	2
β-strand	159-162	4	2
α-helix	169-172	4
β-strand	175	1	44
α-helix	184-186	3
α-helix	191-201	11
α-helix	203-206	4
α-helix	208-214	7
α-helix	216-219	4
β-strand	222-225	4	44
α-helix	232-240	9
β-strand	246-250	5	44
β-strand	259	1	38
α-helix	262-276	15
β-strand	280-284	5	44
α-helix	287-289	3
β-strand	292	1	45
α-helix	293-294	2
α-helix	300-316	17
α-helix	321-322	2
β-strand	325-331	7	44
β-strand	337	1	45
β-strand	349-352	4	44
α-helix	354	1
α-helix	356	1
α-helix	358-368	11
β-strand	374	1	46
α-helix	381-384	4
α-helix	392-408	17
β-strand	414	1	46
α-helix	416-426	11
β-strand	439	1	26

Chain c: 12 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	30-34	5	37
α-helix	35-47	13
β-strand	54-63	10	37
β-strand	66-75	10	37
α-helix	76-77	2
α-helix	89-102	14
β-strand	107-114	8	37
α-helix	124-136	13
β-strand	141-145	5	37
β-strand	157-162	6	37
α-helix	163-164	2
α-helix	165-168	4
α-helix	189-192	4
β-strand	200-208	9	37
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: 21 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	22-66	45
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	98-99	2	1
α-helix	105-107	3
β-strand	115-116	2	1
β-strand	122-125	4	1
α-helix	128-130	3
α-helix	133-136	4
β-strand	139	1	3
α-helix	148-150	3
α-helix	155-165	11
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	188-189	2	5
α-helix	198-205	8
β-strand	210-213	4	3
β-strand	223	1	6
α-helix	226-240	15
β-strand	244-247	4	3
β-strand	249	1	5
α-helix	252-255	4
β-strand	256	1	7
α-helix	259-260	2
α-helix	268-280	13
β-strand	289-291	3	3
β-strand	294-295	2	5
β-strand	301	1	7
β-strand	313	1	4
β-strand	316	1	5
α-helix	318-320	3
α-helix	322-331	10
β-strand	337-338	2	8
α-helix	344-349	6
α-helix	357-371	15
β-strand	377-378	2	8
α-helix	380-390	11
α-helix	399-402	4
β-strand	405	1	9

Chain D: 19 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	40-81	42
β-strand	87-91	5	2
β-strand	95	1	10
β-strand	101	1	10
α-helix	103	1
β-strand	104-105	2	2
β-strand	110	1	2
β-strand	111-112	2	1
β-strand	113	1	10
β-strand	115	1	2
α-helix	121-123	3
β-strand	129-133	5	2
β-strand	139-141	3	2
α-helix	142-145	4
β-strand	153	1	11
α-helix	171-181	11
α-helix	183-186	4
α-helix	188-192	5
α-helix	197-199	3
β-strand	201-205	5	11
α-helix	212-221	10
β-strand	226-231	6	11
α-helix	232-235	4
α-helix	243-256	14
β-strand	260-265	6	11
α-helix	267-269	3
β-strand	272	1	12
α-helix	273-274	2
α-helix	280-296	17
β-strand	305-311	7	11
β-strand	317	1	12
β-strand	329	1	11
β-strand	332	1	11
α-helix	334-336	3
α-helix	338-349	12
β-strand	354	1	13
α-helix	361-364	4
α-helix	372-388	17
β-strand	394	1	13
α-helix	396-407	12

Chain E: 18 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	34-51	18
β-strand	55-60	6	2
β-strand	69-73	5	2
β-strand	78-83	6	2
β-strand	97-101	5	2
β-strand	106-111	6	2
α-helix	112-114	3
α-helix	122-124	3
α-helix	139-145	7
α-helix	146-150	5
α-helix	151-154	4
α-helix	157-162	6
α-helix	165-167	3
β-strand	170-173	4	47
α-helix	180-190	11
β-strand	194-198	5	48
α-helix	200-203	4
α-helix	210-224	15
β-strand	228-232	5	48
α-helix	235-237	3
α-helix	248-264	17
β-strand	274-275	2	48
β-strand	278-279	2	47
α-helix	287-289	3
β-strand	291	1	49
β-strand	294	1	49
β-strand	296-300	5	47
α-helix	308-317	10
β-strand	322	1	50
α-helix	328-334	7
α-helix	340-355	16
β-strand	361	1	50
α-helix	364-376	13

Chain F: 19 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	59-84	26
β-strand	88-97	10	2
β-strand	121-126	6	2
β-strand	131-133	3	2
β-strand	138	1	2
α-helix	142-144	3
β-strand	150-153	4	2
β-strand	160-163	4	2
α-helix	164-165	2
α-helix	172-175	4
α-helix	192-201	10
α-helix	204-207	4
α-helix	209-215	7
α-helix	218-220	3
β-strand	224-226	3	51
α-helix	233-242	10
β-strand	249-250	2	51
α-helix	264-277	14
β-strand	283-286	4	51
α-helix	289-292	4
β-strand	293	1	52
α-helix	294-295	2
α-helix	302-304	3
α-helix	306-319	14
β-strand	328-332	5	51
β-strand	338	1	52
β-strand	345	1	53
β-strand	347	1	53
β-strand	351-353	3	51
α-helix	355-357	3
α-helix	359-368	10
β-strand	375	1	54
α-helix	381-387	7
α-helix	393-410	18
β-strand	415	1	54
α-helix	417-427	11

Chain G: 12 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	15-17	3
α-helix	23-32	10
α-helix	33-35	3
β-strand	38-43	6	14
β-strand	47-53	7	14
β-strand	61	1	15
α-helix	63-65	3
β-strand	69-73	5	16
β-strand	76-82	7	16
α-helix	84-105	22
α-helix	108-110	3
α-helix	111-127	17
α-helix	132-134	3
β-strand	136-144	9	16
β-strand	148-154	7	16
β-strand	160-163	4	16
β-strand	165-169	5	14
α-helix	172-182	11
α-helix	191-206	16
α-helix	212-214	3
β-strand	215-221	7	14
β-strand	228-229	2	14
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)
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 14	c	protein	424	Homo sapiens	O00487
Substrate polypeptide	v	protein	11	Homo sapiens
26S proteasome regulatory subunit 7	A	protein	433	Homo sapiens	P35998
26S proteasome regulatory subunit 4	B	protein	440	Homo sapiens	P62191

3 more molecules are not listed.

Sequence of entity 1 (C), FASTA

>9PDN_1 26S protease regulatory subunit 8 (chains C)
MALDGPEQMELEEGKAGSGLRQYYLSKIEELQLIVNDKSQNLRRLQAQRNELNAKVRLLR
EELQLLQEQGSYVGEVVRAMDKKKVLVKVHPEGKFVVDVDKNIDINDVTPNCRVALRNDS
YTLHKILPNKVDPLVSLMMVEKVPDSTYEMIGGLDKQIKEIKEVIELPVKHPELFEALGI
AQPKGVLLYGPPGTGKTLLARAVAHHTDCTFIRVSGSELVQKFIGEGARMVRELFVMARE
HAPSIIFMDEIDSIGSSRLEGGSGGDSEVQRTMLELLNQLDGFEATKNIKVIMATNRIDI
LDSALLRPGRIDRKIEFPPPNEEARLDILKIHSRKMNLTRGINLRKIAELMPGASGAEVK
GVCTEAGMYALRERRVHVTQEDFEMAVAKVMQKDSEKNMSIKKLWK

Sequence of entity 2 (D), FASTA

>9PDN_2 26S proteasome regulatory subunit 6B (chains D)
MEEIGILVEKAQDEIPALSVSRPQTGLSFLGPEPEDLEDLYSRYKKLQQELEFLEVQEEY
IKDEQKNLKKEFLHAQEEVKRIQSIPLVIGQFLEAVDQNTAIVGSTTGSNYYVRILSTID
RELLKPNASVALHKHSNALVDVLPPEADSSIMMLTSDQKPDVMYADIGGMDIQKQEVREA
VELPLTHFELYKQIGIDPPRGVLMYGPPGCGKTMLAKAVAHHTTAAFIRVVGSEFVQKYL
GEGPRMVRDVFRLAKENAPAIIFIDEIDAIATKRFDAQTGADREVQRILLELLNQMDGFD
QNVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLIFSTITSKMNLSEEVDL
EDYVARPDKISGADINSICQESGMLAVRENRYIVLAKDFEKAYKTVIKKDEQEHEFYK

Sequence of entity 3 (G), FASTA

>9PDN_3 Proteasome subunit alpha type-6 (chains G)
MSRGSSAGFDRHITIFSPEGRLYQVEYAFKAINQGGLTSVAVRGKDCAVIVTQKKVPDKL
LDSSTVTHLFKITENIGCVMTGMTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKRIAD
ISQVYTQNAEMRPLGCCMILIGIDEEQGPQVYKCDPAGYYCGFKATAAGVKQTESTSFLE
KKVKKKFDWTFEQTVETAITCLSTVLSIDFKPSEIEVGVVTVENPKFRILTEAEIDAHLV
ALAERD

Sequence of entity 4 (H), FASTA

>9PDN_4 Proteasome subunit alpha type-2 (chains H)
MAERGYSFSLTTFSPSGKLVQIEYALAAVAGGAPSVGIKAANGVVLATEKKQKSILYDER
SVHKVEPITKHIGLVYSGMGPDYRVLVHRARKLAQQYYLVYQEPIPTAQLVQRVASVMQE
YTQSGGVRPFGVSLLICGWNEGRPYLFQSDPSGAYFAWKATAMGKNYVNGKTFLEKRYNE
DLELEDAIHTAILTLKESFEGQMTEDNIEVGICNEAGFRRLTPTEVKDYLAAIA

Sequence of entity 5 (I), FASTA

>9PDN_5 Proteasome subunit alpha type-4 (chains I)
MSRRYDSRTTIFSPEGRLYQVEYAMEAIGHAGTCLGILANDGVLLAAERRNIHKLLDEVF
FSEKIYKLNEDMACSVAGITSDANVLTNELRLIAQRYLLQYQEPIPCEQLVTALCDIKQA
YTQFGGKRPFGVSLLYIGWDKHYGFQLYQSDPSGNYGGWKATCIGNNSAAAVSMLKQDYK
EGEMTLKSALALAIKVLNKTMDVSKLSAEKVEIATLTRENGKTVIRVLKQKEVEQLIKKH
EEEEAKAEREKKEKEQKEKDK

Sequence of entity 6 (J), FASTA

>9PDN_6 Proteasome subunit alpha type-7 (chains J)
MSYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVEKKSVAKLQDERTVR
KICALDDNVCMAFAGLTADARIVINRARVECQSHRLTVEDPVTVEYITRYIASLKQRYTQ
SNGRRPFGISALIVGFDFDGTPRLYQTDPSGTYHAWKANAIGRGAKSVREFLEKNYTDEA
IETDDLTIKLVIKALLEVVQSGGKNIELAVMRRDQSLKILNPEEIEKYVAEIEKEKEENE
KKKQKKAS

Sequence of entity 7 (L), FASTA

>9PDN_7 Proteasome subunit alpha type-1 (chains L)
MFRNQYDNDVTVWSPQGRIHQIEYAMEAVKQGSATVGLKSKTHAVLVALKRAQSELAAHQ
KKILHVDNHIGISIAGLTADARLLCNFMRQECLDSRFVFDRPLPVSRLVSLIGSKTQIPT
QRYGRRPYGVGLLIAGYDDMGPHIFQTCPSANYFDCRAMSIGARSQSARTYLERHMSEFM
ECNLNELVKHGLRALRETLPAEQDLTTKNVSIGIVGKDLEFTIYDDDDVSPFLEGLEERP
QRKAQPAQPADEPAEKADEPMEH

Sequence of entity 8 (M), FASTA

>9PDN_8 Proteasome subunit alpha type-3 (chains M)
MSSIGTGYDLSASTFSPDGRVFQVEYAMKAVENSSTAIGIRCKDGVVFGVEKLVLSKLYE
EGSNKRLFNVDRHVGMAVAGLLADARSLADIAREEASNFRSNFGYNIPLKHLADRVAMYV
HAYTLYSAVRPFGCSFMLGSYSVNDGAQLYMIDPSGVSYGYWGCAIGKARQAAKTEIEKL
QMKEMTCRDIVKEVAKIIYIVHDEVKDKAFELELSWVGELTNGRHEIVPKDIREEAEKYA
KESLKEEDESDDDNM

Sequence of entity 9 (c), FASTA

>9PDN_9 26S proteasome non-ATPase regulatory subunit 14 (chains c)
MDRLLRLGGGMPGLGQGPPTDAPAVDTAEQVYISSLALLKMLKHGRAGVPMEVMGLMLGE
FVDDYTVRVIDVFAMPQSGTGVSVEAVDPVFQAKMLDMLKQTGRPEMVVGWYHSHPGFGC
WLSGVDINTQQSFEALSERAVAVVVDPIQSVKGKVVIDAFRLINANMMVLGHEPRQTTSN
LGHLNKPSIQALIHGLNRHYYSITINYRKNELEQKMLLNLHKKSWMEGLTLQDYSEHCKH
NESVVKEMLELAKNYNKAVEEEDKMTPEQLAIKNVGKQDPKRHLEEHVDVLMTSNIVQCL
AAMLDTVVFKLINHHHHHHDYDIPTTASENLYFQGELGMRGSAGKAGEGEIPAPLAGTVS
KILVKEGDTVKAGQTVLVLEAMKMETEINAPTDGKVEKVLVKERDAVQGGQGLIKIGVHH
HHHH

Sequence of entity 10 (v), FASTA

>9PDN_10 Substrate polypeptide (chains v)
XXXXXXXXXXX

Sequence of entity 11 (A), FASTA

>9PDN_11 26S proteasome regulatory subunit 7 (chains A)
MPDYLGADQRKTKEDEKDDKPIRALDEGDIALLKTYGQSTYSRQIKQVEDDIQQLLKKIN
ELTGIKESDTGLAPPALWDLAADKQTLQSEQPLQVARCTKIINADSEDPKYIINVKQFAK
FVVDLSDQVAPTDIEEGMRVGVDRNKYQIHIPLPPKIDPTVTMMQVEEKPDVTYSDVGGC
KEQIEKLREVVETPLLHPERFVNLGIEPPKGVLLFGPPGTGKTLCARAVANRTDACFIRV
IGSELVQKYVGEGARMVRELFEMARTKKACLIFFDEIDAIGGARFDDGAGGDNEVQRTML
ELINQLDGFDPRGNIKVLMATNRPDTLDPALMRPGRLDRKIEFSLPDLEGRTHIFKIHAR
SMSVERDIRFELLARLCPNSTGAEIRSVCTEAGMFAIRARRKIATEKDFLEAVNKVIKSY
AKFSATPRYMTYN

Sequence of entity 12 (B), FASTA

>9PDN_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
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	2
MG	Magnesium ion	Mg	5
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	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 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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