9U3L: Substrate-engaged human 26S proteasome

Substrate-engaged human 26S proteasome bound to midnolin with RPT2 at top of spiral staircase. Determined by electron microscopy at 2.91 Å resolution. Released 25 Mar 2026.

Method: Electron microscopy
Resolution: 2.91 Å
Organism: Homo sapiens
Chains: 47
Atoms: 104,750
Mol. weight: 1668.49 kDa
Ligands: ADP, ATP, MG, LDZ
Released: 25 Mar 2026

Explore 9U3L in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9U3L contains 606 α-helices and 542 β-strands across 46 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: 24 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	5-10	6
α-helix	18	1
α-helix	19-23	5
α-helix	24-30	7
α-helix	36-46	11
α-helix	54-66	13
α-helix	73-87	15
α-helix	90-102	13
α-helix	111-120	10
α-helix	131-141	11
α-helix	150-161	12
α-helix	170-182	13
α-helix	190-203	14
α-helix	220-223	4
α-helix	231-241	11
α-helix	249-256	8
α-helix	265-273	9
α-helix	277-283	7
β-strand	291-292	2	132
α-helix	293-299	7
α-helix	304-317	14
β-strand	323-325	3	132
α-helix	326-328	3
β-strand	330-332	3	132
α-helix	343-345	3
α-helix	346-370	25
α-helix	372-375	4

Chain A: 21 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	27-35	9
α-helix	42-62	21
α-helix	72-74	3
α-helix	75-80	6
α-helix	81-85	5
α-helix	86-90	5
β-strand	96-97	2	1
β-strand	101-103	3	2
β-strand	112-113	2	2
α-helix	131-133	3
β-strand	142	1	1
β-strand	149	1	1
α-helix	181-196	16
α-helix	198-203	6
β-strand	211-214	4	3
α-helix	226-230	5
α-helix	242-245	4
α-helix	252-266	15
β-strand	272	1	3
β-strand	275	1	3
α-helix	277-279	3
α-helix	285-288	4
α-helix	295-304	10
β-strand	317-320	4	3
α-helix	329-332	4
β-strand	339-341	3	3
α-helix	348-359	12
β-strand	364	1	4
α-helix	370-376	7
α-helix	382-398	17
β-strand	404	1	4
α-helix	406-420	15
α-helix	427-431	5
β-strand	432	1	5

Chain b: 7 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	140
β-strand	13	1	141
α-helix	14-16	3
α-helix	25-43	19
β-strand	48-52	5	140
β-strand	55	1	142
β-strand	65	1	140
α-helix	69-75	7
β-strand	82	1	141
β-strand	84	1	142
α-helix	87-97	11
β-strand	106-113	8	140
α-helix	121-132	12
β-strand	137-142	6	140
α-helix	151-160	10
β-strand	171	1	140
α-helix	181-185	5

Chain B: 22 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	33-38	6
α-helix	59-84	26
α-helix	94-102	9
β-strand	107-114	8	1
β-strand	120	1	7
β-strand	122-124	3	1
β-strand	130-132	3	1
β-strand	134	1	7
β-strand	135	1	1
β-strand	149-152	4	1
β-strand	159-162	4	1
α-helix	163-164	2
α-helix	169-173	5
β-strand	175	1	8
α-helix	184-186	3
α-helix	191-197	7
α-helix	198-202	5
α-helix	203-206	4
α-helix	209-212	4
α-helix	217-219	3
β-strand	221-225	5	8
α-helix	232-241	10
β-strand	247-251	5	8
α-helix	252-255	4
α-helix	262-276	15
β-strand	281-285	5	8
α-helix	287-289	3
α-helix	303-316	14
β-strand	326-330	5	8
α-helix	339-342	4
β-strand	349-352	4	8
α-helix	354-356	3
α-helix	360-368	9
β-strand	374	1	9
α-helix	380-386	7
α-helix	392-408	17
β-strand	414	1	9
α-helix	416-427	12
β-strand	439	1	10

Chain c: 10 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	31-34	4	143
α-helix	35-47	13
β-strand	54-60	7	143
β-strand	67-71	5	143
β-strand	74	1	143
α-helix	89-100	12
β-strand	108-114	7	143
α-helix	124-136	13
β-strand	141-145	5	143
β-strand	157-162	6	143
α-helix	189-193	5
β-strand	196	1	143
β-strand	200-203	4	143
β-strand	205-208	4	143
α-helix	214-221	8
α-helix	226-229	4
α-helix	237-261	25
α-helix	267-270	4
α-helix	279-283	5
α-helix	286-308	23

Chain C: 17 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	14-16	3
α-helix	17-21	5
α-helix	22-66	45
α-helix	69-70	2
β-strand	71-76	6	1
β-strand	84-88	5	1
β-strand	94-99	6	1
β-strand	112-116	5	1
β-strand	122-127	6	1
α-helix	155-170	16
α-helix	173-178	6
α-helix	181-183	3
β-strand	185-189	5	16
α-helix	198-205	8
β-strand	210-215	6	16
α-helix	226-240	15
β-strand	244-249	6	16
α-helix	269-279	11
β-strand	289-294	6	16
β-strand	313-316	4	16
α-helix	318-320	3
α-helix	322-332	11
α-helix	338-339	2
α-helix	344-348	5
α-helix	359-372	14
α-helix	380-390	11
α-helix	400-404	5

Chain d: 15 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	17-29	13
α-helix	42-64	23
α-helix	68-81	14
α-helix	90-92	3
α-helix	95-108	14
α-helix	112-116	5
α-helix	131-144	14
α-helix	148-153	6
α-helix	154-156	3
α-helix	164-182	19
β-strand	188-189	2	6
α-helix	191-193	3
α-helix	194-198	5
α-helix	206-212	7
β-strand	222-223	2	6
α-helix	224-226	3
α-helix	240-253	14

Chain D: 16 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	42-80	39
α-helix	87	1
β-strand	88-97	10	20
β-strand	100-105	6	20
β-strand	106	1	21
β-strand	108	1	21
β-strand	111-112	2	1
β-strand	113-114	2	20
β-strand	128-132	5	20
β-strand	139-142	4	20
α-helix	143-144	2
α-helix	164-166	3
α-helix	171-177	7
α-helix	178-182	5
α-helix	183-186	4
α-helix	188-194	7
β-strand	201-205	5	22
α-helix	212-222	11
β-strand	226-230	5	22
α-helix	242-256	15
β-strand	260-264	5	22
β-strand	272	1	23
α-helix	282-297	16
β-strand	305-311	7	22
β-strand	317	1	23
α-helix	319-322	4
β-strand	329-332	4	22
α-helix	341-350	10
α-helix	360-363	4
α-helix	372-388	17
α-helix	398-407	10

38 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 proteasome regulatory subunit 8	C	protein	398	Homo sapiens	P62195 (AlphaFold model)
26S proteasome regulatory subunit 6B	D	protein	418	Homo sapiens	P43686 (AlphaFold model)
Proteasome 26S subunit, ATPase 6	E	protein	403	Homo sapiens	A0A087X2I1
Proteasome subunit alpha type-6	G, g	protein	245	Homo sapiens	P60900
Proteasome subunit alpha type-2	H, h	protein	233	Homo sapiens	P25787
Proteasome subunit alpha type-4	I, i	protein	260	Homo sapiens	P25789
Proteasome subunit alpha type-7	J, j	protein	247	Homo sapiens	O14818
Isoform Long of Proteasome subunit alpha type-1	L, l	protein	268	Homo sapiens	P25786
Proteasome subunit alpha type-3	M, m	protein	254	Homo sapiens	P25788
Proteasome subunit beta type-6	N, n	protein	238	Homo sapiens	P28072

21 more molecules are not listed.

Sequence of entity 1 (A), FASTA

>9U3L_1 26S proteasome regulatory subunit 7 (chains A)
MPDYLGADQRKTKEDEKDDKPIRALDEGDIALLKTYGQSTYSRQIKQVEDDIQQLLKKIN
ELTGIKESDTGLAPPALWDLAADKQTLQSEQPLQVARCTKIINADSEDPKYIINVKQFAK
FVVDLSDQVAPTDIEEGMRVGVDRNKYQIHIPLPPKIDPTVTMMQVEEKPDVTYSDVGGC
KEQIEKLREVVETPLLHPERFVNLGIEPPKGVLLFGPPGTGKTLCARAVANRTDACFIRV
IGSELVQKYVGEGARMVRELFEMARTKKACLIFFDEIDAIGGARFDDGAGGDNEVQRTML
ELINQLDGFDPRGNIKVLMATNRPDTLDPALMRPGRLDRKIEFSLPDLEGRTHIFKIHAR
SMSVERDIRFELLARLCPNSTGAEIRSVCTEAGMFAIRARRKIATEKDFLEAVNKVIKSY
AKFSATPRYMTYN

Sequence of entity 2 (B), FASTA

>9U3L_2 26S proteasome regulatory subunit 4 (chains B)
MGQSQSGGHGPGGGKKDDKDKKKKYEPPVPTRVGKKKKKTKGPDAASKLPLVTPHTQCRL
KLLKLERIKDYLLMEEEFIRNQEQMKPLEEKQEEERSKVDDLRGTPMSVGTLEEIIDDNH
AIVSTSVGSEHYVSILSFVDKDLLEPGCSVLLNHKVHAVIGVLMDDTDPLVTVMKVEKAP
QETYADIGGLDNQIQEIKESVELPLTHPEYYEEMGIKPPKGVILYGPPGTGKTLLAKAVA
NQTSATFLRVVGSELIQKYLGDGPKLVRELFRVAEEHAPSIVFIDEIDAIGTKRYDSNSG
GEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDEKT
KKRIFQIHTSRMTLADDVTLDDLIMAKDDLSGADIKAICTEAGLMALRERRMKVTNEDFK
KSKENVLYKKQEGTPEGLYL

Sequence of entity 3 (C), FASTA

>9U3L_3 26S proteasome regulatory subunit 8 (chains C)
MELEEGKAGSGLRQYYLSKIEELQLIVNDKSQNLRRLQAQRNELNAKVRLLREELQLLQE
QGSYVGEVVRAMDKKKVLVKVHPEGKFVVDVDKNIDINDVTPNCRVALRNDSYTLHKILP
NKVDPLVSLMMVEKVPDSTYEMIGGLDKQIKEIKEVIELPVKHPELFEALGIAQPKGVLL
YGPPGTGKTLLARAVAHHTDCTFIRVSGSELVQKFIGEGARMVRELFVMAREHAPSIIFM
DEIDSIGSSRLEGGSGGDSEVQRTMLELLNQLDGFEATKNIKVIMATNRIDILDSALLRP
GRIDRKIEFPPPNEEARLDILKIHSRKMNLTRGINLRKIAELMPGASGAEVKGVCTEAGM
YALRERRVHVTQEDFEMAVAKVMQKDSEKNMSIKKLWK

Sequence of entity 4 (D), FASTA

>9U3L_4 26S proteasome regulatory subunit 6B (chains D)
MEEIGILVEKAQDEIPALSVSRPQTGLSFLGPEPEDLEDLYSRYKKLQQELEFLEVQEEY
IKDEQKNLKKEFLHAQEEVKRIQSIPLVIGQFLEAVDQNTAIVGSTTGSNYYVRILSTID
RELLKPNASVALHKHSNALVDVLPPEADSSIMMLTSDQKPDVMYADIGGMDIQKQEVREA
VELPLTHFELYKQIGIDPPRGVLMYGPPGCGKTMLAKAVAHHTTAAFIRVVGSEFVQKYL
GEGPRMVRDVFRLAKENAPAIIFIDEIDAIATKRFDAQTGADREVQRILLELLNQMDGFD
QNVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLIFSTITSKMNLSEEVDL
EDYVARPDKISGADINSICQESGMLAVRENRYIVLAKDFEKAYKTVIKKDEQEHEFYK

Sequence of entity 5 (E), FASTA

>9U3L_5 Proteasome 26S subunit, ATPase 6 (chains E)
MAIPGIPYERRLLIMADPRDKALQDYRKKLLEHKEIDGRLKELREQLKELTKQYEKSEND
LKALQSVGQIVGEVLKQLTEEKFIVKATNGPRYVVGCRRQLDKSKLKPGTRVALDMTTLT
IMRYLPREVDPLVYNMSHEDPGNVSYSEIGGLSEQIRELREVIELPLTNPELFQRVGIIP
PKGCLLYGPPGTGKTLLARAVASQLDCNFLKVVSSSIVDKYIGESARLIREMFNYARDHQ
PCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQMDGFDTLHRVKMIMATNRPDTLD
PALLRPGRLDRKIHIDLPNEQARLDILKIHAGPITKHGEIDYEAIVKLSDGFNGADLRNV
CTEAGMFAIRADHDFVVQEDFMKAVRKVADSKKLESKLDYKPV

Sequence of entity 6 (G, g), FASTA

>9U3L_6 Proteasome subunit alpha type-6 (chains G, g)
SRGSSAGFDRHITIFSPEGRLYQVEYAFKAINQGGLTSVAVRGKDCAVIVTQKKVPDKLL
DSSTVTHLFKITENIGCVMTGMTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKRIADI
SQVYTQNAEMRPLGCCMILIGIDEEQGPQVYKCDPAGYYCGFKATAAGVKQTESTSFLEK
KVKKKFDWTFEQTVETAITCLSTVLSIDFKPSEIEVGVVTVENPKFRILTEAEIDAHLVA
LAERD

Sequence of entity 7 (H, h), FASTA

>9U3L_7 Proteasome subunit alpha type-2 (chains H, h)
AERGYSFSLTTFSPSGKLVQIEYALAAVAGGAPSVGIKAANGVVLATEKKQKSILYDERS
VHKVEPITKHIGLVYSGMGPDYRVLVHRARKLAQQYYLVYQEPIPTAQLVQRVASVMQEY
TQSGGVRPFGVSLLICGWNEGRPYLFQSDPSGAYFAWKATAMGKNYVNGKTFLEKRYNED
LELEDAIHTAILTLKESFEGQMTEDNIEVGICNEAGFRRLTPTEVKDYLAAIA

Sequence of entity 8 (I, i), FASTA

>9U3L_8 Proteasome subunit alpha type-4 (chains I, i)
SRRYDSRTTIFSPEGRLYQVEYAMEAIGHAGTCLGILANDGVLLAAERRNIHKLLDEVFF
SEKIYKLNEDMACSVAGITSDANVLTNELRLIAQRYLLQYQEPIPCEQLVTALCDIKQAY
TQFGGKRPFGVSLLYIGWDKHYGFQLYQSDPSGNYGGWKATCIGNNSAAAVSMLKQDYKE
GEMTLKSALALAIKVLNKTMDVSKLSAEKVEIATLTRENGKTVIRVLKQKEVEQLIKKHE
EEEAKAEREKKEKEQKEKDK

Sequence of entity 9 (J, j), FASTA

>9U3L_9 Proteasome subunit alpha type-7 (chains J, j)
SYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVEKKSVAKLQDERTVRK
ICALDDNVCMAFAGLTADARIVINRARVECQSHRLTVEDPVTVEYITRYIASLKQRYTQS
NGRRPFGISALIVGFDFDGTPRLYQTDPSGTYHAWKANAIGRGAKSVREFLEKNYTDEAI
ETDDLTIKLVIKALLEVVQSGGKNIELAVMRRDQSLKILNPEEIEKYVAEIEKEKEENEK
KKQKKAS

Sequence of entity 10 (L, l), FASTA

>9U3L_10 Isoform Long of Proteasome subunit alpha type-1 (chains L, l)
QLSKVKFRNQYDNDVTVWSPQGRIHQIEYAMEAVKQGSATVGLKSKTHAVLVALKRAQSE
LAAHQKKILHVDNHIGISIAGLTADARLLCNFMRQECLDSRFVFDRPLPVSRLVSLIGSK
TQIPTQRYGRRPYGVGLLIAGYDDMGPHIFQTCPSANYFDCRAMSIGARSQSARTYLERH
MSEFMECNLNELVKHGLRALRETLPAEQDLTTKNVSIGIVGKDLEFTIYDDDDVSPFLEG
LEERPQRKAQPAQPADEPAEKADEPMEH

Sequence of entity 11 (M, m), FASTA

>9U3L_11 Proteasome subunit alpha type-3 (chains M, m)
SSIGTGYDLSASTFSPDGRVFQVEYAMKAVENSSTAIGIRCKDGVVFGVEKLVLSKLYEE
GSNKRLFNVDRHVGMAVAGLLADARSLADIAREEASNFRSNFGYNIPLKHLADRVAMYVH
AYTLYSAVRPFGCSFMLGSYSVNDGAQLYMIDPSGVSYGYWGCAIGKARQAAKTEIEKLQ
MKEMTCRDIVKEVAKIIYIVHDEVKDKAFELELSWVGELTNGRHEIVPKDIREEAEKYAK
ESLKEEDESDDDNM

Sequence of entity 12 (N, n), FASTA

>9U3L_12 Proteasome subunit beta type-6 (chains N, n)
AATLLAARGAGPAPAWGPEAFTPDWESREVSTGTTIMAVQFDGGVVLGADSRTTTGSYIA
NRVTDKLTPIHDRIFCCRSGSAADTQAVADAVTYQLGFHSIELNEPPLVHTAASLFKEMC
YRYREDLMAGIIIAGWDPQEGGQVYSVPMGGMMVRQSFAIGGSGSSYIYGYVDATYREGM
TKEECLQFTANALALAMERDGSSGGVIRLAAIAESGVERQVLLGDQIPKFAVATLPPA

Ligands and cofactors

ID	Name	Formula	Copies
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	3
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	3
MG	Magnesium ion	Mg	3
LDZ	N-[(benzyloxy)carbonyl]-L-leucyl-N-[(2S)-4-methyl-1-oxopentan-2-yl]-L-leucinami…	C26 H41 N3 O5	6
ZN	Zinc ion	Zn	1

Primary citation

Structural dynamics of the midnolin-proteasome during ubiquitin-independent substrate turnover. Zhu, C., Qin, L., Dai, Z. et al. Nat Commun (2026) 17. DOI 10.1038/s41467-026-71002-0 · 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…
9NKI 2.94 Å, Structure of substrate engaged MIDN-bound human 26S proteasome, EB MIDN_UBL state…

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