9MBP: Substrate-engaged human 26S proteasome

Substrate-engaged human 26S proteasome bound to midnolin with RPT1 at top of spiral staircase. Determined by electron microscopy at 2.75 Å resolution. Released 25 Mar 2026.

Method: Electron microscopy
Resolution: 2.75 Å
Organism: Homo sapiens
Chains: 48
Atoms: 105,160
Mol. weight: 1717.62 kDa
Ligands: ZN, ATP, LDZ, ADP
Released: 25 Mar 2026

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

Secondary structure: helices and β-sheets

9MBP contains 587 α-helices and 553 β-strands across 48 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, 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	35-44	10
α-helix	54-67	14
α-helix	73-87	15
α-helix	92-102	11
α-helix	109-122	14
α-helix	131-140	10
α-helix	150-162	13
α-helix	169-182	14
α-helix	190-205	16
α-helix	215-217	3
α-helix	231-242	12
α-helix	247-256	10
α-helix	265-283	19
β-strand	290-292	3	17
α-helix	293-300	8
α-helix	304-317	14
β-strand	320-325	6	17
β-strand	330-335	6	17
α-helix	343-370	28

Chain A: 21 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	27-35	9
α-helix	42-62	21
α-helix	75-79	5
α-helix	84-90	7
β-strand	96-104	9	62
β-strand	111-114	4	62
β-strand	120-125	6	62
β-strand	139-142	4	62
β-strand	148-152	5	62
α-helix	154-156	3
α-helix	159-163	5
β-strand	165	1	63
α-helix	174-176	3
α-helix	181-191	11
α-helix	199-202	4
β-strand	211-215	5	63
α-helix	222-231	10
β-strand	236-240	5	63
α-helix	252-266	15
β-strand	270-275	6	63
α-helix	277-279	3
α-helix	293-306	14
β-strand	315-321	7	63
α-helix	324-326	3
α-helix	329-332	4
β-strand	339-342	4	63
α-helix	348-359	12
β-strand	364	1	64
α-helix	370-375	6
α-helix	382-398	17
β-strand	404	1	64
α-helix	406-413	8
α-helix	414-418	5
α-helix	427-429	3
β-strand	432	1	65

Chain b: 5 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	42
β-strand	13	1	43
α-helix	25-43	19
β-strand	48-53	6	42
β-strand	55	1	44
β-strand	65	1	42
α-helix	69-75	7
β-strand	82	1	43
β-strand	84	1	44
α-helix	87-98	12
β-strand	106-113	8	42
α-helix	121-134	14
β-strand	137-142	6	42
α-helix	151-160	10
β-strand	171	1	42

Chain B: 19 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	59-82	24
α-helix	96-102	7
β-strand	107-111	5	69
β-strand	115-116	2	70
β-strand	120-121	2	70
α-helix	123	1
β-strand	124-125	2	69
β-strand	129-130	2	69
β-strand	131-132	2	62
β-strand	133-134	2	70
β-strand	135	1	69
β-strand	149-152	4	69
β-strand	159-162	4	69
α-helix	169-173	5
β-strand	175	1	71
α-helix	184-186	3
α-helix	191-201	11
α-helix	203-206	4
α-helix	209-212	4
β-strand	221-225	5	71
α-helix	232-242	11
β-strand	246-250	5	71
α-helix	253-255	3
β-strand	259	1	72
α-helix	260-262	3
α-helix	263-277	15
β-strand	280-284	5	71
α-helix	287-289	3
α-helix	300-316	17
β-strand	325-331	7	71
β-strand	349-352	4	71
α-helix	354-356	3
α-helix	358-368	11
β-strand	374	1	73
α-helix	381-384	4
α-helix	392-408	17
β-strand	414	1	73
α-helix	416-426	11
β-strand	439	1	74

Chain c: 12 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	30-34	5	49
α-helix	35-47	13
β-strand	54-60	7	49
β-strand	66-74	9	49
α-helix	75-77	3
α-helix	89-101	13
β-strand	107-114	8	49
α-helix	125-136	12
β-strand	141-145	5	49
β-strand	157-162	6	49
α-helix	163-164	2
α-helix	185-188	4
α-helix	189-194	6
β-strand	196	1	49
β-strand	200-203	4	49
β-strand	205-208	4	49
α-helix	214-217	4
α-helix	227-229	3
α-helix	236-259	24
α-helix	267-273	7
α-helix	282-308	27

Chain C: 22 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	14-16	3
α-helix	17-21	5
α-helix	22-66	45
β-strand	71-79	9	69
β-strand	85-88	4	69
β-strand	94-99	6	69
α-helix	100	1
α-helix	105-107	3
β-strand	113-116	4	69
β-strand	122-126	5	69
α-helix	133-136	4
β-strand	139	1	77
α-helix	143-144	2
α-helix	148-150	3
α-helix	156-165	10
α-helix	167-170	4
α-helix	172-178	7
α-helix	180-183	4
β-strand	185-189	5	77
α-helix	196-205	10
β-strand	210-214	5	77
β-strand	223	1	78
α-helix	226-240	15
β-strand	244-249	6	77
α-helix	267-280	14
β-strand	289-295	7	77
β-strand	313-316	4	77
α-helix	318-320	3
α-helix	322-332	11
α-helix	338-339	2
α-helix	344-349	6
α-helix	357-372	16
α-helix	380-390	11
α-helix	400-404	5

Chain d: 12 helices, 0 β-strands

Element	Residues	Length
α-helix	17-29	13
α-helix	45-65	21
α-helix	68-82	15
α-helix	95-108	14
α-helix	112-119	8
α-helix	131-145	15
α-helix	148-154	7
α-helix	164-178	15
α-helix	179-181	3
α-helix	191-197	7
α-helix	205-213	9
α-helix	239-254	16

Chain D: 16 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	40-80	41
α-helix	81-83	3
β-strand	88-97	10	69
β-strand	100-105	6	69
β-strand	110-113	4	69
β-strand	129-132	4	69
β-strand	139-142	4	69
β-strand	153	1	82
α-helix	164-166	3
α-helix	172-181	10
α-helix	183-186	4
α-helix	189-194	6
β-strand	201-205	5	82
α-helix	212-222	11
β-strand	226-231	6	82
α-helix	232-235	4
β-strand	239	1	83
α-helix	242-256	15
β-strand	260-265	6	82
α-helix	267-269	3
β-strand	272	1	84
α-helix	273-274	2
α-helix	282-296	15
β-strand	305-311	7	82
β-strand	317	1	84
β-strand	329-332	4	82
α-helix	340-348	9
β-strand	354	1	85
α-helix	361-364	4
α-helix	372-388	17
β-strand	394	1	85
α-helix	397-407	11

40 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 non-ATPase regulatory subunit 1	U	protein	953	Homo sapiens	Q99460 (AlphaFold model)
26S proteasome non-ATPase regulatory subunit 3	V	protein	533	Homo sapiens	O43242 (AlphaFold model)
26S proteasome non-ATPase regulatory subunit 12	W	protein	456	Homo sapiens	O00232 (AlphaFold model)
26S proteasome non-ATPase regulatory subunit 11	X	protein	422	Homo sapiens	O00231 (AlphaFold model)
26S proteasome non-ATPase regulatory subunit 6	Y	protein	389	Homo sapiens	Q15008
26S proteasome non-ATPase regulatory subunit 7	Z	protein	324	Homo sapiens	P51665
26S proteasome non-ATPase regulatory subunit 13	a	protein	376	Homo sapiens	Q9UNM6
26S proteasome non-ATPase regulatory subunit 4	b	protein	377	Homo sapiens	P55036
26S proteasome non-ATPase regulatory subunit 14	c	protein	309	Homo sapiens	O00487
26S proteasome non-ATPase regulatory subunit 8	d	protein	349	Homo sapiens	P48556
26S proteasome complex subunit SEM1	e	protein	70	Homo sapiens	P60896
26S proteasome regulatory subunit 7	A	protein	433	Homo sapiens	P35998

22 more molecules are not listed.

Sequence of entity 1 (U), FASTA

>9MBP_1 26S proteasome non-ATPase regulatory subunit 1 (chains U)
MITSAAGIISLLDEDEPQLKEFALHKLNAVVNDFWAEISESVDKIEVLYEDEGFRSRQFA
ALVASKVFYHLGAFEESLNYALGAGDLFNVNDNSEYVETIIAKCIDHYTKQCVENADLPE
GEKKPIDQRLEGIVNKMFQRCLDDHKYKQAIGIALETRRLDVFEKTILESNDVPGMLAYS
LKLCMSLMQNKQFRNKVLRVLVKIYMNLEKPDFINVCQCLIFLDDPQAVSDILEKLVKED
NLLMAYQICFDLYESASQQFLSSVIQNLRTVGTPIASVPGSTNTGTVPGSEKDSDSMETE
EKTSSAFVGKTPEASPEPKDQTLKMIKILSGEMAIELHLQFLIRNNNTDLMILKNTKDAV
RNSVCHTATVIANSFMHCGTTSDQFLRDNLEWLARATNWAKFTATASLGVIHKGHEKEAL
QLMATYLPKDTSPGSAYQEGGGLYALGLIHANHGGDIIDYLLNQLKNASNDIVRHGGSLG
LGLAAMGTARQDVYDLLKTNLYQDDAVTGEAAGLALGLVMLGSKNAQAIEDMVGYAQETQ
HEKILRGLAVGIALVMYGRMEEADALIESLCRDKDPILRRSGMYTVAMAYCGSGNNKAIR
RLLHVAVSDVNDDVRRAAVESLGFILFRTPEQCPSVVSLLSESYNPHVRYGAAMALGICC
AGTGNKEAINLLEPMTNDPVNYVRQGALIASALIMIQQTEITCPKVNQFRQLYSKVINDK
HDDVMAKFGAILAQGILDAGGHNVTISLQSRTGHTHMPSVVGVLVFTQFWFWFPLSHFLS
LAYTPTCVIGLNKDLKMPKVQYKSNCKPSTFAYPAPLEVPKEKEKEKVSTAVLSITAKAK
KKEKEKEKKEEEKMEVDEAEKKEEKEKKKEPEPNFQLLDNPARVMPAQLKVLTMPETCRY
QPFKPLSIGGIIILKDTSEDIEELVEPVAAHGPKIEEEEQEPEPPEPFEYIDD

Sequence of entity 2 (V), FASTA

>9MBP_2 26S proteasome non-ATPase regulatory subunit 3 (chains V)
KQEGSARRRGADKAKPPPGGGEQEPPPPPAPQDVEMKEEAATGGGSTGEADGKTAAAAAE
HSQRELDTVTLEDIKEHVKQLEKAVSGKEPRFVLRALRMLPSTSRRLNHYVLYKAVQGFF
TSNNATRDFLLPFLEEPMDTEADLQFRPRTGKAASTPLLPEVEAYLQLLVVIFMMNSKRY
KEAQKISDDLMQKISTQNRRALDLVAAKCYYYHARVYEFLDKLDVVRSFLHARLRTATLR
HDADGQATLLNLLLRNYLHYSLYDQAEKLVSKSVFPEQANNNEWARYLYYTGRIKAIQLE
YSEARRTMTNALRKAPQHTAVGFKQTVHKLLIVVELLLGEIPDRLQFRQPSLKRSLMPYF
LLTQAVRTGNLAKFNQVLDQFGEKFQADGTYTLIIRLRHNVIKTGVRMISLSYSRISLAD
IAQKLQLDSPEDAEFIVAKAIRDGVIEASINHEKGYVQSKEMIDIYSTREPQLAFHQRIS
FCLDIHNMSVKAMRFPPKSYNKDLESAEERREREQQDLEFAKEMAEDDDDSFP

Sequence of entity 3 (W), FASTA

>9MBP_3 26S proteasome non-ATPase regulatory subunit 12 (chains W)
MADGGSERADGRIVKMEVDYSATVDQRLPECAKLAKEGRLQEVIETLLSLEKQTRTASDM
VSTSRILVAVVKMCYEAKEWDLLNENIMLLSKRRSQLKQAVAKMVQQCCTYVEEITDLPI
KLRLIDTLRMVTEGKIYVEIERARLTKTLATIKEQNGDVKEAASILQELQVETYGSMEKK
ERVEFILEQMRLCLAVKDYIRTQIISKKINTKFFQEENTEKLKLKYYNLMIQLDQHEGSY
LSICKHYRAIYDTPCIQAESEKWQQALKSVVLYVILAPFDNEQSDLVHRISGDKKLEEIP
KYKDLLKLFTTMELMRWSTLVEDYGMELRKGSLESPATDVFGSTEEGEKRWKDLKNRVVE
HNIRIMAKYYTRITMKRMAQLLDLSVDESEAFLSNLVVNKTIFAKVDRLAGIINFQRPKD
PNNLLNDWSQKLNSLMSLVNKTTHLIAKEEMIHNLQ

Sequence of entity 4 (X), FASTA

>9MBP_4 26S proteasome non-ATPase regulatory subunit 11 (chains X)
MAAAAVVEFQRAQSLLSTDREASIDILHSIVKRDIQENDEEAVQVKEQSILELGSLLAKT
GQAAELGGLLKYVRPFLNSISKAKAARLVRSLLDLFLDMEAATGQEVELCLECIEWAKSE
KRTFLRQALEARLVSLYFDTKRYQEALHLGSQLLRELKKMDDKALLVEVQLLESKTYHAL
SNLPKARAALTSARTTANAIYCPPKLQATLDMQSGIIHAAEEKDWKTAYSYFYEAFEGYD
SIDSPKAITSLKYMLLCKIMLNTPEDVQALVSGKLALRYAGRQTEALKCVAQASKNRSLA
DFEKALTDYRAELRDDPIISTHLAKLYDNLLEQNLIRVIEPFSRVQIEHISSLIKLSKAD
VERKLSQMILDKKFHGILDQGEGVLIIFDEPPVDKTYEAALETIQNMSKVVDSLYNKAKK
LT

Sequence of entity 5 (Y), FASTA

>9MBP_5 26S proteasome non-ATPase regulatory subunit 6 (chains Y)
MPLENLEEEGLPKNPDLRIAQLRFLLSLPEHRGDAAVRDELMAAVRDNNMAPYYEALCKS
LDWQIDVDLLNKMKKANEDELKRLDEELEDAEKNLGESEIRDAMMAKAEYLCRIGDKEGA
LTAFRKTYDKTVALGHRLDIVFYLLRIGLFYMDNDLITRNTEKAKSLIEEGGDWDRRNRL
KVYQGLYCVAIRDFKQAAELFLDTVSTFTSYELMDYKTFVTYTVYVSMIALERPDLREKV
IKGAEILEVLHSLPAVRQYLFSLYECRYSVFFQSLAVVEQEMKKDWLFAPHYRYYVREMR
IHAYSQLLESYRSLTLGYMAEAFGVGVEFIDQELSRFIAAGRLHCKIDKVNEIVETNRPD
SKNWQYQETIKKGDLLLNRVQKLSRVINM

Sequence of entity 6 (Z), FASTA

>9MBP_6 26S proteasome non-ATPase regulatory subunit 7 (chains Z)
MPELAVQKVVVHPLVLLSVVDHFNRIGKVGNQKRVVGVLLGSWQKKVLDVSNSFAVPFDE
DDKDDSVWFLDHDYLENMYGMFKKVNARERIVGWYHTGPKLHKNDIAINELMKRYCPNSV
LVIIDVKPKDLGLPTEAYISVEEVHDDGTPTSKTFEHVTSEIGAEEAEEVGVEHLLRDIK
DTTVGTLSQRITNQVHGLKGLNSKLLDIRSYLEKVATGKLPINHQIIYQLQDVFNLLPDV
SLQEFVKAFYLKTNDQMVVVYLASLIRSVVALHNLINNKIANRDAEKKEGQEKEESKKDR
KEDKEKDKDKEKSDVKKEEKKEKK

Sequence of entity 7 (a), FASTA

>9MBP_7 26S proteasome non-ATPase regulatory subunit 13 (chains a)
MKDVPGFLQQSQNSGPGQPAVWHRLEELYTKKLWHQLTLQVLDFVQDPCFAQGDGLIKLY
ENFISEFEHRVNPLSLVEIILHVVRQMTDPNVALTFLEKTREKVKSSDEAVILCKTAIGA
LKLNIGDLQVTKETIEDVEEMLNNLPGVTSVHSRFYDLSSKYYQTIGNHASYYKDALRFL
GCVDIKDLPVSEQQERAFTLGLAGLLGEGVFNFGELLMHPVLESLRNTDRQWLIDTLYAF
NSGNVERFQTLKTAWGQQPDLAANEAQLLRKIQLLCLMEMTFTRPANHRQLTFEEIAKSA
KITVNEVELLVMKALSVGLVKGSIDEVDKRVHMTWVQPRVLDLQQIKGMKDRLEFWCTDV
KSMEMLVEHQAHDILT

Sequence of entity 8 (b), FASTA

>9MBP_8 26S proteasome non-ATPase regulatory subunit 4 (chains b)
MVLESTMVCVDNSEYMRNGDFLPTRLQAQQDAVNIVCHSKTRSNPENNVGLITLANDCEV
LTTLTPDTGRILSKLHTVQPKGKITFCTGIRVAHLALKHRQGKNHKMRIIAFVGSPVEDN
EKDLVKLAKRLKKEKVNVDIINFGEEEVNTEKLTAFVNTLNGKDGTGSHLVTVPPGPSLA
DALISSPILAGEGGAMLGLGASDFEFGVDPSADPELALALRVSMEEQRQRQEEEARRAAA
ASAAEAGIATTGTEDSDDALLKMTISQQEFGRTGLPDLSSMTEEEQIAYAMQMSLQGAEF
GQAESADIDASSAMDTSEPAKEEDDYDVMQDPEFLQSVLENLPGVDPNNEAIRNAMGSLA
SQATKDGKKDKKEEDKK

Sequence of entity 9 (c), FASTA

>9MBP_9 26S proteasome non-ATPase regulatory subunit 14 (chains c)
DRLLRLGGGMPGLGQGPPTDAPAVDTAEQVYISSLALLKMLKHGRAGVPMEVMGLMLGEF
VDDYTVRVIDVFAMPQSGTGVSVEAVDPVFQAKMLDMLKQTGRPEMVVGWYHSHPGFGCW
LSGVDINTQQSFEALSERAVAVVVDPIQSVKGKVVIDAFRLINANMMVLGHEPRQTTSNL
GHLNKPSIQALIHGLNRHYYSITINYRKNELEQKMLLNLHKKSWMEGLTLQDYSEHCKHN
ESVVKEMLELAKNYNKAVEEEDKMTPEQLAIKNVGKQDPKRHLEEHVDVLMTSNIVQCLA
AMLDTVVFK

Sequence of entity 10 (d), FASTA

>9MBP_10 26S proteasome non-ATPase regulatory subunit 8 (chains d)
FIKGRAPRAPPRERRRATRGGLRQVVAPPRALGSTSRPHFRRASVCRRRCRKSGGLLAAS
RKMAAAAVNGAAGFSSSGPAATSGAVLQAATGMYEQLKGEWNRKSPNLSKCGEELGRLKL
VLLELNFLPTTGTKLTKQQLILARDILEIGAQWSILRKDIPSFERYMAQLKCYYFDYKEQ
LPESAYMHQLLGLNLLFLLSQNRVAEFHTELERLPAKDIQTNVYIKHPVSLEQYLMEGSY
NKVFLAKGNIPAESYTFFIDILLDTIRDEIAGCIEKAYEKILFTEATRILFFNTPKKMTD
YAKKRGWVLGPNNYYSFASQQQKPEDTTIPSTELAKQVIEYARQLEMIV

Sequence of entity 11 (e), FASTA

>9MBP_11 26S proteasome complex subunit SEM1 (chains e)
MSEKKQPVDLGLLEEDDEFEEFPAEDWAGLDEDEDAHVWEDNWDDDNVEDDFSNQLRAEL
EKHGYKMETS

Sequence of entity 12 (A), FASTA

>9MBP_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
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	4
LDZ	N-[(benzyloxy)carbonyl]-L-leucyl-N-[(2S)-4-methyl-1-oxopentan-2-yl]-L-leucinami…	C26 H41 N3 O5	6
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	2
MG	Magnesium ion	Mg	5

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 Q99460 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5V1Y 1.42 Å, Crystal structure of the ternary RPN13 PRU-RPN2 (940-953)-ubiquitin complex
6OI4 1.76 Å, RPN13 (19-132)-RPN2 (940-952) pY950-Ub complex
5V1Z 2.0 Å, Crystal structure of the RPN13 PRU-RPN2 (932-953)-ubiquitin complex
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
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…

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