9BV2: M2B Midnolin-Proteasome

M2B Midnolin-Proteasome (translocating). Determined by electron microscopy at 3.4 Å resolution. Released 11 Jun 2025.

Method: Electron microscopy
Resolution: 3.4 Å
Organism: Homo sapiens
Chains: 40
Atoms: 88,606
Mol. weight: 1523.41 kDa
Ligands: ZN, ADP, ATP
Released: 11 Jun 2025

Explore 9BV2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9BV2 contains 496 α-helices and 441 β-strands across 40 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: 22 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	3-14	12
α-helix	21-31	11
α-helix	37-46	10
α-helix	54-59	6
α-helix	60-64	5
α-helix	65	1
α-helix	73-85	13
α-helix	90-103	14
α-helix	108-124	17
α-helix	128-142	15
α-helix	150-166	17
α-helix	169-182	14
α-helix	190-205	16
α-helix	220-222	3
α-helix	231-241	11
α-helix	245-255	11
α-helix	259-263	5
α-helix	265-283	19
α-helix	286-288	3
β-strand	290-292	3	22
α-helix	293-298	6
α-helix	307-317	11
β-strand	320-325	6	22
β-strand	330-336	7	22
α-helix	343-370	28

Chain A: 18 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	27-36	10
α-helix	42-61	20
α-helix	65-67	3
β-strand	72	1	65
α-helix	73-74	2
α-helix	81-88	8
β-strand	93-97	5	66
β-strand	98-100	3	67
α-helix	102-105	4
β-strand	111-113	3	67
β-strand	121-123	3	67
α-helix	131-134	4
β-strand	139-142	4	66
β-strand	149-151	3	66
α-helix	182-191	10
α-helix	193-196	4
α-helix	199-204	6
β-strand	212-213	2	68
α-helix	222-230	9
α-helix	254-265	12
β-strand	273	1	68
α-helix	294-306	13
β-strand	318-319	2	68
α-helix	348-359	12
β-strand	364	1	69
α-helix	370-376	7
α-helix	382-399	18
β-strand	404	1	69
α-helix	406-417	12
α-helix	430-432	3

Chain b: 8 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	4-11	8	45
α-helix	14-17	4
α-helix	25-42	18
β-strand	48-54	7	45
β-strand	59-65	7	45
α-helix	69-76	8
α-helix	86-99	14
β-strand	106-112	7	45
α-helix	121-133	13
β-strand	137-142	6	45
α-helix	146-161	16
β-strand	169-172	4	45
α-helix	179-184	6
α-helix	187-190	4

Chain B: 18 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	59-85	27
α-helix	95-102	8
β-strand	108-116	9	66
β-strand	120-124	5	66
β-strand	130-135	6	66
β-strand	139	1	65
β-strand	149-152	4	66
β-strand	159-161	3	66
α-helix	169-174	6
β-strand	175	1	74
α-helix	184-186	3
α-helix	191-201	11
α-helix	203-206	4
α-helix	210-213	4
α-helix	217-219	3
β-strand	221-225	5	74
α-helix	232-242	11
β-strand	246-251	6	74
α-helix	252-254	3
α-helix	262-276	15
β-strand	280-285	6	74
α-helix	287-289	3
β-strand	292	1	75
α-helix	301-315	15
β-strand	325-331	7	74
β-strand	337	1	75
β-strand	349-352	4	74
α-helix	354-356	3
α-helix	358-369	12
α-helix	382-385	4
α-helix	392-408	17
α-helix	416-426	11

Chain c: 11 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	26	1	50
β-strand	30-34	5	51
α-helix	35-46	12
β-strand	54-61	8	51
β-strand	66-74	9	51
α-helix	84-86	3
α-helix	89-102	14
β-strand	107-114	8	51
α-helix	124-136	13
β-strand	142-145	4	51
β-strand	157-162	6	51
α-helix	165-170	6
β-strand	176	1	50
α-helix	189-193	5
β-strand	200-208	9	51
α-helix	211-218	8
α-helix	222-224	3
α-helix	225-229	5
α-helix	234-265	32
α-helix	279-306	28

Chain C: 16 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	19-67	49
β-strand	71-78	8	66
β-strand	84-89	6	66
β-strand	94-98	5	66
β-strand	113-117	5	66
β-strand	123	1	66
α-helix	127-130	4
α-helix	148-150	3
α-helix	155-170	16
α-helix	172-178	7
α-helix	181-183	3
β-strand	185-189	5	80
α-helix	196-206	11
β-strand	210-215	6	80
α-helix	227-240	14
β-strand	244-249	6	80
α-helix	267-280	14
β-strand	289-295	7	80
α-helix	303-306	4
β-strand	313-316	4	80
α-helix	318-320	3
α-helix	323-333	11
α-helix	344-350	7
α-helix	356-372	17
α-helix	380-390	11
α-helix	400-403	4
β-strand	405	1	81

Chain d: 15 helices, 0 β-strands

Element	Residues	Length
α-helix	84-102	19
α-helix	110-125	16
α-helix	139-158	20
α-helix	161-177	17
α-helix	183-184	2
α-helix	189-202	14
α-helix	205-214	10
α-helix	217-222	6
α-helix	227-238	12
α-helix	241-247	7
α-helix	259-276	18
α-helix	284-290	7
α-helix	296-298	3
α-helix	317-320	4
α-helix	332-347	16

Chain D: 18 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	40-72	33
α-helix	75-82	8
β-strand	88-97	10	66
β-strand	100-105	6	66
β-strand	109-113	5	66
β-strand	115	1	66
α-helix	116	1
β-strand	128-132	5	66
β-strand	139-142	4	66
α-helix	143-144	2
α-helix	171-181	11
α-helix	183-186	4
α-helix	188-194	7
β-strand	202-205	4	82
α-helix	213-218	6
β-strand	226-231	6	82
α-helix	242-257	16
β-strand	260-265	6	82
α-helix	267-269	3
α-helix	281-296	16
β-strand	307-311	5	82
α-helix	320-322	3
β-strand	331-332	2	82
α-helix	334-336	3
α-helix	338-349	12
β-strand	354	1	83
α-helix	360-365	6
α-helix	372-388	17
β-strand	394	1	83
α-helix	396-407	12
α-helix	415-417	3

32 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	534	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	310	Homo sapiens	O00487
26S proteasome non-ATPase regulatory subunit 8	d	protein	350	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

21 more molecules are not listed.

Sequence of entity 1 (U), FASTA

>9BV2_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

>9BV2_2 26S proteasome non-ATPase regulatory subunit 3 (chains V)
MKQEGSARRRGADKAKPPPGGGEQEPPPPPAPQDVEMKEEAATGGGSTGEADGKTAAAAA
EHSQRELDTVTLEDIKEHVKQLEKAVSGKEPRFVLRALRMLPSTSRRLNHYVLYKAVQGF
FTSNNATRDFLLPFLEEPMDTEADLQFRPRTGKAASTPLLPEVEAYLQLLVVIFMMNSKR
YKEAQKISDDLMQKISTQNRRALDLVAAKCYYYHARVYEFLDKLDVVRSFLHARLRTATL
RHDADGQATLLNLLLRNYLHYSLYDQAEKLVSKSVFPEQANNNEWARYLYYTGRIKAIQL
EYSEARRTMTNALRKAPQHTAVGFKQTVHKLLIVVELLLGEIPDRLQFRQPSLKRSLMPY
FLLTQAVRTGNLAKFNQVLDQFGEKFQADGTYTLIIRLRHNVIKTGVRMISLSYSRISLA
DIAQKLQLDSPEDAEFIVAKAIRDGVIEASINHEKGYVQSKEMIDIYSTREPQLAFHQRI
SFCLDIHNMSVKAMRFPPKSYNKDLESAEERREREQQDLEFAKEMAEDDDDSFP

Sequence of entity 3 (W), FASTA

>9BV2_3 26S proteasome non-ATPase regulatory subunit 12 (chains W)
MADGGSERADGRIVKMEVDYSATVDQRLPECAKLAKEGRLQEVIETLLSLEKQTRTASDM
VSTSRILVAVVKMCYEAKEWDLLNENIMLLSKRRSQLKQAVAKMVQQCCTYVEEITDLPI
KLRLIDTLRMVTEGKIYVEIERARLTKTLATIKEQNGDVKEAASILQELQVETYGSMEKK
ERVEFILEQMRLCLAVKDYIRTQIISKKINTKFFQEENTEKLKLKYYNLMIQLDQHEGSY
LSICKHYRAIYDTPCIQAESEKWQQALKSVVLYVILAPFDNEQSDLVHRISGDKKLEEIP
KYKDLLKLFTTMELMRWSTLVEDYGMELRKGSLESPATDVFGSTEEGEKRWKDLKNRVVE
HNIRIMAKYYTRITMKRMAQLLDLSVDESEAFLSNLVVNKTIFAKVDRLAGIINFQRPKD
PNNLLNDWSQKLNSLMSLVNKTTHLIAKEEMIHNLQ

Sequence of entity 4 (X), FASTA

>9BV2_4 26S proteasome non-ATPase regulatory subunit 11 (chains X)
MAAAAVVEFQRAQSLLSTDREASIDILHSIVKRDIQENDEEAVQVKEQSILELGSLLAKT
GQAAELGGLLKYVRPFLNSISKAKAARLVRSLLDLFLDMEAATGQEVELCLECIEWAKSE
KRTFLRQALEARLVSLYFDTKRYQEALHLGSQLLRELKKMDDKALLVEVQLLESKTYHAL
SNLPKARAALTSARTTANAIYCPPKLQATLDMQSGIIHAAEEKDWKTAYSYFYEAFEGYD
SIDSPKAITSLKYMLLCKIMLNTPEDVQALVSGKLALRYAGRQTEALKCVAQASKNRSLA
DFEKALTDYRAELRDDPIISTHLAKLYDNLLEQNLIRVIEPFSRVQIEHISSLIKLSKAD
VERKLSQMILDKKFHGILDQGEGVLIIFDEPPVDKTYEAALETIQNMSKVVDSLYNKAKK
LT

Sequence of entity 5 (Y), FASTA

>9BV2_5 26S proteasome non-ATPase regulatory subunit 6 (chains Y)
MPLENLEEEGLPKNPDLRIAQLRFLLSLPEHRGDAAVRDELMAAVRDNNMAPYYEALCKS
LDWQIDVDLLNKMKKANEDELKRLDEELEDAEKNLGESEIRDAMMAKAEYLCRIGDKEGA
LTAFRKTYDKTVALGHRLDIVFYLLRIGLFYMDNDLITRNTEKAKSLIEEGGDWDRRNRL
KVYQGLYCVAIRDFKQAAELFLDTVSTFTSYELMDYKTFVTYTVYVSMIALERPDLREKV
IKGAEILEVLHSLPAVRQYLFSLYECRYSVFFQSLAVVEQEMKKDWLFAPHYRYYVREMR
IHAYSQLLESYRSLTLGYMAEAFGVGVEFIDQELSRFIAAGRLHCKIDKVNEIVETNRPD
SKNWQYQETIKKGDLLLNRVQKLSRVINM

Sequence of entity 6 (Z), FASTA

>9BV2_6 26S proteasome non-ATPase regulatory subunit 7 (chains Z)
MPELAVQKVVVHPLVLLSVVDHFNRIGKVGNQKRVVGVLLGSWQKKVLDVSNSFAVPFDE
DDKDDSVWFLDHDYLENMYGMFKKVNARERIVGWYHTGPKLHKNDIAINELMKRYCPNSV
LVIIDVKPKDLGLPTEAYISVEEVHDDGTPTSKTFEHVTSEIGAEEAEEVGVEHLLRDIK
DTTVGTLSQRITNQVHGLKGLNSKLLDIRSYLEKVATGKLPINHQIIYQLQDVFNLLPDV
SLQEFVKAFYLKTNDQMVVVYLASLIRSVVALHNLINNKIANRDAEKKEGQEKEESKKDR
KEDKEKDKDKEKSDVKKEEKKEKK

Sequence of entity 7 (a), FASTA

>9BV2_7 26S proteasome non-ATPase regulatory subunit 13 (chains a)
MKDVPGFLQQSQNSGPGQPAVWHRLEELYTKKLWHQLTLQVLDFVQDPCFAQGDGLIKLY
ENFISEFEHRVNPLSLVEIILHVVRQMTDPNVALTFLEKTREKVKSSDEAVILCKTAIGA
LKLNIGDLQVTKETIEDVEEMLNNLPGVTSVHSRFYDLSSKYYQTIGNHASYYKDALRFL
GCVDIKDLPVSEQQERAFTLGLAGLLGEGVFNFGELLMHPVLESLRNTDRQWLIDTLYAF
NSGNVERFQTLKTAWGQQPDLAANEAQLLRKIQLLCLMEMTFTRPANHRQLTFEEIAKSA
KITVNEVELLVMKALSVGLVKGSIDEVDKRVHMTWVQPRVLDLQQIKGMKDRLEFWCTDV
KSMEMLVEHQAHDILT

Sequence of entity 8 (b), FASTA

>9BV2_8 26S proteasome non-ATPase regulatory subunit 4 (chains b)
MVLESTMVCVDNSEYMRNGDFLPTRLQAQQDAVNIVCHSKTRSNPENNVGLITLANDCEV
LTTLTPDTGRILSKLHTVQPKGKITFCTGIRVAHLALKHRQGKNHKMRIIAFVGSPVEDN
EKDLVKLAKRLKKEKVNVDIINFGEEEVNTEKLTAFVNTLNGKDGTGSHLVTVPPGPSLA
DALISSPILAGEGGAMLGLGASDFEFGVDPSADPELALALRVSMEEQRQRQEEEARRAAA
ASAAEAGIATTGTEDSDDALLKMTISQQEFGRTGLPDLSSMTEEEQIAYAMQMSLQGAEF
GQAESADIDASSAMDTSEPAKEEDDYDVMQDPEFLQSVLENLPGVDPNNEAIRNAMGSLA
SQATKDGKKDKKEEDKK

Sequence of entity 9 (c), FASTA

>9BV2_9 26S proteasome non-ATPase regulatory subunit 14 (chains c)
MDRLLRLGGGMPGLGQGPPTDAPAVDTAEQVYISSLALLKMLKHGRAGVPMEVMGLMLGE
FVDDYTVRVIDVFAMPQSGTGVSVEAVDPVFQAKMLDMLKQTGRPEMVVGWYHSHPGFGC
WLSGVDINTQQSFEALSERAVAVVVDPIQSVKGKVVIDAFRLINANMMVLGHEPRQTTSN
LGHLNKPSIQALIHGLNRHYYSITINYRKNELEQKMLLNLHKKSWMEGLTLQDYSEHCKH
NESVVKEMLELAKNYNKAVEEEDKMTPEQLAIKNVGKQDPKRHLEEHVDVLMTSNIVQCL
AAMLDTVVFK

Sequence of entity 10 (d), FASTA

>9BV2_10 26S proteasome non-ATPase regulatory subunit 8 (chains d)
MFIKGRAPRAPPRERRRATRGGLRQVVAPPRALGSTSRPHFRRASVCRRRCRKSGGLLAA
SRKMAAAAVNGAAGFSSSGPAATSGAVLQAATGMYEQLKGEWNRKSPNLSKCGEELGRLK
LVLLELNFLPTTGTKLTKQQLILARDILEIGAQWSILRKDIPSFERYMAQLKCYYFDYKE
QLPESAYMHQLLGLNLLFLLSQNRVAEFHTELERLPAKDIQTNVYIKHPVSLEQYLMEGS
YNKVFLAKGNIPAESYTFFIDILLDTIRDEIAGCIEKAYEKILFTEATRILFFNTPKKMT
DYAKKRGWVLGPNNYYSFASQQQKPEDTTIPSTELAKQVIEYARQLEMIV

Sequence of entity 11 (e), FASTA

>9BV2_11 26S proteasome complex subunit SEM1 (chains e)
MSEKKQPVDLGLLEEDDEFEEFPAEDWAGLDEDEDAHVWEDNWDDDNVEDDFSNQLRAEL
EKHGYKMETS

Sequence of entity 12 (A), FASTA

>9BV2_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	1
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	4

Primary citation

Structural basis for the midnolin-proteasome pathway and its role in suppressing myeloma. Nardone, C., Gao, J., Seo, H.S. et al. Mol Cell (2025) 85:2597-2609.e11. DOI 10.1016/j.molcel.2025.05.030 · 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
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

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