9NKI: 26S proteasome regulatory subunit 7

Structure of substrate engaged MIDN-bound human 26S proteasome, EB MIDN_UBL state (Composite map). Determined by electron microscopy at 2.94 Å resolution. Released 7 May 2025.

Method: Electron microscopy
Resolution: 2.94 Å
Organism: Homo sapiens
Chains: 48
Atoms: 102,622
Mol. weight: 1717.71 kDa
Ligands: ATP, MG, ADP, ZN
Released: 7 May 2025

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

Secondary structure: helices and β-sheets

9NKI contains 612 α-helices and 584 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: 21 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	5-10	6
α-helix	11-13	3
α-helix	18-29	12
α-helix	34-46	13
α-helix	54-64	11
α-helix	73-84	12
α-helix	90-103	14
α-helix	111-123	13
α-helix	131-137	7
α-helix	149-164	16
α-helix	169-182	14
α-helix	190-206	17
α-helix	223-225	3
α-helix	231-242	12
α-helix	245-250	6
α-helix	252-255	4
α-helix	259-263	5
α-helix	266-283	18
β-strand	290-292	3	148
α-helix	293-300	8
α-helix	304-317	14
β-strand	320-322	3	159
β-strand	325	1	148
β-strand	330-332	3	148
β-strand	333-336	4	159
α-helix	345-370	26

Chain A: 23 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	42-63	22
β-strand	72	1	1
α-helix	75-77	3
α-helix	86-89	4
β-strand	96-104	9	2
β-strand	111-115	5	2
β-strand	119-123	5	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	159-162	4
β-strand	165	1	3
α-helix	182-187	6
α-helix	188-192	5
α-helix	193-196	4
α-helix	198-204	7
β-strand	211-215	5	3
α-helix	222-232	11
β-strand	236-241	6	3
α-helix	242-244	3
β-strand	249	1	4
α-helix	252-266	15
β-strand	270-275	6	3
α-helix	277-279	3
α-helix	282-284	3
α-helix	294-306	13
α-helix	311-312	2
β-strand	315-321	7	3
β-strand	339-342	4	3
α-helix	343	1
α-helix	348-358	11
β-strand	364	1	5
α-helix	370-376	7
α-helix	382-398	17
β-strand	404	1	5
α-helix	406-413	8
α-helix	414-418	5

Chain b: 8 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	6
β-strand	8-9	2	7
α-helix	14-17	4
α-helix	26-43	18
β-strand	48	1	6
β-strand	49-53	5	7
β-strand	59-65	7	7
α-helix	69-75	7
α-helix	86-98	13
β-strand	106-107	2	6
β-strand	110-112	3	7
α-helix	121-133	13
β-strand	139-142	4	7
α-helix	154-160	7
β-strand	169-172	4	7
α-helix	180-183	4
α-helix	186-189	4

Chain B: 22 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	48-50	3
α-helix	59-85	27
α-helix	89-92	4
α-helix	95-102	8
β-strand	107-109	3	8
β-strand	111-115	5	2
β-strand	120-124	5	2
β-strand	130-134	5	2
β-strand	135	1	8
β-strand	139	1	1
α-helix	141-143	3
β-strand	150-152	3	8
β-strand	159-162	4	8
α-helix	171-174	4
β-strand	175	1	9
α-helix	184-186	3
α-helix	192-197	6
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	9
α-helix	232-242	11
β-strand	246-251	6	9
α-helix	252-255	4
α-helix	263-270	8
β-strand	280-285	6	9
α-helix	287-289	3
α-helix	302-316	15
β-strand	325-331	7	9
β-strand	349-352	4	9
α-helix	354-356	3
α-helix	359-368	10
β-strand	374	1	10
α-helix	380-384	5
α-helix	392-408	17
β-strand	414	1	10
α-helix	416-427	12

Chain c: 10 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	26	1	146
β-strand	30-33	4	147
α-helix	35-47	13
β-strand	54-60	7	147
β-strand	66-74	9	147
β-strand	77-80	4	28
β-strand	83-86	4	28
α-helix	90-101	12
β-strand	107-114	8	147
α-helix	124-136	13
β-strand	141-145	5	147
β-strand	157-162	6	147
β-strand	176	1	146
α-helix	189-193	5
β-strand	196	1	147
β-strand	200-206	7	147
α-helix	211-219	9
α-helix	222-224	3
α-helix	226-229	4
α-helix	234-259	26
α-helix	269-273	5
α-helix	280-308	29

Chain C: 17 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	21-65	45
β-strand	71-80	10	8
β-strand	84-88	5	8
β-strand	94-99	6	8
α-helix	105-107	3
β-strand	113-116	4	8
β-strand	122-123	2	8
α-helix	155-161	7
α-helix	162-166	5
α-helix	167-170	4
α-helix	174-178	5
α-helix	180-183	4
β-strand	185-189	5	11
α-helix	196-206	11
β-strand	210	1	11
α-helix	216-219	4
α-helix	226-240	15
β-strand	244-248	5	11
α-helix	251-253	3
α-helix	268-280	13
β-strand	289-295	7	11
β-strand	314-315	2	11
α-helix	318-320	3
α-helix	322-332	11
β-strand	338	1	12
α-helix	344-349	6
α-helix	356-372	17
β-strand	378	1	12
α-helix	380-405	26

Chain d: 16 helices, 0 β-strands

Element	Residues	Length
α-helix	82-102	21
α-helix	111-125	15
α-helix	138-157	20
α-helix	161-177	17
α-helix	183-185	3
α-helix	188-201	14
α-helix	205-214	10
α-helix	218-222	5
α-helix	224-237	14
α-helix	241-246	6
α-helix	247-249	3
α-helix	254-256	3
α-helix	257-277	21
α-helix	287-290	4
α-helix	298-305	8
α-helix	333-347	15

Chain D: 16 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	40-79	40
β-strand	87-95	9	8
β-strand	100-105	6	8
β-strand	110-115	6	8
α-helix	121-123	3
β-strand	128-132	5	8
β-strand	139-142	4	8
α-helix	143-144	2
α-helix	171-181	11
α-helix	196-199	4
β-strand	201-205	5	13
α-helix	212-222	11
β-strand	226-231	6	13
α-helix	232-235	4
α-helix	242-256	15
β-strand	260-265	6	13
α-helix	267-269	3
β-strand	272	1	14
α-helix	281-296	16
β-strand	305-311	7	13
β-strand	317	1	14
α-helix	319-322	4
β-strand	329-332	4	13
α-helix	334-336	3
α-helix	338-349	12
α-helix	360-365	6
α-helix	372-388	17
α-helix	396-406	11
β-strand	417	1	15

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 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 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)
26S proteasome regulatory subunit 10B	E	protein	403	Homo sapiens	A0A087X2I1
26S proteasome regulatory subunit 6A	F	protein	439	Homo sapiens	P17980
Proteasome subunit alpha type-6	G, g	protein	246	Homo sapiens	P60900
Proteasome subunit alpha type-2	H, h	protein	234	Homo sapiens	P25787
Proteasome subunit alpha type-4	I, i	protein	261	Homo sapiens	P25789
Proteasome subunit alpha type-7	J, j	protein	248	Homo sapiens	O14818
Proteasome subunit alpha type-5	K, k	protein	241	Homo sapiens	P28066
Proteasome subunit alpha type-1	L, l	protein	263	Homo sapiens	P25786

22 more molecules are not listed.

Sequence of entity 1 (A), FASTA

>9NKI_1 26S proteasome regulatory subunit 7 (chains A)
MPDYLGADQRKTKEDEKDDKPIRALDEGDIALLKTYGQSTYSRQIKQVEDDIQQLLKKIN
ELTGIKESDTGLAPPALWDLAADKQTLQSEQPLQVARCTKIINADSEDPKYIINVKQFAK
FVVDLSDQVAPTDIEEGMRVGVDRNKYQIHIPLPPKIDPTVTMMQVEEKPDVTYSDVGGC
KEQIEKLREVVETPLLHPERFVNLGIEPPKGVLLFGPPGTGKTLCARAVANRTDACFIRV
IGSELVQKYVGEGARMVRELFEMARTKKACLIFFDEIDAIGGARFDDGAGGDNEVQRTML
ELINQLDGFDPRGNIKVLMATNRPDTLDPALMRPGRLDRKIEFSLPDLEGRTHIFKIHAR
SMSVERDIRFELLARLCPNSTGAEIRSVCTEAGMFAIRARRKIATEKDFLEAVNKVIKSY
AKFSATPRYMTYN

Sequence of entity 2 (B), FASTA

>9NKI_2 26S proteasome regulatory subunit 4 (chains B)
MGQSQSGGHGPGGGKKDDKDKKKKYEPPVPTRVGKKKKKTKGPDAASKLPLVTPHTQCRL
KLLKLERIKDYLLMEEEFIRNQEQMKPLEEKQEEERSKVDDLRGTPMSVGTLEEIIDDNH
AIVSTSVGSEHYVSILSFVDKDLLEPGCSVLLNHKVHAVIGVLMDDTDPLVTVMKVEKAP
QETYADIGGLDNQIQEIKESVELPLTHPEYYEEMGIKPPKGVILYGPPGTGKTLLAKAVA
NQTSATFLRVVGSELIQKYLGDGPKLVRELFRVAEEHAPSIVFIDEIDAIGTKRYDSNSG
GEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDEKT
KKRIFQIHTSRMTLADDVTLDDLIMAKDDLSGADIKAICTEAGLMALRERRMKVTNEDFK
KSKENVLYKKQEGTPEGLYL

Sequence of entity 3 (C), FASTA

>9NKI_3 26S protease regulatory subunit 8 (chains C)
MALDGPEQMELEEGKAGSGLRQYYLSKIEELQLIVNDKSQNLRRLQAQRNELNAKVRLLR
EELQLLQEQGSYVGEVVRAMDKKKVLVKVHPEGKFVVDVDKNIDINDVTPNCRVALRNDS
YTLHKILPNKVDPLVSLMMVEKVPDSTYEMIGGLDKQIKEIKEVIELPVKHPELFEALGI
AQPKGVLLYGPPGTGKTLLARAVAHHTDCTFIRVSGSELVQKFIGEGARMVRELFVMARE
HAPSIIFMDEIDSIGSSRLEGGSGGDSEVQRTMLELLNQLDGFEATKNIKVIMATNRIDI
LDSALLRPGRIDRKIEFPPPNEEARLDILKIHSRKMNLTRGINLRKIAELMPGASGAEVK
GVCTEAGMYALRERRVHVTQEDFEMAVAKVMQKDSEKNMSIKKLWK

Sequence of entity 4 (D), FASTA

>9NKI_4 26S proteasome regulatory subunit 6B (chains D)
MEEIGILVEKAQDEIPALSVSRPQTGLSFLGPEPEDLEDLYSRYKKLQQELEFLEVQEEY
IKDEQKNLKKEFLHAQEEVKRIQSIPLVIGQFLEAVDQNTAIVGSTTGSNYYVRILSTID
RELLKPNASVALHKHSNALVDVLPPEADSSIMMLTSDQKPDVMYADIGGMDIQKQEVREA
VELPLTHFELYKQIGIDPPRGVLMYGPPGCGKTMLAKAVAHHTTAAFIRVVGSEFVQKYL
GEGPRMVRDVFRLAKENAPAIIFIDEIDAIATKRFDAQTGADREVQRILLELLNQMDGFD
QNVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLIFSTITSKMNLSEEVDL
EDYVARPDKISGADINSICQESGMLAVRENRYIVLAKDFEKAYKTVIKKDEQEHEFYK

Sequence of entity 5 (E), FASTA

>9NKI_5 26S proteasome regulatory subunit 10B (chains E)
MAIPGIPYERRLLIMADPRDKALQDYRKKLLEHKEIDGRLKELREQLKELTKQYEKSEND
LKALQSVGQIVGEVLKQLTEEKFIVKATNGPRYVVGCRRQLDKSKLKPGTRVALDMTTLT
IMRYLPREVDPLVYNMSHEDPGNVSYSEIGGLSEQIRELREVIELPLTNPELFQRVGIIP
PKGCLLYGPPGTGKTLLARAVASQLDCNFLKVVSSSIVDKYIGESARLIREMFNYARDHQ
PCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQMDGFDTLHRVKMIMATNRPDTLD
PALLRPGRLDRKIHIDLPNEQARLDILKIHAGPITKHGEIDYEAIVKLSDGFNGADLRNV
CTEAGMFAIRADHDFVVQEDFMKAVRKVADSKKLESKLDYKPV

Sequence of entity 6 (F), FASTA

>9NKI_6 26S proteasome regulatory subunit 6A (chains F)
MNLLPNIESPVTRQEKMATVWDEAEQDGIGEEVLKMSTEEIIQRTRLLDSEIKIMKSEVL
RVTHELQAMKDKIKENSEKIKVNKTLPYLVSNVIELLDVDPNDQEEDGANIDLDSQRKGK
CAVIKTSTRQTYFLPVIGLVDAEKLKPGDLVGVNKDSYLILETLPTEYDSRVKAMEVDER
PTEQYSDIGGLDKQIQELVEAIVLPMNHKEKFENLGIQPPKGVLMYGPPGTGKTLLARAC
AAQTKATFLKLAGPQLVQMFIGDGAKLVRDAFALAKEKAPSIIFIDELDAIGTKRFDSEK
AGDREVQRTMLELLNQLDGFQPNTQVKVIAATNRVDILDPALLRSGRLDRKIEFPMPNEE
ARARIMQIHSRKMNVSPDVNYEELARCTDDFNGAQCKAVCVEAGMIALRRGATELTHEDY
MEGILEVQAKKKANLQYYA

Sequence of entity 7 (G, g), FASTA

>9NKI_7 Proteasome subunit alpha type-6 (chains G, g)
MSRGSSAGFDRHITIFSPEGRLYQVEYAFKAINQGGLTSVAVRGKDCAVIVTQKKVPDKL
LDSSTVTHLFKITENIGCVMTGMTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKRIAD
ISQVYTQNAEMRPLGCCMILIGIDEEQGPQVYKCDPAGYYCGFKATAAGVKQTESTSFLE
KKVKKKFDWTFEQTVETAITCLSTVLSIDFKPSEIEVGVVTVENPKFRILTEAEIDAHLV
ALAERD

Sequence of entity 8 (H, h), FASTA

>9NKI_8 Proteasome subunit alpha type-2 (chains H, h)
MAERGYSFSLTTFSPSGKLVQIEYALAAVAGGAPSVGIKAANGVVLATEKKQKSILYDER
SVHKVEPITKHIGLVYSGMGPDYRVLVHRARKLAQQYYLVYQEPIPTAQLVQRVASVMQE
YTQSGGVRPFGVSLLICGWNEGRPYLFQSDPSGAYFAWKATAMGKNYVNGKTFLEKRYNE
DLELEDAIHTAILTLKESFEGQMTEDNIEVGICNEAGFRRLTPTEVKDYLAAIA

Sequence of entity 9 (I, i), FASTA

>9NKI_9 Proteasome subunit alpha type-4 (chains I, i)
MSRRYDSRTTIFSPEGRLYQVEYAMEAIGHAGTCLGILANDGVLLAAERRNIHKLLDEVF
FSEKIYKLNEDMACSVAGITSDANVLTNELRLIAQRYLLQYQEPIPCEQLVTALCDIKQA
YTQFGGKRPFGVSLLYIGWDKHYGFQLYQSDPSGNYGGWKATCIGNNSAAAVSMLKQDYK
EGEMTLKSALALAIKVLNKTMDVSKLSAEKVEIATLTRENGKTVIRVLKQKEVEQLIKKH
EEEEAKAEREKKEKEQKEKDK

Sequence of entity 10 (J, j), FASTA

>9NKI_10 Proteasome subunit alpha type-7 (chains J, j)
MSYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVEKKSVAKLQDERTVR
KICALDDNVCMAFAGLTADARIVINRARVECQSHRLTVEDPVTVEYITRYIASLKQRYTQ
SNGRRPFGISALIVGFDFDGTPRLYQTDPSGTYHAWKANAIGRGAKSVREFLEKNYTDEA
IETDDLTIKLVIKALLEVVQSGGKNIELAVMRRDQSLKILNPEEIEKYVAEIEKEKEENE
KKKQKKAS

Sequence of entity 11 (K, k), FASTA

>9NKI_11 Proteasome subunit alpha type-5 (chains K, k)
MFLTRSEYYRGVNTFSPEGRLFQVEYAIEAIKLGSTAIGIQTSEGVCLAVEKRITSPLME
PSSIEKIVEIDAHIGCAMSGLIADAKTLIDKARVETQNHWFTYNETMTVESVTQAVSNLA
LQFGEEDADPGAMSRPFGVALLFGGVDEKGPQLFHMDPSGTFVQCDARAIGSASEGAQSS
LQEVYHKSMTLKEAIKSSLIILKQVMEEKLNATNIELATVQPGQNFHMFTKEELEEVIKD
I

Sequence of entity 12 (L, l), FASTA

>9NKI_12 Proteasome subunit alpha type-1 (chains L, l)
MFRNQYDNDVTVWSPQGRIHQIEYAMEAVKQGSATVGLKSKTHAVLVALKRAQSELAAHQ
KKILHVDNHIGISIAGLTADARLLCNFMRQECLDSRFVFDRPLPVSRLVSLIGSKTQIPT
QRYGRRPYGVGLLIAGYDDMGPHIFQTCPSANYFDCRAMSIGARSQSARTYLERHMSEFM
ECNLNELVKHGLRALRETLPAEQDLTTKNVSIGIVGKDLEFTIYDDDDVSPFLEGLEERP
QRKAQPAQPADEPAEKADEPMEH

Ligands and cofactors

ID	Name	Formula	Copies
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	4
MG	Magnesium ion	Mg	4
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	1
ZN	Zinc ion	Zn	1

Primary citation

Structural insights into the ubiquitin-independent midnolin-proteasome pathway. Peddada, N., Zhong, X., Yin, Y. et al. Proc Natl Acad Sci U S A (2025) 122:e2505345122-e2505345122. DOI 10.1073/pnas.2505345122 · 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…
9U3L 2.91 Å, Substrate-engaged human 26S proteasome bound to midnolin with RPT2 at top of spiral…

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