9NKF: 26S proteasome regulatory subunit 7

Structure of human substrate-free 26S proteasome in the presence of ATPgS and MG-132,SA-like state (composite map). Determined by electron microscopy at 2.9 Å resolution. Released 7 May 2025.

Method: Electron microscopy
Resolution: 2.9 Å
Organism: Homo sapiens
Chains: 46
Atoms: 101,338
Mol. weight: 1670.6 kDa
Ligands: ATP, MG, ADP, LDZ
Released: 7 May 2025

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

Secondary structure: helices and β-sheets

9NKF contains 588 α-helices and 539 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: 22 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	6-11	6
α-helix	18-30	13
α-helix	35-45	11
α-helix	53-57	5
α-helix	58-66	9
α-helix	73-87	15
α-helix	90-102	13
α-helix	111-121	11
α-helix	132-138	7
α-helix	150-166	17
α-helix	171-179	9
α-helix	190-204	15
α-helix	222-224	3
α-helix	232-241	10
α-helix	246-249	4
α-helix	252-254	3
α-helix	265-281	17
β-strand	292	1	136
α-helix	293-300	8
α-helix	304-306	3
α-helix	307-317	11
β-strand	320-326	7	136
β-strand	330-336	7	136
α-helix	337-338	2
α-helix	345-370	26

Chain A: 16 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	75-80	6
α-helix	83-89	7
α-helix	94-95	2
β-strand	96-103	8	1
β-strand	111-115	5	1
β-strand	121-123	3	1
α-helix	131-133	3
β-strand	139-142	4	1
β-strand	149-153	5	1
α-helix	154-156	3
α-helix	159-162	4
β-strand	165	1	2
α-helix	181-186	6
β-strand	212-215	4	3
α-helix	222-232	11
β-strand	236-240	5	2
α-helix	255-265	11
β-strand	270-274	5	2
α-helix	294-304	11
β-strand	315-318	4	2
β-strand	319-321	3	3
β-strand	333	1	4
β-strand	336	1	4
β-strand	339-342	4	3
α-helix	344-346	3
α-helix	348-358	11
α-helix	370-375	6
α-helix	382-392	11
α-helix	394-399	6
α-helix	406-416	11

Chain b: 9 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	140
β-strand	9-10	2	140
α-helix	14-17	4
α-helix	24-40	17
β-strand	49	1	140
β-strand	52-53	2	140
β-strand	59-60	2	140
β-strand	65	1	140
α-helix	69-75	7
α-helix	87-98	12
β-strand	106-111	6	140
α-helix	123-133	11
β-strand	137-140	4	140
β-strand	141	1	141
α-helix	148-150	3
α-helix	154-161	8
β-strand	171	1	141
α-helix	181-183	3
α-helix	186-189	4

Chain B: 17 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	60-85	26
α-helix	94-102	9
β-strand	107-110	4	6
β-strand	111-114	4	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	6
β-strand	150-152	3	6
β-strand	159-161	3	6
α-helix	164-166	3
α-helix	169-173	5
α-helix	194-197	4
α-helix	198-202	5
α-helix	203-206	4
α-helix	210-213	4
α-helix	217-219	3
β-strand	222-225	4	8
α-helix	232-241	10
β-strand	246-251	6	8
α-helix	266-276	11
β-strand	280-285	6	8
α-helix	302-316	15
β-strand	325-331	7	8
β-strand	349-352	4	8
α-helix	354-357	4
α-helix	358-368	11
α-helix	380-384	5
α-helix	393-407	15
α-helix	416-425	10

Chain c: 11 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	31-32	2	5
α-helix	37-47	11
β-strand	54-61	8	5
β-strand	67-74	8	5
α-helix	89-99	11
β-strand	107-114	8	5
α-helix	124-136	13
β-strand	141-145	5	5
β-strand	160-162	3	5
α-helix	165-170	6
α-helix	186-188	3
α-helix	189-193	5
β-strand	196	1	5
β-strand	200-202	3	5
β-strand	205-206	2	5
α-helix	211-215	5
α-helix	227-229	3
α-helix	234-260	27
α-helix	267-272	6
α-helix	280-308	29

Chain C: 17 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	24-65	42
β-strand	71-79	9	6
β-strand	84-89	6	6
β-strand	94-99	6	6
β-strand	113-116	4	6
β-strand	122-123	2	6
α-helix	129-132	4
α-helix	133-140	8
α-helix	148-150	3
α-helix	156-165	10
α-helix	167-170	4
α-helix	180-183	4
β-strand	186-189	4	9
α-helix	196-205	10
β-strand	210-213	4	9
α-helix	234-238	5
β-strand	244-248	5	9
α-helix	271-276	6
β-strand	289-295	7	9
β-strand	313-316	4	9
α-helix	318-320	3
α-helix	322-333	12
β-strand	338	1	10
α-helix	339	1
α-helix	344-349	6
α-helix	363-372	10
β-strand	378	1	10
α-helix	380-387	8
α-helix	388-393	6

Chain d: 11 helices, 0 β-strands

Element	Residues	Length
α-helix	19-32	14
α-helix	46-64	19
α-helix	68-83	16
α-helix	95-108	14
α-helix	112-119	8
α-helix	131-144	14
α-helix	149-155	7
α-helix	164-182	19
α-helix	193-196	4
α-helix	205-212	8
α-helix	236-254	19

Chain D: 24 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	41-76	36
α-helix	79-82	4
β-strand	87-91	5	11
β-strand	92-97	6	6
β-strand	100-103	4	6
β-strand	111-113	3	6
α-helix	121-123	3
β-strand	129-133	5	11
β-strand	139-142	4	11
α-helix	143-145	3
α-helix	156-158	3
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
α-helix	196-199	4
β-strand	202-205	4	12
α-helix	212-219	8
β-strand	226-231	6	12
α-helix	232-235	4
α-helix	243-256	14
β-strand	260-265	6	12
α-helix	267-269	3
α-helix	281-296	16
β-strand	305-310	6	12
α-helix	314-316	3
α-helix	319-322	4
β-strand	324	1	13
β-strand	326	1	13
β-strand	330-332	3	12
α-helix	334-336	3
α-helix	338-350	13
α-helix	360-363	4
α-helix	373-386	14
α-helix	396-403	8
α-helix	415-417	3

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 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
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
Proteasome subunit alpha type-3	M, m	protein	255	Homo sapiens	P25788

20 more molecules are not listed.

Sequence of entity 1 (A), FASTA

>9NKF_1 26S proteasome regulatory subunit 7 (chains A)
MPDYLGADQRKTKEDEKDDKPIRALDEGDIALLKTYGQSTYSRQIKQVEDDIQQLLKKIN
ELTGIKESDTGLAPPALWDLAADKQTLQSEQPLQVARCTKIINADSEDPKYIINVKQFAK
FVVDLSDQVAPTDIEEGMRVGVDRNKYQIHIPLPPKIDPTVTMMQVEEKPDVTYSDVGGC
KEQIEKLREVVETPLLHPERFVNLGIEPPKGVLLFGPPGTGKTLCARAVANRTDACFIRV
IGSELVQKYVGEGARMVRELFEMARTKKACLIFFDEIDAIGGARFDDGAGGDNEVQRTML
ELINQLDGFDPRGNIKVLMATNRPDTLDPALMRPGRLDRKIEFSLPDLEGRTHIFKIHAR
SMSVERDIRFELLARLCPNSTGAEIRSVCTEAGMFAIRARRKIATEKDFLEAVNKVIKSY
AKFSATPRYMTYN

Sequence of entity 2 (B), FASTA

>9NKF_2 26S proteasome regulatory subunit 4 (chains B)
MGQSQSGGHGPGGGKKDDKDKKKKYEPPVPTRVGKKKKKTKGPDAASKLPLVTPHTQCRL
KLLKLERIKDYLLMEEEFIRNQEQMKPLEEKQEEERSKVDDLRGTPMSVGTLEEIIDDNH
AIVSTSVGSEHYVSILSFVDKDLLEPGCSVLLNHKVHAVIGVLMDDTDPLVTVMKVEKAP
QETYADIGGLDNQIQEIKESVELPLTHPEYYEEMGIKPPKGVILYGPPGTGKTLLAKAVA
NQTSATFLRVVGSELIQKYLGDGPKLVRELFRVAEEHAPSIVFIDEIDAIGTKRYDSNSG
GEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDEKT
KKRIFQIHTSRMTLADDVTLDDLIMAKDDLSGADIKAICTEAGLMALRERRMKVTNEDFK
KSKENVLYKKQEGTPEGLYL

Sequence of entity 3 (C), FASTA

>9NKF_3 26S protease regulatory subunit 8 (chains C)
MALDGPEQMELEEGKAGSGLRQYYLSKIEELQLIVNDKSQNLRRLQAQRNELNAKVRLLR
EELQLLQEQGSYVGEVVRAMDKKKVLVKVHPEGKFVVDVDKNIDINDVTPNCRVALRNDS
YTLHKILPNKVDPLVSLMMVEKVPDSTYEMIGGLDKQIKEIKEVIELPVKHPELFEALGI
AQPKGVLLYGPPGTGKTLLARAVAHHTDCTFIRVSGSELVQKFIGEGARMVRELFVMARE
HAPSIIFMDEIDSIGSSRLEGGSGGDSEVQRTMLELLNQLDGFEATKNIKVIMATNRIDI
LDSALLRPGRIDRKIEFPPPNEEARLDILKIHSRKMNLTRGINLRKIAELMPGASGAEVK
GVCTEAGMYALRERRVHVTQEDFEMAVAKVMQKDSEKNMSIKKLWK

Sequence of entity 4 (D), FASTA

>9NKF_4 26S proteasome regulatory subunit 6B (chains D)
MEEIGILVEKAQDEIPALSVSRPQTGLSFLGPEPEDLEDLYSRYKKLQQELEFLEVQEEY
IKDEQKNLKKEFLHAQEEVKRIQSIPLVIGQFLEAVDQNTAIVGSTTGSNYYVRILSTID
RELLKPNASVALHKHSNALVDVLPPEADSSIMMLTSDQKPDVMYADIGGMDIQKQEVREA
VELPLTHFELYKQIGIDPPRGVLMYGPPGCGKTMLAKAVAHHTTAAFIRVVGSEFVQKYL
GEGPRMVRDVFRLAKENAPAIIFIDEIDAIATKRFDAQTGADREVQRILLELLNQMDGFD
QNVNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLIFSTITSKMNLSEEVDL
EDYVARPDKISGADINSICQESGMLAVRENRYIVLAKDFEKAYKTVIKKDEQEHEFYK

Sequence of entity 5 (E), FASTA

>9NKF_5 26S proteasome regulatory subunit 10B (chains E)
MAIPGIPYERRLLIMADPRDKALQDYRKKLLEHKEIDGRLKELREQLKELTKQYEKSEND
LKALQSVGQIVGEVLKQLTEEKFIVKATNGPRYVVGCRRQLDKSKLKPGTRVALDMTTLT
IMRYLPREVDPLVYNMSHEDPGNVSYSEIGGLSEQIRELREVIELPLTNPELFQRVGIIP
PKGCLLYGPPGTGKTLLARAVASQLDCNFLKVVSSSIVDKYIGESARLIREMFNYARDHQ
PCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQMDGFDTLHRVKMIMATNRPDTLD
PALLRPGRLDRKIHIDLPNEQARLDILKIHAGPITKHGEIDYEAIVKLSDGFNGADLRNV
CTEAGMFAIRADHDFVVQEDFMKAVRKVADSKKLESKLDYKPV

Sequence of entity 6 (G, g), FASTA

>9NKF_6 Proteasome subunit alpha type-6 (chains G, g)
MSRGSSAGFDRHITIFSPEGRLYQVEYAFKAINQGGLTSVAVRGKDCAVIVTQKKVPDKL
LDSSTVTHLFKITENIGCVMTGMTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKRIAD
ISQVYTQNAEMRPLGCCMILIGIDEEQGPQVYKCDPAGYYCGFKATAAGVKQTESTSFLE
KKVKKKFDWTFEQTVETAITCLSTVLSIDFKPSEIEVGVVTVENPKFRILTEAEIDAHLV
ALAERD

Sequence of entity 7 (H, h), FASTA

>9NKF_7 Proteasome subunit alpha type-2 (chains H, h)
MAERGYSFSLTTFSPSGKLVQIEYALAAVAGGAPSVGIKAANGVVLATEKKQKSILYDER
SVHKVEPITKHIGLVYSGMGPDYRVLVHRARKLAQQYYLVYQEPIPTAQLVQRVASVMQE
YTQSGGVRPFGVSLLICGWNEGRPYLFQSDPSGAYFAWKATAMGKNYVNGKTFLEKRYNE
DLELEDAIHTAILTLKESFEGQMTEDNIEVGICNEAGFRRLTPTEVKDYLAAIA

Sequence of entity 8 (I, i), FASTA

>9NKF_8 Proteasome subunit alpha type-4 (chains I, i)
MSRRYDSRTTIFSPEGRLYQVEYAMEAIGHAGTCLGILANDGVLLAAERRNIHKLLDEVF
FSEKIYKLNEDMACSVAGITSDANVLTNELRLIAQRYLLQYQEPIPCEQLVTALCDIKQA
YTQFGGKRPFGVSLLYIGWDKHYGFQLYQSDPSGNYGGWKATCIGNNSAAAVSMLKQDYK
EGEMTLKSALALAIKVLNKTMDVSKLSAEKVEIATLTRENGKTVIRVLKQKEVEQLIKKH
EEEEAKAEREKKEKEQKEKDK

Sequence of entity 9 (J, j), FASTA

>9NKF_9 Proteasome subunit alpha type-7 (chains J, j)
MSYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVEKKSVAKLQDERTVR
KICALDDNVCMAFAGLTADARIVINRARVECQSHRLTVEDPVTVEYITRYIASLKQRYTQ
SNGRRPFGISALIVGFDFDGTPRLYQTDPSGTYHAWKANAIGRGAKSVREFLEKNYTDEA
IETDDLTIKLVIKALLEVVQSGGKNIELAVMRRDQSLKILNPEEIEKYVAEIEKEKEENE
KKKQKKAS

Sequence of entity 10 (K, k), FASTA

>9NKF_10 Proteasome subunit alpha type-5 (chains K, k)
MFLTRSEYDRGVNTFSPEGRLFQVEYAIEAIKLGSTAIGIQTSEGVCLAVEKRITSPLME
PSSIEKIVEIDAHIGCAMSGLIADAKTLIDKARVETQNHWFTYNETMTVESVTQAVSNLA
LQFGEEDADPGAMSRPFGVALLFGGVDEKGPQLFHMDPSGTFVQCDARAIGSASEGAQSS
LQEVYHKSMTLKEAIKSSLIILKQVMEEKLNATNIELATVQPGQNFHMFTKEELEEVIKD
I

Sequence of entity 11 (L, l), FASTA

>9NKF_11 Proteasome subunit alpha type-1 (chains L, l)
MFRNQYDNDVTVWSPQGRIHQIEYAMEAVKQGSATVGLKSKTHAVLVALKRAQSELAAHQ
KKILHVDNHIGISIAGLTADARLLCNFMRQECLDSRFVFDRPLPVSRLVSLIGSKTQIPT
QRYGRRPYGVGLLIAGYDDMGPHIFQTCPSANYFDCRAMSIGARSQSARTYLERHMSEFM
ECNLNELVKHGLRALRETLPAEQDLTTKNVSIGIVGKDLEFTIYDDDDVSPFLEGLEERP
QRKAQPAQPADEPAEKADEPMEH

Sequence of entity 12 (M, m), FASTA

>9NKF_12 Proteasome subunit alpha type-3 (chains M, m)
MSSIGTGYDLSASTFSPDGRVFQVEYAMKAVENSSTAIGIRCKDGVVFGVEKLVLSKLYE
EGSNKRLFNVDRHVGMAVAGLLADARSLADIAREEASNFRSNFGYNIPLKHLADRVAMYV
HAYTLYSAVRPFGCSFMLGSYSVNDGAQLYMIDPSGVSYGYWGCAIGKARQAAKTEIEKL
QMKEMTCRDIVKEVAKIIYIVHDEVKDKAFELELSWVGELTNGRHEIVPKDIREEAEKYA
KESLKEEDESDDDNM

Ligands and cofactors

ID	Name	Formula	Copies
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	4
MG	Magnesium ion	Mg	5
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	2
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 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
9U3L 2.91 Å, Substrate-engaged human 26S proteasome bound to midnolin with RPT2 at top of spiral…
9NKI 2.94 Å, Structure of substrate engaged MIDN-bound human 26S proteasome, EB MIDN_UBL state…

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