9NKG: Proteasome subunit alpha type-6

Structure of substrate engaged MIDN-bound human 26S proteasome, EB-MIDN (Composite map). Determined by electron microscopy at 2.8 Å resolution. Released 7 May 2025.

Method: Electron microscopy
Resolution: 2.8 Å
Organism: Homo sapiens
Chains: 48
Atoms: 103,066
Mol. weight: 1720.57 kDa
Ligands: LDZ, ATP, MG, ADP
Released: 7 May 2025

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

Secondary structure: helices and β-sheets

9NKG contains 603 α-helices and 575 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, 3 β-strands

Element	Residues	Length	Sheet
α-helix	5-12	8
α-helix	18-31	14
α-helix	34-44	11
α-helix	53-55	3
α-helix	58-68	11
α-helix	73-86	14
α-helix	90-104	15
α-helix	105-107	3
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	245-255	11
α-helix	259-263	5
α-helix	266-283	18
β-strand	290-292	3	69
α-helix	293-300	8
α-helix	305-317	13
β-strand	320-325	6	69
β-strand	330-336	7	69
α-helix	343-371	29

Chain A: 26 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	42-63	22
β-strand	72	1	21
α-helix	73-74	2
α-helix	75-77	3
α-helix	87-90	4
β-strand	96-104	9	22
β-strand	111-115	5	22
β-strand	119-123	5	22
β-strand	125	1	22
α-helix	131-133	3
β-strand	139-143	5	22
β-strand	149-153	5	22
α-helix	154-156	3
α-helix	159-162	4
β-strand	165	1	23
α-helix	174-176	3
α-helix	182-191	10
α-helix	193-196	4
α-helix	199-203	5
β-strand	211-215	5	23
α-helix	222-232	11
β-strand	236-241	6	23
α-helix	242-245	4
β-strand	249	1	24
α-helix	253-266	14
β-strand	270-275	6	23
α-helix	277-279	3
β-strand	282	1	25
α-helix	283-284	2
α-helix	293-306	14
α-helix	311-312	2
β-strand	315-321	7	23
α-helix	324-326	3
β-strand	327	1	25
α-helix	329-332	4
β-strand	339-342	4	23
α-helix	348-359	12
β-strand	364	1	26
α-helix	370-376	7
α-helix	382-398	17
β-strand	404	1	26
α-helix	406-413	8
α-helix	414-418	5
α-helix	419-422	4

Chain b: 8 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	94
α-helix	14-17	4
α-helix	25-43	19
β-strand	48-53	6	94
β-strand	59-65	7	94
α-helix	69-75	7
α-helix	86-96	11
β-strand	106-112	7	94
α-helix	121-134	14
β-strand	137-141	5	94
α-helix	154-160	7
β-strand	169-171	3	94
α-helix	180-183	4
α-helix	186-189	4

Chain B: 20 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	59-85	27
α-helix	89-92	4
α-helix	95-102	8
β-strand	107-109	3	22
β-strand	111-115	5	22
β-strand	120-124	5	22
β-strand	130-135	6	22
β-strand	139	1	21
α-helix	141-143	3
β-strand	150-152	3	22
β-strand	159-162	4	22
α-helix	171-174	4
β-strand	175	1	31
α-helix	192-197	6
α-helix	198-202	5
α-helix	203-206	4
α-helix	209-214	6
α-helix	216-219	4
β-strand	221-225	5	31
α-helix	232-242	11
β-strand	246-251	6	31
α-helix	252-255	4
α-helix	262-275	14
β-strand	280-285	6	31
α-helix	287-289	3
α-helix	302-316	15
β-strand	325-331	7	31
β-strand	349-352	4	31
α-helix	354-356	3
α-helix	360-368	9
β-strand	374	1	32
α-helix	380-385	6
α-helix	392-409	18
β-strand	414	1	32
α-helix	416-427	12

Chain c: 10 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	26	1	120
β-strand	30-33	4	121
α-helix	35-47	13
β-strand	54-60	7	121
β-strand	66-74	9	121
β-strand	77-80	4	55
β-strand	83-86	4	55
α-helix	90-100	11
β-strand	107-114	8	121
α-helix	124-136	13
β-strand	141-145	5	121
β-strand	157-162	6	121
β-strand	176	1	120
α-helix	189-194	6
β-strand	196	1	121
β-strand	200-206	7	121
α-helix	211-219	9
α-helix	222-224	3
α-helix	225-229	5
α-helix	234-260	27
α-helix	269-273	5
α-helix	280-308	29

Chain C: 17 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	21-65	45
β-strand	71-79	9	22
β-strand	85-88	4	22
β-strand	94-99	6	22
α-helix	105-107	3
β-strand	113-116	4	22
β-strand	122-123	2	22
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	37
α-helix	196-207	12
β-strand	210	1	37
β-strand	213-214	2	38
α-helix	216-219	4
α-helix	226-240	15
β-strand	244-246	3	37
β-strand	247-248	2	38
α-helix	268-282	15
β-strand	289-295	7	37
α-helix	303-305	3
β-strand	313-316	4	37
α-helix	318-320	3
α-helix	322-333	12
β-strand	338	1	39
α-helix	344-350	7
α-helix	356-373	18
β-strand	378	1	39
α-helix	380-405	26

Chain d: 14 helices, 0 β-strands

Element	Residues	Length
α-helix	82-102	21
α-helix	110-123	14
α-helix	138-158	21
α-helix	161-176	16
α-helix	188-202	15
α-helix	205-214	10
α-helix	219-222	4
α-helix	227-238	12
α-helix	241-247	7
α-helix	256-277	22
α-helix	287-291	5
α-helix	296-299	4
α-helix	300-305	6
α-helix	333-347	15

Chain D: 20 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	40-78	39
α-helix	79-82	4
β-strand	87-95	9	22
β-strand	101-105	5	22
β-strand	110-113	4	22
α-helix	114	1
β-strand	115	1	22
α-helix	116	1
α-helix	121-123	3
β-strand	128-132	5	22
β-strand	139-142	4	22
α-helix	151-153	3
α-helix	171-180	10
α-helix	196-199	4
β-strand	201-205	5	43
α-helix	212-222	11
β-strand	226-231	6	43
α-helix	232-235	4
α-helix	242-256	15
β-strand	260-265	6	43
α-helix	267-269	3
β-strand	272	1	44
α-helix	281-297	17
β-strand	305-311	7	43
β-strand	317	1	44
α-helix	319-322	4
β-strand	324	1	45
β-strand	326	1	45
β-strand	329-332	4	43
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
α-helix	411-414	4

39 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
Proteasome subunit alpha type-6	G, g	protein	246	Homo sapiens	P60900 (AlphaFold model)
Proteasome subunit alpha type-2	H, h	protein	234	Homo sapiens	P25787 (AlphaFold model)
Proteasome subunit alpha type-4	I, i	protein	261	Homo sapiens	P25789 (AlphaFold model)
Proteasome subunit alpha type-7	J, j	protein	248	Homo sapiens	O14818 (AlphaFold model)
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
Proteasome subunit beta type-6	N, n	protein	239	Homo sapiens	P28072
Proteasome subunit beta type-7	O, o	protein	277	Homo sapiens	Q99436
Proteasome subunit beta type-3	P, p	protein	205	Homo sapiens	P49720
Proteasome subunit beta type-2	Q, q	protein	201	Homo sapiens	P49721
Proteasome subunit beta type-5	R, r	protein	263	Homo sapiens	P28074

22 more molecules are not listed.

Sequence of entity 1 (G, g), FASTA

>9NKG_1 Proteasome subunit alpha type-6 (chains G, g)
MSRGSSAGFDRHITIFSPEGRLYQVEYAFKAINQGGLTSVAVRGKDCAVIVTQKKVPDKL
LDSSTVTHLFKITENIGCVMTGMTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKRIAD
ISQVYTQNAEMRPLGCCMILIGIDEEQGPQVYKCDPAGYYCGFKATAAGVKQTESTSFLE
KKVKKKFDWTFEQTVETAITCLSTVLSIDFKPSEIEVGVVTVENPKFRILTEAEIDAHLV
ALAERD

Sequence of entity 2 (H, h), FASTA

>9NKG_2 Proteasome subunit alpha type-2 (chains H, h)
MAERGYSFSLTTFSPSGKLVQIEYALAAVAGGAPSVGIKAANGVVLATEKKQKSILYDER
SVHKVEPITKHIGLVYSGMGPDYRVLVHRARKLAQQYYLVYQEPIPTAQLVQRVASVMQE
YTQSGGVRPFGVSLLICGWNEGRPYLFQSDPSGAYFAWKATAMGKNYVNGKTFLEKRYNE
DLELEDAIHTAILTLKESFEGQMTEDNIEVGICNEAGFRRLTPTEVKDYLAAIA

Sequence of entity 3 (I, i), FASTA

>9NKG_3 Proteasome subunit alpha type-4 (chains I, i)
MSRRYDSRTTIFSPEGRLYQVEYAMEAIGHAGTCLGILANDGVLLAAERRNIHKLLDEVF
FSEKIYKLNEDMACSVAGITSDANVLTNELRLIAQRYLLQYQEPIPCEQLVTALCDIKQA
YTQFGGKRPFGVSLLYIGWDKHYGFQLYQSDPSGNYGGWKATCIGNNSAAAVSMLKQDYK
EGEMTLKSALALAIKVLNKTMDVSKLSAEKVEIATLTRENGKTVIRVLKQKEVEQLIKKH
EEEEAKAEREKKEKEQKEKDK

Sequence of entity 4 (J, j), FASTA

>9NKG_4 Proteasome subunit alpha type-7 (chains J, j)
MSYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVEKKSVAKLQDERTVR
KICALDDNVCMAFAGLTADARIVINRARVECQSHRLTVEDPVTVEYITRYIASLKQRYTQ
SNGRRPFGISALIVGFDFDGTPRLYQTDPSGTYHAWKANAIGRGAKSVREFLEKNYTDEA
IETDDLTIKLVIKALLEVVQSGGKNIELAVMRRDQSLKILNPEEIEKYVAEIEKEKEENE
KKKQKKAS

Sequence of entity 5 (K, k), FASTA

>9NKG_5 Proteasome subunit alpha type-5 (chains K, k)
MFLTRSEYYRGVNTFSPEGRLFQVEYAIEAIKLGSTAIGIQTSEGVCLAVEKRITSPLME
PSSIEKIVEIDAHIGCAMSGLIADAKTLIDKARVETQNHWFTYNETMTVESVTQAVSNLA
LQFGEEDADPGAMSRPFGVALLFGGVDEKGPQLFHMDPSGTFVQCDARAIGSASEGAQSS
LQEVYHKSMTLKEAIKSSLIILKQVMEEKLNATNIELATVQPGQNFHMFTKEELEEVIKD
I

Sequence of entity 6 (L, l), FASTA

>9NKG_6 Proteasome subunit alpha type-1 (chains L, l)
MFRNQYDNDVTVWSPQGRIHQIEYAMEAVKQGSATVGLKSKTHAVLVALKRAQSELAAHQ
KKILHVDNHIGISIAGLTADARLLCNFMRQECLDSRFVFDRPLPVSRLVSLIGSKTQIPT
QRYGRRPYGVGLLIAGYDDMGPHIFQTCPSANYFDCRAMSIGARSQSARTYLERHMSEFM
ECNLNELVKHGLRALRETLPAEQDLTTKNVSIGIVGKDLEFTIYDDDDVSPFLEGLEERP
QRKAQPAQPADEPAEKADEPMEH

Sequence of entity 7 (M, m), FASTA

>9NKG_7 Proteasome subunit alpha type-3 (chains M, m)
MSSIGTGYDLSASTFSPDGRVFQVEYAMKAVENSSTAIGIRCKDGVVFGVEKLVLSKLYE
EGSNKRLFNVDRHVGMAVAGLLADARSLADIAREEASNFRSNFGYNIPLKHLADRVAMYV
HAYTLYSAVRPFGCSFMLGSYSVNDGAQLYMIDPSGVSYGYWGCAIGKARQAAKTEIEKL
QMKEMTCRDIVKEVAKIIYIVHDEVKDKAFELELSWVGELTNGRHEIVPKDIREEAEKYA
KESLKEEDESDDDNM

Sequence of entity 8 (N, n), FASTA

>9NKG_8 Proteasome subunit beta type-6 (chains N, n)
MAATLLAARGAGPAPAWGPEAFTPDWESREVSTGTTIMAVQFDGGVVLGADSRTTTGSYI
ANRVTDKLTPIHDRIFCCRSGSAADTQAVADAVTYQLGFHSIELNEPPLVHTAASLFKEM
CYRYREDLMAGIIIAGWDPQEGGQVYSVPMGGMMVRQSFAIGGSGSSYIYGYVDATYREG
MTKEECLQFTANALALAMERDGSSGGVIRLAAIAESGVERQVLLGDQIPKFAVATLPPA

Sequence of entity 9 (O, o), FASTA

>9NKG_9 Proteasome subunit beta type-7 (chains O, o)
MAAVSVYAPPVGGFSFDNCRRNAVLEADFAKRGYKLPKVRKTGTTIAGVVYKDGIVLGAD
TRATEGMVVADKNCSKIHFISPNIYCCGAGTAADTDMTTQLISSNLELHSLSTGRLPRVV
TANRMLKQMLFRYQGYIGAALVLGGVDVTGPHLYSIYPHGSTDKLPYVTMGSGSLAAMAV
FEDKFRPDMEEEEAKNLVSEAIAAGIFNDLGSGSNIDLCVISKNKLDFLRPYTVPNKKGT
RLGRYRCEKGTTAVLTEKITPLEIEVLEETVQTMDTS

Sequence of entity 10 (P, p), FASTA

>9NKG_10 Proteasome subunit beta type-3 (chains P, p)
MSIMSYNGGAVMAMKGKNCVAIAADRRFGIQAQMVTTDFQKIFPMGDRLYIGLAGLATDV
QTVAQRLKFRLNLYELKEGRQIKPYTLMSMVANLLYEKRFGPYYTEPVIAGLDPKTFKPF
ICSLDLIGCPMVTDDFVVSGTCAEQMYGMCESLWEPNMDPDHLFETISQAMLNAVDRDAV
SGMGVIVHIIEKDKITTRTLKARMD

Sequence of entity 11 (Q, q), FASTA

>9NKG_11 Proteasome subunit beta type-2 (chains Q, q)
MEYLIGIQGPDYVLVASDRVAASNIVQMKDDHDKMFKMSEKILLLCVGEAGDTVQFAEYI
QKNVQLYKMRNGYELSPTAAANFTRRNLADCLRSRTPYHVNLLLAGYDEHEGPALYYMDY
LAALAKAPFAAHGYGAFLTLSILDRYYTPTISRERAVELLRKCLEELQKRFILNLPTFSV
RIIDKNGIHDLDNISFPKQGS

Sequence of entity 12 (R, r), FASTA

>9NKG_12 Proteasome subunit beta type-5 (chains R, r)
MALASVLERPLPVNQRGFFGLGGRADLLDLGPGSLSDGLSLAAPGWGVPEEPGIEMLHGT
TTLAFKFRHGVIVAADSRATAGAYIASQTVKKVIEINPYLLGTMAGGAADCSFWERLLAR
QCRIYELRNKERISVAAASKLLANMVYQYKGMGLSMGTMICGWDKRGPGLYYVDSEGNRI
SGATFSVGSGSVYAYGVMDRGYSYDLEVEQAYDLARRAIYQATYRDAYSGGAVNLYHVRE
DGWIRVSSDNVADLHEKYSGSTP

Ligands and cofactors

ID	Name	Formula	Copies
LDZ	N-[(benzyloxy)carbonyl]-L-leucyl-N-[(2S)-4-methyl-1-oxopentan-2-yl]-L-leucinami…	C26 H41 N3 O5	6
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 P60900 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5LE5 1.8 Å, Native human 20S proteasome at 1.8 Angstrom
9TMN 1.85 Å, Human sperm 20S proteasome complex isolated from native source
5LEY 1.9 Å, Human 20S proteasome complex with Oprozomib at 1.9 Angstrom
5LF4 1.99 Å, Human 20S proteasome complex with Delanzomib at 2.0 Angstrom
5LF1 2.0 Å, Human 20S proteasome complex with Dihydroeponemycin at 2.0 Angstrom
5LF7 2.0 Å, Human 20S proteasome complex with Ixazomib at 2.0 Angstrom
8UD9 2.04 Å, Structure of human constitutive 20S proteasome complexed with the inhibitor TDI-8304
5LF6 2.07 Å, Human 20S proteasome complex with Z-LLY-ketoaldehyde at 2.1 Angstrom
5LF3 2.1 Å, Human 20S proteasome complex with Bortezomib at 2.1 Angstrom
8BZL 2.14 Å, Human 20S Proteasome in complex with peptide activator peptide BLM42
5LEZ 2.19 Å, Human 20S proteasome complex with Oprozomib in Mg-Acetate at 2.2 Angstrom
5LEX 2.2 Å, Native human 20S proteasome in Mg-Acetate at 2.2 Angstrom

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