9HMN: Human 20S proteasome

CryoEM structure of human 20S proteasome in complex with proteasome inhibitor Salinosporamid A. Determined by electron microscopy at 2.55 Å resolution. Released 5 Mar 2025.

Method: Electron microscopy
Resolution: 2.55 Å
Organism: Homo sapiens
Chains: 28
Atoms: 48,800
Mol. weight: 718.64 kDa
Ligands: SA1
Released: 5 Mar 2025

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

Secondary structure: helices and β-sheets

9HMN contains 221 α-helices and 394 β-strands across 28 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.

Chains a and I: 5 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	7
β-strand	11-17	7	7
β-strand	20-22	3	8
β-strand	25-28	4	8
β-strand	34-38	5	9
β-strand	41-47	7	9
α-helix	49-70	22
α-helix	76-89	14
β-strand	96-104	9	9
β-strand	107-113	7	9
β-strand	119-121	3	9
β-strand	124-128	5	7
α-helix	131-141	11
α-helix	148-165	18
β-strand	166	1	40
β-strand	173-179	7	7
β-strand	183-190	8	7
α-helix	195-198	4
β-strand	211-218	8	85

Chain A: 10 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	23-32	10
β-strand	38-43	6	1
β-strand	47-53	7	1
β-strand	61	1	2
α-helix	63-65	3
β-strand	69-71	3	3
β-strand	77-82	6	3
α-helix	84-105	22
α-helix	108-110	3
α-helix	111-127	17
β-strand	128	1	4
β-strand	131	1	5
α-helix	132-134	3
β-strand	136-144	9	3
β-strand	148-154	7	3
β-strand	160-162	3	3
β-strand	163	1	6
β-strand	165-169	5	1
α-helix	172-184	13
α-helix	191-206	16
α-helix	209-211	3
β-strand	215-221	7	1
β-strand	228-229	2	1
α-helix	232-243	12

Chains b and L: 6 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	15
β-strand	11-16	6	15
β-strand	20-22	3	16
β-strand	25-28	4	16
β-strand	34-38	5	17
β-strand	41-44	4	17
β-strand	46-47	2	17
α-helix	49-70	22
α-helix	73-75	3
α-helix	76-88	13
β-strand	97-105	9	17
β-strand	108-115	8	17
β-strand	120-122	3	17
β-strand	125-129	5	15
α-helix	132-142	11
α-helix	149-166	18
β-strand	167	1	32
β-strand	173-180	8	15
β-strand	183-191	9	15
α-helix	192-199	8

Chains B and P: 8 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	9	1	10
β-strand	13	1	11
β-strand	19	1	11
α-helix	20-30	11
β-strand	35-39	5	12
β-strand	44-49	6	12
β-strand	57	1	6
β-strand	66-67	2	13
β-strand	73-78	6	13
α-helix	80-101	22
α-helix	104-106	3
α-helix	107-120	14
β-strand	125	1	10
β-strand	127	1	4
β-strand	132-140	9	13
β-strand	143-149	7	13
β-strand	155-157	3	13
β-strand	158	1	14
β-strand	160-163	4	12
α-helix	167-177	11
α-helix	184-196	13
β-strand	208-214	7	12
β-strand	217-220	4	12
α-helix	221-222	2
α-helix	223-233	11

Chains C and Q: 10 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	19-28	10
β-strand	34-38	5	18
β-strand	42-48	7	18
β-strand	56	1	14
β-strand	65-67	3	19
β-strand	72-78	7	19
α-helix	80-101	22
α-helix	104-106	3
α-helix	107-123	17
β-strand	124	1	20
α-helix	128-130	3
β-strand	132-140	9	19
β-strand	144-150	7	19
β-strand	156-159	4	19
β-strand	161-164	4	18
α-helix	168-178	11
α-helix	186-200	15
α-helix	208-210	3
β-strand	211-219	9	18
β-strand	222-227	6	18
α-helix	228-229	2
α-helix	230-253	24

Chains D and Y: 8 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	45
β-strand	10	1	46
β-strand	16	1	46
α-helix	17-27	11
β-strand	32-36	5	47
β-strand	40-46	7	47
β-strand	54	1	19
β-strand	63-64	2	48
β-strand	69-75	7	48
α-helix	77-98	22
α-helix	101-103	3
α-helix	104-118	15
β-strand	121	1	25
β-strand	122	1	45
β-strand	124	1	20
β-strand	129-136	8	48
β-strand	142-147	6	48
β-strand	153-155	3	48
β-strand	156	1	23
β-strand	158-161	4	47
α-helix	165-175	11
α-helix	179-181	3
α-helix	184-198	15
β-strand	206-212	7	47
β-strand	219-220	2	47
α-helix	222-237	16

Chains E and R: 10 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	14	1
β-strand	15	1	21
α-helix	16	1
β-strand	21	1	21
α-helix	22-31	10
β-strand	37-42	6	22
β-strand	45-51	7	22
β-strand	59	1	23
α-helix	61-63	3
β-strand	67-71	5	24
β-strand	74-80	7	24
α-helix	85-103	19
α-helix	106-108	3
α-helix	109-117	9
β-strand	123	1	25
β-strand	133	1	25
β-strand	139-147	9	24
β-strand	150-156	7	24
β-strand	162-164	3	24
β-strand	167-170	4	22
α-helix	174-184	11
α-helix	191-205	15
β-strand	215-220	6	22
β-strand	226-228	3	22
α-helix	231-240	10

Chains F and S: 12 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	12-14	3
α-helix	20-31	12
β-strand	35-39	5	26
β-strand	43-49	7	26
α-helix	58-61	4
β-strand	63-67	5	27
β-strand	70-76	7	27
α-helix	78-99	22
α-helix	102-104	3
α-helix	105-117	13
α-helix	118-121	4
β-strand	122	1	28
β-strand	130-138	9	27
β-strand	141-147	7	27
β-strand	153-156	4	27
β-strand	158-161	4	26
α-helix	165-179	15
α-helix	184-196	13
β-strand	210-216	7	26
β-strand	219-225	7	26
α-helix	226-229	4
α-helix	230-233	4
α-helix	237-239	3

7 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	A, O	protein	246	Homo sapiens	P60900 (AlphaFold model)
Proteasome subunit alpha type-2	B, P	protein	233	Homo sapiens	P25787 (AlphaFold model)
Proteasome subunit alpha type-4	C, Q	protein	261	Homo sapiens	P25789 (AlphaFold model)
Proteasome subunit alpha type-5	E, R	protein	241	Homo sapiens	P28066 (AlphaFold model)
Proteasome subunit alpha type-1	F, S	protein	263	Homo sapiens	P25786
Proteasome subunit alpha type-3	G, T	protein	254	Homo sapiens	P25788
Proteasome subunit beta type-3	J, U	protein	204	Homo sapiens	P49720
Proteasome subunit beta type-2	K, V	protein	201	Homo sapiens	P49721
Proteasome subunit beta type-1	M, W	protein	213	Homo sapiens	P20618
Proteasome subunit beta type-4	N, X	protein	219	Homo sapiens	P28070
Proteasome subunit alpha type-7	D, Y	protein	248	Homo sapiens	O14818
Proteasome subunit beta type-6	H, Z	protein	205	Homo sapiens	P28072

2 more molecules are not listed.

Sequence of entity 1 (A, O), FASTA

>9HMN_1 Proteasome subunit alpha type-6 (chains A, O)
MSRGSSAGFDRHITIFSPEGRLYQVEYAFKAINQGGLTSVAVRGKDCAVIVTQKKVPDKL
LDSSTVTHLFKITENIGCVMTGMTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKRIAD
ISQVYTQNAEMRPLGCCMILIGIDEEQGPQVYKCDPAGYYCGFKATAAGVKQTESTSFLE
KKVKKKFDWTFEQTVETAITCLSTVLSIDFKPSEIEVGVVTVENPKFRILTEAEIDAHLV
ALAERD

Sequence of entity 2 (B, P), FASTA

>9HMN_2 Proteasome subunit alpha type-2 (chains B, P)
AERGYSFSLTTFSPSGKLVQIEYALAAVAGGAPSVGIKAANGVVLATEKKQKSILYDERS
VHKVEPITKHIGLVYSGMGPDYRVLVHRARKLAQQYYLVYQEPIPTAQLVQRVASVMQEY
TQSGGVRPFGVSLLICGWNEGRPYLFQSDPSGAYFAWKATAMGKNYVNGKTFLEKRYNED
LELEDAIHTAILTLKESFEGQMTEDNIEVGICNEAGFRRLTPTEVKDYLAAIA

Sequence of entity 3 (C, Q), FASTA

>9HMN_3 Proteasome subunit alpha type-4 (chains C, Q)
MSRRYDSRTTIFSPEGRLYQVEYAMEAIGHAGTCLGILANDGVLLAAERRNIHKLLDEVF
FSEKIYKLNEDMACSVAGITSDANVLTNELRLIAQRYLLQYQEPIPCEQLVTALCDIKQA
YTQFGGKRPFGVSLLYIGWDKHYGFQLYQSDPSGNYGGWKATCIGNNSAAAVSMLKQDYK
EGEMTLKSALALAIKVLNKTMDVSKLSAEKVEIATLTRENGKTVIRVLKQKEVEQLIKKH
EEEEAKAEREKKEKEQKEKDK

Sequence of entity 4 (E, R), FASTA

>9HMN_4 Proteasome subunit alpha type-5 (chains E, R)
MFLTRSEYDRGVNTFSPEGRLFQVEYAIEAIKLGSTAIGIQTSEGVCLAVEKRITSPLME
PSSIEKIVEIDAHIGCAMSGLIADAKTLIDKARVETQNHWFTYNETMTVESVTQAVSNLA
LQFGEEDADPGAMSRPFGVALLFGGVDEKGPQLFHMDPSGTFVQCDARAIGSASEGAQSS
LQEVYHKSMTLKEAIKSSLIILKQVMEEKLNATNIELATVQPGQNFHMFTKEELEEVIKD
I

Sequence of entity 5 (F, S), FASTA

>9HMN_5 Proteasome subunit alpha type-1 (chains F, S)
MFRNQYDNDVTVWSPQGRIHQIEYAMEAVKQGSATVGLKSKTHAVLVALKRAQSELAAHQ
KKILHVDNHIGISIAGLTADARLLCNFMRQECLDSRFVFDRPLPVSRLVSLIGSKTQIPT
QRYGRRPYGVGLLIAGYDDMGPHIFQTCPSANYFDCRAMSIGARSQSARTYLERHMSEFM
ECNLNELVKHGLRALRETLPAEQDLTTKNVSIGIVGKDLEFTIYDDDDVSPFLEGLEERP
QRKAQPAQPADEPAEKADEPMEH

Sequence of entity 6 (G, T), FASTA

>9HMN_6 Proteasome subunit alpha type-3 (chains G, T)
SSIGTGYDLSASTFSPDGRVFQVEYAMKAVENSSTAIGIRCKDGVVFGVEKLVLSKLYEE
GSNKRLFNVDRHVGMAVAGLLADARSLADIAREEASNFRSNFGYNIPLKHLADRVAMYVH
AYTLYSAVRPFGCSFMLGSYSVNDGAQLYMIDPSGVSYGYWGCAIGKARQAAKTEIEKLQ
MKEMTCRDIVKEVAKIIYIVHDEVKDKAFELELSWVGELTNGRHEIVPKDIREEAEKYAK
ESLKEEDESDDDNM

Sequence of entity 7 (J, U), FASTA

>9HMN_7 Proteasome subunit beta type-3 (chains J, U)
SIMSYNGGAVMAMKGKNCVAIAADRRFGIQAQMVTTDFQKIFPMGDRLYIGLAGLATDVQ
TVAQRLKFRLNLYELKEGRQIKPYTLMSMVANLLYEKRFGPYYTEPVIAGLDPKTFKPFI
CSLDLIGCPMVTDDFVVSGTCAEQMYGMCESLWEPNMDPDHLFETISQAMLNAVDRDAVS
GMGVIVHIIEKDKITTRTLKARMD

Sequence of entity 8 (K, V), FASTA

>9HMN_8 Proteasome subunit beta type-2 (chains K, V)
MEYLIGIQGPDYVLVASDRVAASNIVQMKDDHDKMFKMSEKILLLCVGEAGDTVQFAEYI
QKNVQLYKMRNGYELSPTAAANFTRRNLADCLRSRTPYHVNLLLAGYDEHEGPALYYMDY
LAALAKAPFAAHGYGAFLTLSILDRYYTPTISRERAVELLRKCLEELQKRFILNLPTFSV
RIIDKNGIHDLDNISFPKQGS

Sequence of entity 9 (M, W), FASTA

>9HMN_9 Proteasome subunit beta type-1 (chains M, W)
RFSPYVFNGGTILAIAGEDFAIVASDTRLSEGFSIHTRDSPKCYKLTDKTVIGCSGFHGD
CLTLTKIIEARLKMYKHSNNKAMTTGAIAAMLSTILYSRRFFPYYVYNIIGGLDEEGKGA
VYSFDPVGSYQRDSFKAGGSASAMLQPLLDNQVGFKNMQNVEHVPLSLDRAMRLVKDVFI
SAAERDVYTGDALRICIVTKEGIREETVSLRKD

Sequence of entity 10 (N, X), FASTA

>9HMN_10 Proteasome subunit beta type-4 (chains N, X)
TQNPMVTGTSVLGVKFEGGVVIAADMLGSYGSLARFRNISRIMRVNNSTMLGASGDYADF
QYLKQVLGQMVIDEELLGDGHSYSPRAIHSWLTRAMYSRRSKMNPLWNTMVIGGYADGES
FLGYVDMLGVAYEAPSLATGYGAYLAQPLLREVLEKQPVLSQTEARDLVERCMRVLYYRD
ARSYNRFQIATVTEKGVEIEGPLSTETNWDIAHMISGFE

Sequence of entity 11 (D, Y), FASTA

>9HMN_11 Proteasome subunit alpha type-7 (chains D, Y)
MSYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVEKKSVAKLQDERTVR
KICALDDNVCMAFAGLTADARIVINRARVECQSHRLTVEDPVTVEYITRYIASLKQRYTQ
SNGRRPFGISALIVGFDFDGTPRLYQTDPSGTYHAWKANAIGRGAKSVREFLEKNYTDEA
IETDDLTIKLVIKALLEVVQSGGKNIELAVMRRDQSLKILNPEEIEKYVAEIEKEKEENE
KKKQKKAS

Sequence of entity 12 (H, Z), FASTA

>9HMN_12 Proteasome subunit beta type-6 (chains H, Z)
TTIMAVQFDGGVVLGADSRTTTGSYIANRVTDKLTPIHDRIFCCRSGSAADTQAVADAVT
YQLGFHSIELNEPPLVHTAASLFKEMCYRYREDLMAGIIIAGWDPQEGGQVYSVPMGGMM
VRQSFAIGGSGSSYIYGYVDATYREGMTKEECLQFTANALALAMERDGSSGGVIRLAAIA
ESGVERQVLLGDQIPKFAVATLPPA

Ligands and cofactors

ID	Name	Formula	Copies
SA1	(3AR,6R,6AS)-6-((S)-((S)-cyclohex-2-enyl)(hydroxy)methyl)-6A-methyl-4-oxo-hexah…	C15 H21 N O4	6

Primary citation

Structural Insights into Salinosporamide a Mediated Inhibition of the Human 20S Proteasome. Sulzen, H., Fajtova, P., O'Donoghue, A.J. et al. Molecules (2025) 30. DOI 10.3390/molecules30061386 · 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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