8UD9: Human constitutive 20S proteasome

Structure of human constitutive 20S proteasome complexed with the inhibitor TDI-8304. Determined by electron microscopy at 2.04 Å resolution. Released 20 Dec 2023.

Method: Electron microscopy
Resolution: 2.04 Å
Organism: Homo sapiens
Chains: 28
Atoms: 49,955
Mol. weight: 718.95 kDa
Ligands: YRE
Released: 20 Dec 2023

Explore 8UD9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8UD9 contains 241 α-helices and 399 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 M: 5 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	11-16	6	6
β-strand	21-26	6	6
β-strand	29-31	3	7
β-strand	34-37	4	7
β-strand	43-47	5	8
β-strand	50-56	7	8
α-helix	58-79	22
α-helix	82-84	3
α-helix	85-98	14
β-strand	106-113	8	8
β-strand	119-124	6	8
β-strand	130-133	4	8
β-strand	135-139	5	6
α-helix	142-152	11
α-helix	168-185	18
β-strand	186	1	38
β-strand	193-199	7	6
β-strand	202-208	7	6

Chain A: 12 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	23-32	10
α-helix	33-35	3
β-strand	38-43	6	1
β-strand	47-53	7	1
β-strand	61	1	2
α-helix	63-65	3
β-strand	69-73	5	3
β-strand	76-82	7	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	160-163	4	3
β-strand	165-169	5	1
α-helix	172-185	14
α-helix	191-206	16
α-helix	212-214	3
β-strand	215-221	7	1
β-strand	228-229	2	1
α-helix	230-231	2
α-helix	232-243	12

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

Element	Residues	Length	Sheet
β-strand	6-8	3	14
β-strand	11-16	6	15
β-strand	19-25	7	15
β-strand	28-30	3	14
β-strand	33-36	4	14
β-strand	42-46	5	14
β-strand	49-56	8	14
α-helix	57-77	21
α-helix	85-101	17
β-strand	108-116	9	14
β-strand	119-125	7	14
β-strand	131-133	3	14
β-strand	136-138	3	15
α-helix	142-145	4
α-helix	147-156	10
α-helix	162-179	18
β-strand	180	1	35
β-strand	187-193	7	15
β-strand	196-203	8	15
α-helix	210-212	3

Chains B and P: 9 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	9	1	9
β-strand	13	1	10
β-strand	19	1	10
α-helix	20-30	11
β-strand	35-39	5	11
β-strand	44-49	6	11
β-strand	57	1	3
β-strand	66-69	4	12
β-strand	72-78	7	12
α-helix	80-101	22
α-helix	104-106	3
α-helix	107-120	14
β-strand	125	1	9
β-strand	127	1	4
α-helix	128-130	3
β-strand	132-140	9	12
β-strand	143-149	7	12
β-strand	155-157	3	12
β-strand	158	1	13
β-strand	160-163	4	11
α-helix	167-177	11
α-helix	184-197	14
β-strand	208-213	6	11
β-strand	218-220	3	11
α-helix	221-222	2
α-helix	223-233	11

Chains C and Q: 10 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	19-29	11
β-strand	34-39	6	16
β-strand	42-48	7	16
β-strand	56	1	13
β-strand	65-69	5	17
β-strand	72-78	7	17
α-helix	80-101	22
α-helix	104-106	3
α-helix	107-123	17
β-strand	124	1	18
α-helix	127-130	4
β-strand	132-140	9	17
β-strand	144-150	7	17
β-strand	156-158	3	17
β-strand	159	1	19
β-strand	161-164	4	16
α-helix	168-178	11
α-helix	186-199	14
α-helix	208-210	3
β-strand	211-219	9	16
β-strand	222-227	6	16
α-helix	228-229	2
α-helix	230-250	21

Chain D: 12 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	10	1	20
β-strand	16	1	20
α-helix	17-28	12
α-helix	30-31	2
β-strand	32-36	5	21
β-strand	40-46	7	21
β-strand	54	1	19
α-helix	56-59	4
β-strand	62-64	3	22
β-strand	69-75	7	22
α-helix	77-98	22
α-helix	101-103	3
α-helix	104-118	15
β-strand	121	1	23
β-strand	124	1	18
α-helix	125-127	3
β-strand	129-136	8	22
β-strand	142-147	6	22
β-strand	153-155	3	22
β-strand	156	1	24
β-strand	158-161	4	21
α-helix	165-175	11
α-helix	184-196	13
α-helix	203-205	3
β-strand	206-212	7	21
β-strand	218-219	2	21
α-helix	220-221	2
α-helix	222-243	22

Chain E: 12 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	14	1
β-strand	15	1	25
α-helix	16	1
β-strand	21	1	25
α-helix	22-31	10
α-helix	35-36	2
β-strand	37-42	6	26
β-strand	45-51	7	26
β-strand	59	1	24
α-helix	61-63	3
β-strand	67-71	5	27
β-strand	74-80	7	27
α-helix	82-103	22
α-helix	106-108	3
α-helix	109-117	9
β-strand	123	1	23
β-strand	133	1	23
β-strand	139-147	9	27
β-strand	150-156	7	27
β-strand	162-164	3	27
β-strand	165	1	28
β-strand	167-170	4	26
α-helix	174-184	11
α-helix	191-205	15
α-helix	209-210	2
β-strand	215-220	6	26
β-strand	227-228	2	26
α-helix	231-239	9

Chain F: 13 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	20-31	12
α-helix	33-34	2
β-strand	35-39	5	29
β-strand	43-49	7	29
α-helix	50-51	2
β-strand	57	1	28
α-helix	58-61	4
β-strand	63-67	5	30
β-strand	70-76	7	30
α-helix	78-99	22
α-helix	102-104	3
α-helix	105-117	13
α-helix	118-121	4
β-strand	122	1	31
β-strand	130-138	9	30
β-strand	141-147	7	30
β-strand	153-156	4	30
β-strand	158-161	4	29
α-helix	165-175	11
α-helix	176-178	3
α-helix	184-198	15
β-strand	210-216	7	29
β-strand	222-225	4	29
α-helix	226-229	4
α-helix	230-234	5

11 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	234	Homo sapiens	P25787 (AlphaFold model)
Proteasome subunit alpha type-4	C, Q	protein	261	Homo sapiens	P25789 (AlphaFold model)
Proteasome subunit alpha type-7	D, R	protein	248	Homo sapiens	O14818 (AlphaFold model)
Proteasome subunit alpha type-5	E, S	protein	241	Homo sapiens	P28066
Proteasome subunit alpha type-1	F, T	protein	263	Homo sapiens	P25786
Proteasome subunit alpha type-3	G, U	protein	255	Homo sapiens	P25788
Proteasome subunit beta type-6	H, V	protein	205	Homo sapiens	P28072
Proteasome subunit beta type-7	I, W	protein	234	Homo sapiens	Q99436
Proteasome subunit beta type-3	J, X	protein	205	Homo sapiens	P49720
Proteasome subunit beta type-2	K, Y	protein	201	Homo sapiens	P49721
Proteasome subunit beta type-5	L, Z	protein	204	Homo sapiens	P28074

2 more molecules are not listed.

Sequence of entity 1 (A, O), FASTA

>8UD9_1 Proteasome subunit alpha type-6 (chains A, O)
MSRGSSAGFDRHITIFSPEGRLYQVEYAFKAINQGGLTSVAVRGKDCAVIVTQKKVPDKL
LDSSTVTHLFKITENIGCVMTGMTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKRIAD
ISQVYTQNAEMRPLGCCMILIGIDEEQGPQVYKCDPAGYYCGFKATAAGVKQTESTSFLE
KKVKKKFDWTFEQTVETAITCLSTVLSIDFKPSEIEVGVVTVENPKFRILTEAEIDAHLV
ALAERD

Sequence of entity 2 (B, P), FASTA

>8UD9_2 Proteasome subunit alpha type-2 (chains B, P)
MAERGYSFSLTTFSPSGKLVQIEYALAAVAGGAPSVGIKAANGVVLATEKKQKSILYDER
SVHKVEPITKHIGLVYSGMGPDYRVLVHRARKLAQQYYLVYQEPIPTAQLVQRVASVMQE
YTQSGGVRPFGVSLLICGWNEGRPYLFQSDPSGAYFAWKATAMGKNYVNGKTFLEKRYNE
DLELEDAIHTAILTLKESFEGQMTEDNIEVGICNEAGFRRLTPTEVKDYLAAIA

Sequence of entity 3 (C, Q), FASTA

>8UD9_3 Proteasome subunit alpha type-4 (chains C, Q)
MSRRYDSRTTIFSPEGRLYQVEYAMEAIGHAGTCLGILANDGVLLAAERRNIHKLLDEVF
FSEKIYKLNEDMACSVAGITSDANVLTNELRLIAQRYLLQYQEPIPCEQLVTALCDIKQA
YTQFGGKRPFGVSLLYIGWDKHYGFQLYQSDPSGNYGGWKATCIGNNSAAAVSMLKQDYK
EGEMTLKSALALAIKVLNKTMDVSKLSAEKVEIATLTRENGKTVIRVLKQKEVEQLIKKH
EEEEAKAEREKKEKEQKEKDK

Sequence of entity 4 (D, R), FASTA

>8UD9_4 Proteasome subunit alpha type-7 (chains D, R)
MSYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVEKKSVAKLQDERTVR
KICALDDNVCMAFAGLTADARIVINRARVECQSHRLTVEDPVTVEYITRYIASLKQRYTQ
SNGRRPFGISALIVGFDFDGTPRLYQTDPSGTYHAWKANAIGRGAKSVREFLEKNYTDEA
IETDDLTIKLVIKALLEVVQSGGKNIELAVMRRDQSLKILNPEEIEKYVAEIEKEKEENE
KKKQKKAS

Sequence of entity 5 (E, S), FASTA

>8UD9_5 Proteasome subunit alpha type-5 (chains E, S)
MFLTRSEYDRGVNTFSPEGRLFQVEYAIEAIKLGSTAIGIQTSEGVCLAVEKRITSPLME
PSSIEKIVEIDAHIGCAMSGLIADAKTLIDKARVETQNHWFTYNETMTVESVTQAVSNLA
LQFGEEDADPGAMSRPFGVALLFGGVDEKGPQLFHMDPSGTFVQCDARAIGSASEGAQSS
LQEVYHKSMTLKEAIKSSLIILKQVMEEKLNATNIELATVQPGQNFHMFTKEELEEVIKD
I

Sequence of entity 6 (F, T), FASTA

>8UD9_6 Proteasome subunit alpha type-1 (chains F, T)
MFRNQYDNDVTVWSPQGRIHQIEYAMEAVKQGSATVGLKSKTHAVLVALKRAQSELAAHQ
KKILHVDNHIGISIAGLTADARLLCNFMRQECLDSRFVFDRPLPVSRLVSLIGSKTQIPT
QRYGRRPYGVGLLIAGYDDMGPHIFQTCPSANYFDCRAMSIGARSQSARTYLERHMSEFM
ECNLNELVKHGLRALRETLPAEQDLTTKNVSIGIVGKDLEFTIYDDDDVSPFLEGLEERP
QRKAQPAQPADEPAEKADEPMEH

Sequence of entity 7 (G, U), FASTA

>8UD9_7 Proteasome subunit alpha type-3 (chains G, U)
MSSIGTGYDLSASTFSPDGRVFQVEYAMKAVENSSTAIGIRCKDGVVFGVEKLVLSKLYE
EGSNKRLFNVDRHVGMAVAGLLADARSLADIAREEASNFRSNFGYNIPLKHLADRVAMYV
HAYTLYSAVRPFGCSFMLGSYSVNDGAQLYMIDPSGVSYGYWGCAIGKARQAAKTEIEKL
QMKEMTCRDIVKEVAKIIYIVHDEVKDKAFELELSWVGELTNGRHEIVPKDIREEAEKYA
KESLKEEDESDDDNM

Sequence of entity 8 (H, V), FASTA

>8UD9_8 Proteasome subunit beta type-6 (chains H, V)
TTIMAVQFDGGVVLGADSRTTTGSYIANRVTDKLTPIHDRIFCCRSGSAADTQAVADAVT
YQLGFHSIELNEPPLVHTAASLFKEMCYRYREDLMAGIIIAGWDPQEGGQVYSVPMGGMM
VRQSFAIGGSGSSYIYGYVDATYREGMTKEECLQFTANALALAMERDGSSGGVIRLAAIA
ESGVERQVLLGDQIPKFAVATLPPA

Sequence of entity 9 (I, W), FASTA

>8UD9_9 Proteasome subunit beta type-7 (chains I, W)
TTIAGVVYKDGIVLGADTRATEGMVVADKNCSKIHFISPNIYCCGAGTAADTDMTTQLIS
SNLELHSLSTGRLPRVVTANRMLKQMLFRYQGYIGAALVLGGVDVTGPHLYSIYPHGSTD
KLPYVTMGSGSLAAMAVFEDKFRPDMEEEEAKNLVSEAIAAGIFNDLGSGSNIDLCVISK
NKLDFLRPYTVPNKKGTRLGRYRCEKGTTAVLTEKITPLEIEVLEETVQTMDTS

Sequence of entity 10 (J, X), FASTA

>8UD9_10 Proteasome subunit beta type-3 (chains J, X)
MSIMSYNGGAVMAMKGKNCVAIAADRRFGIQAQMVTTDFQKIFPMGDRLYIGLAGLATDV
QTVAQRLKFRLNLYELKEGRQIKPYTLMSMVANLLYEKRFGPYYTEPVIAGLDPKTFKPF
ICSLDLIGCPMVTDDFVVSGTCAEQMYGMCESLWEPNMDPDHLFETISQAMLNAVDRDAV
SGMGVIVHIIEKDKITTRTLKARMD

Sequence of entity 11 (K, Y), FASTA

>8UD9_11 Proteasome subunit beta type-2 (chains K, Y)
MEYLIGIQGPDYVLVASDRVAASNIVQMKDDHDKMFKMSEKILLLCVGEAGDTVQFAEYI
QKNVQLYKMRNGYELSPTAAANFTRRNLADCLRSRTPYHVNLLLAGYDEHEGPALYYMDY
LAALAKAPFAAHGYGAFLTLSILDRYYTPTISRERAVELLRKCLEELQKRFILNLPTFSV
RIIDKNGIHDLDNISFPKQGS

Sequence of entity 12 (L, Z), FASTA

>8UD9_12 Proteasome subunit beta type-5 (chains L, Z)
TTTLAFKFRHGVIVAADSRATAGAYIASQTVKKVIEINPYLLGTMAGGAADCSFWERLLA
RQCRIYELRNKERISVAAASKLLANMVYQYKGMGLSMGTMICGWDKRGPGLYYVDSEGNR
ISGATFSVGSGSVYAYGVMDRGYSYDLEVEQAYDLARRAIYQATYRDAYSGGAVNLYHVR
EDGWIRVSSDNVADLHEKYSGSTP

Ligands and cofactors

ID	Name	Formula	Copies
YRE	(7S,10S,13S)-N-cyclopentyl-10-[2-(morpholin-4-yl)ethyl]-9,12-dioxo-13-(2-oxopyr…	C32 H47 N5 O6	2

Primary citation

Structures revealing mechanisms of resistance and collateral sensitivity of Plasmodium falciparum to proteasome inhibitors. Hsu, H.C., Li, D., Zhan, W. et al. Nat Commun (2023) 14:8302-8302. DOI 10.1038/s41467-023-44077-2 · 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
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
7AWE 2.29 Å, HUMAN IMMUNOPROTEASOME 20S PARTICLE IN COMPLEX WITH [(1R)-2-(1-benzofuran-3-yl)-1-{[(1S,2…

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