7B12: HUMAN IMMUNOPROTEASOME 20S PARTICLE

HUMAN IMMUNOPROTEASOME 20S PARTICLE IN COMPLEX WITH [2-(3-ethylphenyl)-1-[(2S)-3-phenyl-2-[(pyrazin-2-yl)formamido]propanamido]ethyl]boronic acid. Determined by X-ray diffraction at 2.43 Å resolution. Released 1 Dec 2021.

Method: X-ray diffraction
Resolution: 2.43 Å
Organism: Homo sapiens
Chains: 28
Atoms: 49,338
Mol. weight: 694.45 kDa
Ligands: SKN
Released: 1 Dec 2021

Explore 7B12 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7B12 contains 235 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 1 and M: 6 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	11-16	6	1
β-strand	21-26	6	1
β-strand	29-31	3	2
β-strand	34-37	4	2
β-strand	43-47	5	3
β-strand	50-56	7	3
α-helix	58-79	22
α-helix	82-84	3
α-helix	85-98	14
β-strand	106-113	8	3
β-strand	119-124	6	3
β-strand	130-133	4	3
β-strand	135-139	5	1
α-helix	142-152	11
α-helix	164-167	4
α-helix	168-185	18
β-strand	186	1	4
β-strand	192-199	8	1
β-strand	202-209	8	1

Chain 2: 5 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	7-8	2	8
β-strand	11-16	6	9
β-strand	19-25	7	9
β-strand	28-30	3	8
β-strand	33-36	4	8
β-strand	42-44	3	8
β-strand	49-56	8	8
α-helix	57-77	21
α-helix	85-101	17
β-strand	108-116	9	8
β-strand	119-126	8	8
β-strand	131-133	3	8
β-strand	136-138	3	9
α-helix	142-156	15
α-helix	162-179	18
β-strand	180	1	10
β-strand	187-193	7	9
β-strand	196-203	8	9
α-helix	210-213	4

Chain A: 10 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	23-34	12
β-strand	38-43	6	14
β-strand	47-53	7	14
β-strand	61	1	15
α-helix	63-65	3
β-strand	69-71	3	16
β-strand	77-82	6	16
α-helix	84-105	22
α-helix	108-110	3
α-helix	111-127	17
β-strand	128	1	17
β-strand	131	1	18
α-helix	132-134	3
β-strand	136-144	9	16
β-strand	148-154	7	16
β-strand	160-162	3	16
β-strand	163	1	19
β-strand	165-169	5	14
α-helix	172-184	13
α-helix	191-206	16
β-strand	215-221	7	14
β-strand	228-229	2	14
α-helix	230-231	2
α-helix	232-243	12

Chain B: 11 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	8	1	20
β-strand	12	1	21
β-strand	18	1	21
α-helix	19-29	11
α-helix	32-33	2
β-strand	34-38	5	22
β-strand	43-48	6	22
β-strand	56	1	19
α-helix	58-60	3
β-strand	65-66	2	23
β-strand	71-77	7	23
α-helix	79-100	22
α-helix	103-105	3
α-helix	106-119	14
β-strand	124	1	20
β-strand	126	1	17
α-helix	127-129	3
β-strand	131-139	9	23
β-strand	142-148	7	23
β-strand	154-156	3	23
β-strand	157	1	24
β-strand	159-162	4	22
α-helix	166-176	11
α-helix	183-195	13
β-strand	207-213	7	22
β-strand	216-219	4	22
α-helix	220-221	2
α-helix	222-230	9

Chain C: 9 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	19-30	12
α-helix	32-33	2
β-strand	34-38	5	25
β-strand	42-48	7	25
β-strand	56	1	24
β-strand	65-67	3	26
β-strand	72-78	7	26
α-helix	80-101	22
α-helix	104-106	3
α-helix	107-123	17
β-strand	124	1	27
β-strand	132-140	9	26
β-strand	144-150	7	26
β-strand	156-158	3	26
β-strand	159	1	28
β-strand	161-164	4	25
α-helix	168-178	11
α-helix	186-200	15
β-strand	211-219	9	25
β-strand	222-227	6	25
α-helix	228-229	2
α-helix	230-245	16

Chain D: 11 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	10	1	29
β-strand	16	1	29
α-helix	17-26	10
α-helix	30-31	2
β-strand	32-36	5	30
β-strand	40-46	7	30
β-strand	54	1	28
α-helix	56-59	4
β-strand	62-64	3	31
β-strand	69-75	7	31
α-helix	77-98	22
α-helix	101-103	3
α-helix	104-118	15
β-strand	121	1	32
β-strand	124	1	27
α-helix	125-127	3
β-strand	129-136	8	31
β-strand	142-147	6	31
β-strand	153-155	3	31
β-strand	156	1	33
β-strand	158-161	4	30
α-helix	165-175	11
α-helix	178-182	5
α-helix	184-196	13
β-strand	206-212	7	30
β-strand	217-219	3	30
α-helix	222-234	13

Chain E: 13 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	14	1
β-strand	15	1	34
α-helix	16	1
β-strand	21	1	34
α-helix	22-31	10
α-helix	35-36	2
β-strand	37-42	6	35
β-strand	45-51	7	35
β-strand	59	1	33
α-helix	61-63	3
β-strand	67-71	5	36
β-strand	74-80	7	36
α-helix	82-103	22
α-helix	106-108	3
α-helix	109-118	10
β-strand	123	1	32
β-strand	133	1	32
β-strand	139-147	9	36
β-strand	150-156	7	36
β-strand	162-164	3	36
β-strand	165	1	37
β-strand	167-170	4	35
α-helix	174-184	11
α-helix	191-205	15
α-helix	209-210	2
β-strand	215-221	7	35
β-strand	225-228	4	35
α-helix	229-230	2
α-helix	231-239	9

Chain F: 14 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	12-14	3
α-helix	20-31	12
β-strand	33	1	38
α-helix	34	1
β-strand	35-39	5	39
β-strand	43-49	7	39
α-helix	50-51	2
β-strand	52	1	40
β-strand	57	1	37
α-helix	58	1
β-strand	59	1	40
α-helix	60	1
β-strand	63-65	3	41
β-strand	70-76	7	41
α-helix	78-99	22
α-helix	102-104	3
α-helix	105-117	13
α-helix	118-120	3
β-strand	122	1	42
β-strand	130-138	9	41
β-strand	141-147	7	41
β-strand	153-156	4	41
β-strand	158-161	4	39
β-strand	163	1	38
α-helix	165-175	11
α-helix	176-178	3
α-helix	184-198	15
β-strand	210-216	7	39
β-strand	222-224	3	39
α-helix	230-233	4

19 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 beta type-1	1, M	protein	213	Homo sapiens	P20618 (AlphaFold model)
Proteasome subunit beta type-4	2, N	protein	214	Homo sapiens	P28070 (AlphaFold model)
Proteasome subunit alpha type-6	A, O	protein	242	Homo sapiens	P60900 (AlphaFold model)
Proteasome subunit alpha type-2	B, P	protein	229	Homo sapiens	P25787 (AlphaFold model)
Proteasome subunit alpha type-4	C, Q	protein	248	Homo sapiens	P25789
Proteasome subunit alpha type-7	D, r	protein	235	Homo sapiens	O14818
Proteasome subunit alpha type-5	E, s	protein	232	Homo sapiens	P28066
Proteasome subunit alpha type-1	F, T	protein	236	Homo sapiens	P25786
Proteasome subunit alpha type-3	G, U	protein	244	Homo sapiens	P25788
Proteasome subunit beta type-9	H, V	protein	199	Homo sapiens	P28065
Proteasome subunit beta type-3	J, X	protein	204	Homo sapiens	P49720
Proteasome subunit beta type-2	K, Y	protein	197	Homo sapiens	P49721

2 more molecules are not listed.

Sequence of entity 1 (1, M), FASTA

>7B12_1 Proteasome subunit beta type-1 (chains 1, M)
RFSPYVFNGGTILAIAGEDFAIVASDTRLSEGFSIHTRDSPKCYKLTDKTVIGCSGFHGD
CLTLTKIIEARLKMYKHSNNKAMTTGAIAAMLSTILYSRRFFPYYVYNIIGGLDEEGKGA
VYSFDPVGSYQRDSFKAGGSASAMLQPLLDNQVGFKNMQNVEHVPLSLDRAMRLVKDVFI
SAAERDVYTGDALRICIVTKEGIREETVSLRKD

Sequence of entity 2 (2, N), FASTA

>7B12_2 Proteasome subunit beta type-4 (chains 2, N)
TQNPMVTGTSVLGVKFEGGVVIAADMLGSYGSLARFRNISRIMRVNNSTMLGASGDYADF
QYLKQVLGQMVIDEELLGDGHSYSPRAIHSWLTRAMYSRRSKMNPLWNTMVIGGYADGES
FLGYVDMLGVAYEAPSLATGYGAYLAQPLLREVLEKQPVLSQTEARDLVERCMRVLYYRD
ARSYNRFQIATVTEKGVEIEGPLSTETNWDIAHM

Sequence of entity 3 (A, O), FASTA

>7B12_3 Proteasome subunit alpha type-6 (chains A, O)
GSSAGFDRHITIFSPEGRLYQVEYAFKAINQGGLTSVAVRGKDCAVIVTQKKVPDKLLDS
STVTHLFKITENIGCVMTGMTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKRIADISQ
VYTQNAEMRPLGCCMILIGIDEEQGPQVYKCDPAGYYCGFKATAAGVKQTESTSFLEKKV
KKKFDWTFEQTVETAITCLSTVLSIDFKPSEIEVGVVTVENPKFRILTEAEIDAHLVALA
ER

Sequence of entity 4 (B, P), FASTA

>7B12_4 Proteasome subunit alpha type-2 (chains B, P)
GYSFSLTTFSPSGKLVQIEYALAAVAGGAPSVGIKAANGVVLATEKKQKSILYDERSVHK
VEPITKHIGLVYSGMGPDYRVLVHRARKLAQQYYLVYQEPIPTAQLVQRVASVMQEYTQS
GGVRPFGVSLLICGWNEGRPYLFQSDPSGAYFAWKATAMGKNYVNGKTFLEKRYNEDLEL
EDAIHTAILTLKESFEGQMTEDNIEVGICNEAGFRRLTPTEVKDYLAAI

Sequence of entity 5 (C, Q), FASTA

>7B12_5 Proteasome subunit alpha type-4 (chains C, Q)
SRRYDSRTTIFSPEGRLYQVEYAMEAIGHAGTCLGILANDGVLLAAERRNIHKLLDEVFF
SEKIYKLNEDMACSVAGITSDANVLTNELRLIAQRYLLQYQEPIPCEQLVTALCDIKQAY
TQFGGKRPFGVSLLYIGWDKHYGFQLYQSDPSGNYGGWKATCIGNNSAAAVSMLKQDYKE
GEMTLKSALALAIKVLNKTMDVSKLSAEKVEIATLTRENGKTVIRVLKQKEVEQLIKKHE
EEEAKAER

Sequence of entity 6 (D, r), FASTA

>7B12_6 Proteasome subunit alpha type-7 (chains D, r)
SYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVEKKSVAKLQDERTVRK
ICALDDNVCMAFAGLTADARIVINRARVECQSHRLTVEDPVTVEYITRYIASLKQRYTQS
NGRRPFGISALIVGFDFDGTPRLYQTDPSGTYHAWKANAIGRGAKSVREFLEKNYTDEAI
ETDDLTIKLVIKALLEVVQSGGKNIELAVMRRDQSLKILNPEEIEKYVAEIEKEK

Sequence of entity 7 (E, s), FASTA

>7B12_7 Proteasome subunit alpha type-5 (chains E, s)
DRGVNTFSPEGRLFQVEYAIEAIKLGSTAIGIQTSEGVCLAVEKRITSPLMEPSSIEKIV
EIDAHIGCAMSGLIADAKTLIDKARVETQNHWFTYNETMTVESVTQAVSNLALQFGEEDA
DPGAMSRPFGVALLFGGVDEKGPQLFHMDPSGTFVQCDARAIGSASEGAQSSLQEVYHKS
MTLKEAIKSSLIILKQVMEEKLNATNIELATVQPGQNFHMFTKEELEEVIKD

Sequence of entity 8 (F, T), FASTA

>7B12_8 Proteasome subunit alpha type-1 (chains F, T)
NQYDNDVTVWSPQGRIHQIEYAMEAVKQGSATVGLKSKTHAVLVALKRAQSELAAHQKKI
LHVDNHIGISIAGLTADARLLCNFMRQECLDSRFVFDRPLPVSRLVSLIGSKTQIPTQRY
GRRPYGVGLLIAGYDDMGPHIFQTCPSANYFDCRAMSIGARSQSARTYLERHMSEFMECN
LNELVKHGLRALRETLPAEQDLTTKNVSIGIVGKDLEFTIYDDDDVSPFLEGLEER

Sequence of entity 9 (G, U), FASTA

>7B12_9 Proteasome subunit alpha type-3 (chains G, U)
SIGTGYDLSASTFSPDGRVFQVEYAMKAVENSSTAIGIRCKDGVVFGVEKLVLSKLYEEG
SNKRLFNVDRHVGMAVAGLLADARSLADIAREEASNFRSNFGYNIPLKHLADRVAMYVHA
YTLYSAVRPFGCSFMLGSYSVNDGAQLYMIDPSGVSYGYWGCAIGKARQAAKTEIEKLQM
KEMTCRDIVKEVAKIIYIVHDEVKDKAFELELSWVGELTNGRHEIVPKDIREEAEKYAKE
SLKE

Sequence of entity 10 (H, V), FASTA

>7B12_10 Proteasome subunit beta type-9 (chains H, V)
TTIMAVEFDGGVVMGSDSRVSAGEAVVNRVFDKLSPLHERIYCALSGSAADAQAVADMAA
YQLELHGIELEEPPLVLAAANVVRNISYKYREDLSAHLMVAGWDQREGGQVYGTLGGMLT
RQPFAIGGSGSTFIYGYVDAAYKPGMSPEECRRFTTDAIALAMSRDGSSGGVIYLVTITA
AGVDHRVILGNELPKFYDE

Sequence of entity 11 (J, X), FASTA

>7B12_11 Proteasome subunit beta type-3 (chains J, X)
SIMSYNGGAVMAMKGKNCVAIAADRRFGIQAQMVTTDFQKIFPMGDRLYIGLAGLATDVQ
TVAQRLKFRLNLYELKEGRQIKPYTLMSMVANLLYEKRFGPYYTEPVIAGLDPKTFKPFI
CSLDLIGCPMVTDDFVVSGTCAEQMYGMCESLWEPNMDPDHLFETISQAMLNAVDRDAVS
GMGVIVHIIEKDKITTRTLKARMD

Sequence of entity 12 (K, Y), FASTA

>7B12_12 Proteasome subunit beta type-2 (chains K, Y)
MEYLIGIQGPDYVLVASDRVAASNIVQMKDDHDKMFKMSEKILLLCVGEAGDTVQFAEYI
QKNVQLYKMRNGYELSPTAAANFTRRNLADCLRSRTPYHVNLLLAGYDEHEGPALYYMDY
LAALAKAPFAAHGYGAFLTLSILDRYYTPTISRERAVELLRKCLEELQKRFILNLPTFSV
RIIDKNGIHDLDNISFP

Ligands and cofactors

ID	Name	Formula	Copies
SKN	((R)-2-(3-ethylphenyl)-1-((S)-3-phenyl-2-(pyrazine-2-carboxamido)propanamido)et…	C24 H27 B N4 O4	6

Water and common crystallization additives (SO4, NA) are not listed.

Primary citation

Structure-Based Optimization and Discovery of M3258, a Specific Inhibitor of the Immunoproteasome Subunit LMP7 ( beta 5i). Klein, M., Busch, M., Friese-Hamim, M. et al. J Med Chem (2021) 64:10230-10245. DOI 10.1021/acs.jmedchem.1c00604 · PubMed

Other PDB entries of the same protein (UniProt P20618 (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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