1G65: Proteasome component Y7

Crystal structure of epoxomicin:20s proteasome reveals a molecular basis for selectivity of alpha,beta-epoxyketone proteasome inhibitors. Determined by X-ray diffraction at 2.25 Å resolution. Released 27 Nov 2000.

Method: X-ray diffraction
Resolution: 2.25 Å
Organisms: Saccharomyces cerevisiae, Saccharomyces cerevisiae S288c
Chains: 30
Atoms: 52,508
Mol. weight: 705.53 kDa
Ligands: MG
Released: 27 Nov 2000

Explore 1G65 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1G65 contains 245 α-helices and 398 β-strands across 30 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 1: 8 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	-3--1	3	8
β-strand	3-8	6	9
β-strand	11-17	7	9
β-strand	20-22	3	8
β-strand	25-28	4	8
β-strand	34-36	3	8
β-strand	41-48	8	8
α-helix	49-67	19
α-helix	74-75	2
α-helix	76-92	17
β-strand	97-104	8	8
β-strand	108-114	7	8
β-strand	119-120	2	8
β-strand	124-126	3	9
α-helix	129-132	4
α-helix	134-138	5
α-helix	141D-145	6
α-helix	148-165	18
β-strand	166	1	59
β-strand	172-179	8	9
β-strand	183-191	9	9
α-helix	198-202	5

Chain 2: 7 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3-8	6	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	41-47	7	17
α-helix	49-70	22
α-helix	76-89	14
α-helix	91-94	3
β-strand	97-105	9	17
β-strand	107-113	7	17
β-strand	120-121	2	17
β-strand	124-127	4	15
α-helix	129-134	6
α-helix	135-141	7
α-helix	148-165	18
β-strand	166	1	57
β-strand	173-179	7	15
β-strand	183-187B	7	15
α-helix	187D-187G	4

Chains 3 and 4: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	4	1	46

Chain A: 12 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	11	1	1
α-helix	22-32	11
α-helix	35-36	2
β-strand	37-41	5	2
β-strand	46-51	6	2
β-strand	59	1	3
β-strand	68-71	4	4
β-strand	74-80	7	4
α-helix	82-96	15
α-helix	97-101	5
α-helix	102-103	3
α-helix	106-108	3
α-helix	109-123	15
β-strand	127	1	1
β-strand	129	1	5
β-strand	134-142	9	4
β-strand	146-151	7	4
β-strand	157-159	3	4
β-strand	160	1	6
β-strand	162-165	4	2
α-helix	169-179	11
α-helix	186-200	15
β-strand	210-215	6	2
α-helix	217D-217F	3
β-strand	217I-217J	2	7
β-strand	221-223	3	2
α-helix	224-225	2
α-helix	226-233	8

Chain B: 10 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	6-8	3
β-strand	15	1	10
β-strand	21	1	10
α-helix	22-32	11
α-helix	35-36	2
β-strand	37-41	5	11
β-strand	45-51	7	11
β-strand	59	1	6
β-strand	67-71	5	12
β-strand	74-80	7	12
α-helix	82-103	22
α-helix	106-108	3
α-helix	109-125	17
β-strand	126	1	13
β-strand	134-142	9	12
β-strand	145-151	7	12
β-strand	157-159	3	12
β-strand	160	1	14
β-strand	162-165	4	11
α-helix	169-179	11
α-helix	186-198	13
α-helix	207-209	3
β-strand	210-216	7	11
β-strand	220-223	4	11
α-helix	226-236	11

Chain C: 11 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	22-32	11
α-helix	35-36	2
β-strand	37-41	5	18
β-strand	46-51	6	18
α-helix	52-53	2
β-strand	59	1	14
β-strand	68-71	4	19
β-strand	74-80	7	19
α-helix	82-103	22
α-helix	106-108	3
α-helix	109-122	14
β-strand	129	1	13
α-helix	130-132	3
β-strand	134-141	8	19
β-strand	146-151	6	19
β-strand	157-159	3	19
β-strand	160	1	20
β-strand	162-165	4	18
α-helix	169-179	11
α-helix	186-201	16
α-helix	207-209	3
β-strand	210-216	7	18
β-strand	220-223	4	18
α-helix	226-241	16

Chain D: 13 helices, 16 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	22-32	11
α-helix	35-36	2
β-strand	37-42	6	22
β-strand	45-51	7	22
β-strand	59	1	20
α-helix	61-63	3
β-strand	67-71	5	23
β-strand	74-80	7	23
α-helix	82-85	4
α-helix	86-103	18
α-helix	106-108	3
α-helix	109-120	12
β-strand	123E	1	24
β-strand	123G	1	24
β-strand	134-142	9	23
β-strand	145-151	7	23
β-strand	157-159	3	23
β-strand	160	1	25
β-strand	162-165	4	22
α-helix	169-179	11
α-helix	186-200	15
α-helix	206-207	2
β-strand	210-216	7	22
β-strand	220-223	4	22
α-helix	226-241	15

Chain E: 10 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	5-7	3
α-helix	22-33	12
α-helix	35-36	2
β-strand	37-41	5	26
β-strand	45-51	7	26
β-strand	59	1	25
β-strand	67-71	5	27
β-strand	74-80	7	27
α-helix	82-103	22
α-helix	106-108	3
α-helix	109-122	14
β-strand	126	1	28
β-strand	134-142	9	27
β-strand	145-151	7	27
β-strand	157-159	3	27
β-strand	160	1	29
β-strand	162-165	4	26
α-helix	170-180C	14
α-helix	186-198	13
β-strand	210-216	7	26
β-strand	219-225	7	26
α-helix	226-228	3
α-helix	230-232	3

20 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 component Y7	A, O	protein	250	Saccharomyces cerevisiae	P23639 (AlphaFold model)
Proteasome component Y13	B, P	protein	244	Saccharomyces cerevisiae	P23638 (AlphaFold model)
Proteasome component PRE6	C, Q	protein	241	Saccharomyces cerevisiae	P40303 (AlphaFold model)
Proteasome component PUP2	D, R	protein	242	Saccharomyces cerevisiae	P32379 (AlphaFold model)
Proteasome component PRE5	E, S	protein	233	Saccharomyces cerevisiae	P40302
Proteasome component C1	F, T	protein	244	Saccharomyces cerevisiae	P21242
Proteasome component C7-alpha	G, U	protein	243	Saccharomyces cerevisiae	P21243
Proteasome component PUP1	H, V	protein	222	Saccharomyces cerevisiae S288c	P25043
Proteasome component PUP3	I, W	protein	204	Saccharomyces cerevisiae	P25451
Proteasome component C11	J, X	protein	198	Saccharomyces cerevisiae	P22141
Proteasome component PRE2	K, Y	protein	212	Saccharomyces cerevisiae	P30656
Proteasome component C5	L, Z	protein	222	Saccharomyces cerevisiae	P23724

3 more molecules are not listed.

Sequence of entity 1 (A, O), FASTA

>1G65_1 Proteasome component Y7 (chains A, O)
MTDRYSFSLTTFSPSGKLGQIDYALTAVKQGVTSLGIKATNGVVIATEKKSSSPLAMSET
LSKVSLLTPDIGAVYSGMGPDYRVLVDKSRKVAHTSYKRIYGEYPPTKLLVSEVAKIMQE
ATQSGGVRPFGVSLLIAGHDEFNGFSLYQVDPSGSYFPWKATAIGKGSVAAKTFLEKRWN
DELELEDAIHIALLTLKESVEGEFNGDTIELAIIGDENPDLLGYTGIPTDKGPRFRKLTS
QEINDRLEAL

Sequence of entity 2 (B, P), FASTA

>1G65_2 Proteasome component Y13 (chains B, P)
GSRRYDSRTTIFSPEGRLYQVEYALESISHAGTAIGIMASDGIVLAAERKVTSTLLEQDT
STEKLYKLNDKIAVAVAGLTADAEILINTARIHAQNYLKTYNEDIPVEILVRRLSDIKQG
YTQHGGLRPFGVSFIYAGYDDRYGYQLYTSNPSGNYTGWKAISVGANTSAAQTLLQMDYK
DDMKVDDAIELALKTLSKTTDSSALTYDRLEFATIRKGANDGEVYQKIFKPQEIKDILVK
TGIT

Sequence of entity 3 (C, Q), FASTA

>1G65_3 Proteasome component PRE6 (chains C, Q)
GYDRALSIFSPDGHIFQVEYALEAVKRGTCAVGVKGKNCVVLGCERRSTLKLQDTRITPS
KVSKIDSHVVLSFSGLNADSRILIEKARVEAQSHRLTLEDPVTVEYLTRYVAGVQQRYTQ
SGGVRPFGVSTLIAGFDPRDDEPKLYQTEPSGIYSSWSAQTIGRNSKTVREFLEKNYDRK
EPPATVEECVKLTVRSLLEVVQTGAKNIEITVVKPDSDIVALSSEEINQYVTQIEQEKQE
Q

Sequence of entity 4 (D, R), FASTA

>1G65_4 Proteasome component PUP2 (chains D, R)
DRGVSTFSPEGRLFQVEYSLEAIKLGSTAIGIATKEGVVLGVEKRATSPLLESDSIEKIV
EIDRHIGCAMSGLTADARSMIEHARTAAVTHNLYYDEDINVESLTQSVCDLALRFGEGAS
GEERLMSRPFGVALLIAGHDADDGYQLFHAEPSGTFYRYNAKAIGSGSEGAQAELLNEWH
SSLTLKEAELLVLKILKQVMEEKLDENNAQLSCITKQDGFKIYDNEKTAELIKELKEKEA
AE

Sequence of entity 5 (E, S), FASTA

>1G65_5 Proteasome component PRE5 (chains E, S)
FRNNYDGDTVTFSPTGRLFQVEYALEAIKQGSVTVGLRSNTHAVLVALKRNADELSSYQK
KIIKCDEHMGLSLAGLAPDARVLSNYLRQQCNYSSLVFNRKLAVERAGHLLCDKAQKNTQ
SYGGRPYGVGLLIIGYDKSGAHLLEFQPSGNVTELYGTAIGARSQGAKTYLERTLDTFIK
IDGNPDELIKAGVEAISQSLRDESLTVDNLSIAIVGKDTPFTIYDGEAVAKYI

Sequence of entity 6 (F, T), FASTA

>1G65_6 Proteasome component C1 (chains F, T)
GTGYDLSNSVFSPDGRNFQVEYAVKAVENGTTSIGIKCNDGVVFAVEKLITSKLLVPQKN
VKIQVVDRHIGCVYSGLIPDGRHLVNRGREEAASFKKLYKTPIPIPAFADRLGQYVQAHT
LYNSVRPFGVSTIFGGVDKNGAHLYMLEPSGSYWGYKGAATGKGRQSAKAELEKLVDHHP
EGLSAREAVKQAAKIIYLAHEDNKEKDFELEISWCSLSETNGLHKFVKGDLLQEAIDFAQ
KEIN

Sequence of entity 7 (G, U), FASTA

>1G65_7 Proteasome component C7-alpha (chains G, U)
AGYDRHITIFSPEGRLYQVEYAFKATNQTNINSLAVRGKDCTVVISQKKVPDKLLDPTTV
SYIFCISRTIGMVVNGPIPDARNAALRAKAEAAEFRYKYGYDMPCDVLAKRMANLSQIYT
QRAYMRPLGVILTFVSVDEELGPSIYKTDPAGYYVGYKATATGPKQQEITTNLENHFKKS
KIDHINEESWEKVVEFAITHMIDALGTEFSKNDLEVGVATKDKFFTLSAENIEERLVAIA
EQD

Sequence of entity 8 (H, V), FASTA

>1G65_8 Proteasome component PUP1 (chains H, V)
TTIVGVKFNNGVVIAADTRSTQGPIVADKNCAKLHRISPKIWCAGAGTAADTEAVTQLIG
SNIELHSLYTSREPRVVSALQMLKQHLFKYQGHIGAYLIVAGVDPTGSHLFSIHAHGSTD
VGYYLSLGSGSLAAMAVLESHWKQDLTKEEAIKLASDAIQAGIWNDLGSGSNVDVCVMEI
GKDAEYLRNYLTPNVREEKQKSYKFPRGTTAVLKESIVNICD

Sequence of entity 9 (I, W), FASTA

>1G65_9 Proteasome component PUP3 (chains I, W)
SDPSSINGGIVVAMTGKDCVAIACDLRLGSQSLGVSNKFEKIFHYGHVFLGITGLATDVT
TLNEMFRYKTNLYKLKEERAIEPETFTQLVSSSLYERRFGPYFVGPVVAGINSKSGKPFI
AGFDLIGCIDEAKDFIVSGTASDQLFGMCESLYEPNLEPEDLFETISQALLNAADRDALS
GWGAVVYIIKKDEVVKRYLKMRQD

Sequence of entity 10 (J, X), FASTA

>1G65_10 Proteasome component C11 (chains J, X)
MDIILGIRVQDSVILASSKAVTRGISVLKDSDDKTRQLSPHTLMSFAGEAGDTVQFAEYI
QANIQLYSIREDYELSPQAVSSFVRQELAKSIRSRRPYQVNVLIGGYDKKKNKPELYQID
YLGTKVELPYGAHGYSGFYTFSLLDHHYRPDMTTEEGLDLLKLCVQELEKRMPMDFKGVI
VKIVDKDGIRQVDDFQAQ

Sequence of entity 11 (K, Y), FASTA

>1G65_11 Proteasome component PRE2 (chains K, Y)
TTTLAFRFQGGIIVAVDSRATAGNWVASQTVKKVIEINPFLLGTMAGGAADCQFWETWLG
SQCRLHELREKERISVAAASKILSNLVYQYKGAGLSMGTMICGYTRKEGPTIYYVDSDGT
RLKGDIFCVGSGQTFAYGVLDSNYKWDLSVEDALYLGKRSILAAAHRDAYSGGSVNLYHV
TEDGWIYHGNHDVGELFWKVKEEEGSFNNVIG

Sequence of entity 12 (L, Z), FASTA

>1G65_12 Proteasome component C5 (chains L, Z)
QFNPYGDNGGTILGIAGEDFAVLAGDTRNITDYSINSRYEPKVFDCGDNIVMSANGFAAD
GDALVKRFKNSVKWYHFDHNDKKLSINSAARNIQHLLYGKRFFPYYVHTIIAGLDEDGKG
AVYSFDPVGSYEREQCRAGGAAASLIMPFLDNQVNFKNQYEPGTNGKVKKPLKYLSVEEV
IKLVRDSFTSATERHIQVGDGLEILIVTKDGVRKEFYELKRD

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	10

Primary citation

Crystal Structure of Epoxomicin:20S Proteasome reveals a molecular basis for selectivity of alpha,beta-Epoxyketone Proteasome Inhibitors. Groll, M., Kim, K.B., Kairies, N. et al. J Am Chem Soc (2000) 122:1237-1238. DOI 10.1021/ja993588m · PubMed

Other PDB entries of the same protein (UniProt P23639 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1RYP 1.9 Å, Crystal structure of the 20S proteasome from yeast at 2.4 Å resolution
8RVQ 2.02 Å, 20S proteasome from pre1-1
4R17 2.1 Å, Ligand-induced aziridine-formation at subunit beta5 of the yeast 20S proteasome
8RVL 2.14 Å, Proteasomal late precursor complex from pre1-1
8U7U 2.16 Å, Proteasome 20S Core Particle from Beta 3 D205 deletion
8RVP 2.28 Å, Proteasomal late precursor complex from pre1-1, state 2
4QVP 2.3 Å, yCP beta5-M45T mutant in complex with bortezomib
5CZ4 2.3 Å, Yeast 20S proteasome at 2.3 A resolution
6HWE 2.3 Å, Yeast 20S proteasome beta2-G45A mutant in complex with carfilzomib
9GBK 2.39 Å, Blm10-20S proteasome complex from pre1-1
1G0U 2.4 Å, A gated channel into the proteasome core particle
3NZJ 2.4 Å, Crystal structure of yeast 20S proteasome in complex with ligand 2a

Browse structure collections

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