5WVK: Yeast proteasome-ADP-AlFx

Yeast proteasome-ADP-AlFx. Determined by electron microscopy at 4.2 Å resolution. Released 22 Mar 2017.

Method: Electron microscopy
Resolution: 4.2 Å
Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains: 47
Atoms: 105,261
Mol. weight: 1692.66 kDa
Released: 22 Mar 2017

Explore 5WVK in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5WVK contains 600 α-helices and 520 β-strands across 47 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: 6 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	22-26	5	1
β-strand	31-35	5	1
β-strand	39	1	2
β-strand	47	1	2
β-strand	54	1	3
β-strand	61-62	2	3
β-strand	65-66	2	4
α-helix	68-88	21
α-helix	94-107	14
β-strand	114-115	2	4
β-strand	116-120	5	3
β-strand	128-132	5	3
β-strand	140-141	2	3
β-strand	143-146	4	1
α-helix	149-152	4
α-helix	154-159	6
α-helix	167-183	17
β-strand	185	1	5
β-strand	192-197	6	1
β-strand	202-207	6	1
α-helix	209-212	4

Chain 2: 5 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	31-37	7	11
β-strand	40-47	8	11
β-strand	49-51	3	12
β-strand	54-57	4	12
β-strand	63-67	5	13
β-strand	70-75	6	13
α-helix	80-98	19
α-helix	105-107	3
α-helix	108-118	11
β-strand	126-131	6	13
β-strand	138-142	5	13
β-strand	148-150	3	13
β-strand	153	1	11
β-strand	156-157	2	11
α-helix	160-167	8
α-helix	177-194	18
β-strand	201-208	8	11
β-strand	214-215	2	11
β-strand	220	1	11
β-strand	241-248	8	14

Chain 3: 7 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	4-8	5
β-strand	12-15	4	14
β-strand	21-26	6	14
β-strand	29-31	3	18
β-strand	34-37	4	18
β-strand	43-45	3	19
β-strand	49-55	7	19
α-helix	58-78	21
α-helix	84-95	12
β-strand	105-112	8	19
β-strand	119-123	5	19
β-strand	131	1	19
β-strand	136-137	2	14
α-helix	141-145	5
α-helix	146-152	7
α-helix	160-169	10
α-helix	172-177	6
β-strand	185-190	6	14
β-strand	194-200	7	14

Chain 4: 4 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	22
β-strand	13-18	6	22
β-strand	22	1	23
β-strand	27	1	23
β-strand	36-39	4	24
β-strand	42-48	7	24
α-helix	50-71	22
α-helix	77-90	14
β-strand	100-107	8	24
β-strand	114-119	6	24
β-strand	125-127	3	24
β-strand	130	1	22
α-helix	136-144	9
α-helix	154-170	17
β-strand	179-184	6	22
β-strand	189-191	3	22

Chain 5: 6 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	77-82	6	29
β-strand	87-92	6	29
β-strand	95-96	2	30
β-strand	100	1	31
β-strand	101-103	3	30
β-strand	117-118	2	32
β-strand	121	1	32
α-helix	125-145	21
α-helix	148-150	3
α-helix	151-164	14
β-strand	173-174	2	32
β-strand	176-178	3	32
β-strand	186-191	6	32
β-strand	196-199	4	32
β-strand	202-205	4	29
α-helix	208-217	10
α-helix	225-240	16
β-strand	249-255	7	29
β-strand	260-267	8	29
α-helix	268-276	9

Chain 6: 6 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	31-34	4	37
β-strand	40-45	6	37
β-strand	48-50	3	38
β-strand	53-56	4	38
β-strand	62-64	3	39
β-strand	70-74	5	39
α-helix	77-97	21
α-helix	105-117	13
β-strand	127-133	7	39
β-strand	139-144	6	39
β-strand	152-153	2	39
β-strand	155-157	3	37
α-helix	162-164	3
α-helix	166-172	7
β-strand	179	1	40
β-strand	188	1	40
α-helix	189-191	3
α-helix	196-213	18
β-strand	214	1	41
β-strand	220-226	7	37
β-strand	231-237	7	37

Chain 7: 7 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	39-40	2	44
β-strand	45-48	4	45
β-strand	52-58	7	45
β-strand	59	1	46
β-strand	62-63	2	44
β-strand	66-67	2	44
β-strand	73	1	46
β-strand	75-77	3	47
β-strand	82-88	7	47
α-helix	93-107	15
α-helix	122-138	17
β-strand	145-152	8	47
β-strand	158-164	7	47
β-strand	170-171	2	47
β-strand	175	1	45
α-helix	178-182	5
α-helix	184-191	8
α-helix	197-200	4
α-helix	203-220	18
β-strand	228-234	7	45
β-strand	238-245	8	45
α-helix	253-255	3

Chain a: 8 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	39-40	2	5
β-strand	45-48	4	78
β-strand	52-58	7	78
β-strand	62-63	2	5
β-strand	66	1	5
β-strand	75-78	4	79
β-strand	82-88	7	79
α-helix	90-108	19
α-helix	112-114	3
α-helix	122-137	16
β-strand	145-152	8	79
β-strand	158-163	6	79
β-strand	170-171	2	79
β-strand	175	1	78
α-helix	178-181	4
α-helix	185-191	7
α-helix	195-197	3
α-helix	203-220	18
β-strand	228-234	7	78
β-strand	238-241	4	78
β-strand	245	1	78
α-helix	253-255	3

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 beta type-1	1, b	protein	215	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P38624 (AlphaFold model)
Proteasome subunit beta type-2	2, i	protein	261	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P25043 (AlphaFold model)
Proteasome subunit beta type-3	3, h	protein	205	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P25451 (AlphaFold model)
Proteasome subunit beta type-4	4, g	protein	198	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P22141 (AlphaFold model)
Proteasome subunit beta type-5	5, f	protein	287	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P30656
Proteasome subunit beta type-6	6, e	protein	241	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P23724
Proteasome subunit beta type-7	7, a	protein	266	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P30657
Proteasome subunit alpha type-1	A, c	protein	252	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P21243
Proteasome subunit alpha type-2	B, j	protein	250	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P23639
Proteasome subunit alpha type-3	C, d	protein	258	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P23638
Proteasome subunit alpha type-4	D, n	protein	254	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P40303
Proteasome subunit alpha type-5	E, m	protein	260	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P32379

21 more molecules are not listed.

Sequence of entity 1 (1, b), FASTA

>5WVK_1 Proteasome subunit beta type-1 (chains 1, b)
MNGIQVDINRLKKGEVSLGTSIMAVTFKDGVILGADSRTTTGAYIANRVTDKLTRVHDKI
WCCRSGSAADTQAIADIVQYHLELYTSQYGTPSTETAASVFKELCYENKDNLTAGIIVAG
YDDKNKGEVYTIPLGGSVHKLPYAIAGSGSTFIYGYCDKNFRENMSKEETVDFIKHSLSQ
AIKWDGSSGGVIRMVVLTAAGVERLIFYPDEYEQL

Sequence of entity 2 (2, i), FASTA

>5WVK_2 Proteasome subunit beta type-2 (chains 2, i)
MAGLSFDNYQRNNFLAENSHTQPKATSTGTTIVGVKFNNGVVIAADTRSTQGPIVADKNC
AKLHRISPKIWCAGAGTAADTEAVTQLIGSNIELHSLYTSREPRVVSALQMLKQHLFKYQ
GHIGAYLIVAGVDPTGSHLFSIHAHGSTDVGYYLSLGSGSLAAMAVLESHWKQDLTKEEA
IKLASDAIQAGIWNDLGSGSNVDVCVMEIGKDAEYLRNYLTPNVREEKQKSYKFPRGTTA
VLKESIVNICDIQEEQVDITA

Sequence of entity 3 (3, h), FASTA

>5WVK_3 Proteasome subunit beta type-3 (chains 3, h)
MSDPSSINGGIVVAMTGKDCVAIACDLRLGSQSLGVSNKFEKIFHYGHVFLGITGLATDV
TTLNEMFRYKTNLYKLKEERAIEPETFTQLVSSSLYERRFGPYFVGPVVAGINSKSGKPF
IAGFDLIGCIDEAKDFIVSGTASDQLFGMCESLYEPNLEPEDLFETISQALLNAADRDAL
SGWGAVVYIIKKDEVVKRYLKMRQD

Sequence of entity 4 (4, g), FASTA

>5WVK_4 Proteasome subunit beta type-4 (chains 4, g)
MDIILGIRVQDSVILASSKAVTRGISVLKDSDDKTRQLSPHTLMSFAGEAGDTVQFAEYI
QANIQLYSIREDYELSPQAVSSFVRQELAKSIRSRRPYQVNVLIGGYDKKKNKPELYQID
YLGTKVELPYGAHGYSGFYTFSLLDHHYRPDMTTEEGLDLLKLCVQELEKRMPMDFKGVI
VKIVDKDGIRQVDDFQAQ

Sequence of entity 5 (5, f), FASTA

>5WVK_5 Proteasome subunit beta type-5 (chains 5, f)
MQAIADSFSVPNRLVKELQYDNEQNLESDFVTGASQFQRLAPSLTVPPIASPQQFLRAHT
DDSRNPDCKIKIAHGTTTLAFRFQGGIIVAVDSRATAGNWVASQTVKKVIEINPFLLGTM
AGGAADCQFWETWLGSQCRLHELREKERISVAAASKILSNLVYQYKGAGLSMGTMICGYT
RKEGPTIYYVDSDGTRLKGDIFCVGSGQTFAYGVLDSNYKWDLSVEDALYLGKRSILAAA
HRDAYSGGSVNLYHVTEDGWIYHGNHDVGELFWKVKEEEGSFNNVIG

Sequence of entity 6 (6, e), FASTA

>5WVK_6 Proteasome subunit beta type-6 (chains 6, e)
MATIASEYSSEASNTPIEHQFNPYGDNGGTILGIAGEDFAVLAGDTRNITDYSINSRYEP
KVFDCGDNIVMSANGFAADGDALVKRFKNSVKWYHFDHNDKKLSINSAARNIQHLLYGKR
FFPYYVHTIIAGLDEDGKGAVYSFDPVGSYEREQCRAGGAAASLIMPFLDNQVNFKNQYE
PGTNGKVKKPLKYLSVEEVIKLVRDSFTSATERHIQVGDGLEILIVTKDGVRKEFYELKR
D

Sequence of entity 7 (7, a), FASTA

>5WVK_7 Proteasome subunit beta type-7 (chains 7, a)
MNHDPFSWGRPADSTYGAYNTQIANAGASPMVNTQQPIVTGTSVISMKYDNGVIIAADNL
GSYGSLLRFNGVERLIPVGDNTVVGISGDISDMQHIERLLKDLVTENAYDNPLADAEEAL
EPSYIFEYLATVMYQRRSKMNPLWNAIIVAGVQSNGDQFLRYVNLLGVTYSSPTLATGFG
AHMANPLLRKVVDRESDIPKTTVQVAEEAIVNAMRVLYYRDARSSRNFSLAIIDKNTGLT
FKKNLQVENMKWDFAKDIKGYGTQKI

Sequence of entity 8 (A, c), FASTA

>5WVK_8 Proteasome subunit alpha type-1 (chains A, c)
MSGAAAASAAGYDRHITIFSPEGRLYQVEYAFKATNQTNINSLAVRGKDCTVVISQKKVP
DKLLDPTTVSYIFCISRTIGMVVNGPIPDARNAALRAKAEAAEFRYKYGYDMPCDVLAKR
MANLSQIYTQRAYMRPLGVILTFVSVDEELGPSIYKTDPAGYYVGYKATATGPKQQEITT
NLENHFKKSKIDHINEESWEKVVEFAITHMIDALGTEFSKNDLEVGVATKDKFFTLSAEN
IEERLVAIAEQD

Sequence of entity 9 (B, j), FASTA

>5WVK_9 Proteasome subunit alpha type-2 (chains B, j)
MTDRYSFSLTTFSPSGKLGQIDYALTAVKQGVTSLGIKATNGVVIATEKKSSSPLAMSET
LSKVSLLTPDIGAVYSGMGPDYRVLVDKSRKVAHTSYKRIYGEYPPTKLLVSEVAKIMQE
ATQSGGVRPFGVSLLIAGHDEFNGFSLYQVDPSGSYFPWKATAIGKGSVAAKTFLEKRWN
DELELEDAIHIALLTLKESVEGEFNGDTIELAIIGDENPDLLGYTGIPTDKGPRFRKLTS
QEINDRLEAL

Sequence of entity 10 (C, d), FASTA

>5WVK_10 Proteasome subunit alpha type-3 (chains C, d)
MGSRRYDSRTTIFSPEGRLYQVEYALESISHAGTAIGIMASDGIVLAAERKVTSTLLEQD
TSTEKLYKLNDKIAVAVAGLTADAEILINTARIHAQNYLKTYNEDIPVEILVRRLSDIKQ
GYTQHGGLRPFGVSFIYAGYDDRYGYQLYTSNPSGNYTGWKAISVGANTSAAQTLLQMDY
KDDMKVDDAIELALKTLSKTTDSSALTYDRLEFATIRKGANDGEVYQKIFKPQEIKDILV
KTGITKKDEDEEADEDMK

Sequence of entity 11 (D, n), FASTA

>5WVK_11 Proteasome subunit alpha type-4 (chains D, n)
MSGYDRALSIFSPDGHIFQVEYALEAVKRGTCAVGVKGKNCVVLGCERRSTLKLQDTRIT
PSKVSKIDSHVVLSFSGLNADSRILIEKARVEAQSHRLTLEDPVTVEYLTRYVAGVQQRY
TQSGGVRPFGVSTLIAGFDPRDDEPKLYQTEPSGIYSSWSAQTIGRNSKTVREFLEKNYD
RKEPPATVEECVKLTVRSLLEVVQTGAKNIEITVVKPDSDIVALSSEEINQYVTQIEQEK
QEQQEQDKKKKSNH

Sequence of entity 12 (E, m), FASTA

>5WVK_12 Proteasome subunit alpha type-5 (chains E, m)
MFLTRSEYDRGVSTFSPEGRLFQVEYSLEAIKLGSTAIGIATKEGVVLGVEKRATSPLLE
SDSIEKIVEIDRHIGCAMSGLTADARSMIEHARTAAVTHNLYYDEDINVESLTQSVCDLA
LRFGEGASGEERLMSRPFGVALLIAGHDADDGYQLFHAEPSGTFYRYNAKAIGSGSEGAQ
AELLNEWHSSLTLKEAELLVLKILKQVMEEKLDENNAQLSCITKQDGFKIYDNEKTAELI
KELKEKEAAESPEEADVEMS

Primary citation

High-resolution cryo-EM structure of the proteasome in complex with ADP-AlFx. Ding, Z., Fu, Z., Xu, C. et al. Cell Res (2017) 27:373-385. DOI 10.1038/cr.2017.12 · PubMed

Other PDB entries of the same protein (UniProt P38624 (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
1G65 2.25 Å, Crystal structure of epoxomicin:20s proteasome reveals a molecular basis for selectivity…
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

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