5MP9: 26S proteasome in presence of ATP

26S proteasome in presence of ATP (s1). Determined by electron microscopy at 4.1 Å resolution. Released 8 Mar 2017.

Method: Electron microscopy
Resolution: 4.1 Å
Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains: 34
Atoms: 67,883
Mol. weight: 1061.96 kDa
Ligands: ADP, MG, ATP
Released: 8 Mar 2017

Explore 5MP9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5MP9 contains 333 α-helices and 470 β-strands across 34 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, 12 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	108
β-strand	12-17	6	108
β-strand	20-22	3	78
β-strand	25-28	4	78
β-strand	34-36	3	109
β-strand	41-47	7	109
α-helix	49-70	22
α-helix	75-88	14
β-strand	95-103	9	109
β-strand	107-113	7	109
β-strand	120-121	2	109
β-strand	124-128	5	108
α-helix	130-134	5
α-helix	135-141	7
α-helix	148-165	18
β-strand	173-178	6	108
β-strand	183-188	6	108
α-helix	190-193	4

Chain 2: 9 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	110
β-strand	11-16	6	110
β-strand	20-22	3	74
β-strand	25-28	4	74
β-strand	34-38	5	111
β-strand	41-47	7	111
α-helix	49-70	22
α-helix	73-75	3
α-helix	76-88	13
β-strand	96-103	8	111
β-strand	108-113	6	111
β-strand	119-121	3	111
β-strand	124-127	4	110
α-helix	131-141	11
α-helix	148-165	18
β-strand	166	1	71
α-helix	172	1
β-strand	173-179	7	110
β-strand	184	1	87
β-strand	185-191	7	110
α-helix	197-199	3
α-helix	205-206	2
β-strand	212-217	6	112
α-helix	224	1

Chain 3: 7 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	3-6	4
β-strand	10-15	6	112
β-strand	20-25	6	112
β-strand	28-30	3	69
β-strand	33-36	4	69
β-strand	42-45	4	113
β-strand	48-51	4	113
β-strand	54	1	114
α-helix	56-77	22
α-helix	80-82	3
α-helix	83-96	14
β-strand	104	1	114
β-strand	107-109	3	113
β-strand	120-122	3	113
β-strand	130-132	3	113
β-strand	135-139	5	112
α-helix	142-152	11
α-helix	159-175	17
β-strand	177	1	67
β-strand	184-189	6	112
β-strand	194-199	6	112
α-helix	200	1

Chain 4: 5 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	115
β-strand	13-18	6	115
β-strand	21-23	3	116
β-strand	26-29	4	116
β-strand	35-39	5	117
β-strand	42-48	7	117
α-helix	52-71	20
α-helix	74-76	3
α-helix	77-93	17
β-strand	100-108	9	117
β-strand	113-120	8	117
β-strand	124-127	4	117
β-strand	130-132	3	115
α-helix	136-147	12
α-helix	154-171	18
β-strand	179-184	6	115
β-strand	189-192	4	115

Chain 5: 7 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	118
β-strand	11-16	6	118
β-strand	20-22	3	62
β-strand	25-28	4	62
β-strand	34-36	3	119
β-strand	41-44	4	119
α-helix	49-54	6
α-helix	58-69	12
α-helix	73-75	3
α-helix	76-89	14
β-strand	98-105	8	119
β-strand	109-116	8	119
β-strand	121-124	4	119
β-strand	126-130	5	118
α-helix	133-142	10
α-helix	150-167	18
β-strand	174-181	8	118
β-strand	184-192	9	118
α-helix	193-204	12

Chain 6: 6 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	11-16	6	5
β-strand	21-26	6	5
β-strand	29-31	3	6
β-strand	34-37	4	6
β-strand	44-45	2	7
β-strand	50-56	7	7
α-helix	58-79	22
α-helix	82-85	4
α-helix	86-99	14
β-strand	107-114	8	7
β-strand	120-125	6	7
β-strand	131-134	4	7
β-strand	136-140	5	5
α-helix	143-153	11
β-strand	160	1	8
β-strand	169	1	8
α-helix	170-172	3
α-helix	177-194	18
β-strand	195	1	56
β-strand	201-208	8	5
β-strand	211-218	8	5

Chain 7: 6 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	7-8	2	13
β-strand	11-15	5	14
β-strand	19-25	7	14
β-strand	27-30	4	15
β-strand	33-37	5	15
β-strand	42-44	3	13
β-strand	49-56	8	13
α-helix	57-75	19
α-helix	89-106	18
β-strand	112-119	8	13
β-strand	125-130	6	13
β-strand	136-138	3	13
β-strand	141-143	3	14
α-helix	147-155	9
α-helix	162-164	3
α-helix	170-187	18
β-strand	188	1	51
β-strand	194-201	8	14
β-strand	206-213	8	14
α-helix	214	1

Chain a: 7 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	17-26	10
β-strand	33-37	5	1
β-strand	41-47	7	1
β-strand	55	1	2
β-strand	63-65	3	3
β-strand	70-75	6	3
α-helix	78-99	22
α-helix	105-121	17
β-strand	122	1	4
α-helix	126-128	3
β-strand	131-137	7	3
β-strand	143-148	6	3
β-strand	154-157	4	3
β-strand	159-162	4	1
α-helix	166-180	15
α-helix	191-205	15
β-strand	214-220	7	1
β-strand	223-226	4	1
α-helix	229-241	13

26 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-1	A, a	protein	252	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P21243 (AlphaFold model)
Proteasome subunit alpha type-2	B, b	protein	250	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P23639 (AlphaFold model)
Proteasome subunit alpha type-3	C, c	protein	258	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P23638 (AlphaFold model)
Proteasome subunit alpha type-4	D, d	protein	254	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P40303 (AlphaFold model)
Proteasome subunit alpha type-5	E, e	protein	260	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P32379
Proteasome subunit alpha type-6	F, f	protein	234	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P40302
Probable proteasome subunit alpha type-7	G, g	protein	288	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P21242
Proteasome subunit beta type-1	1, h	protein	215	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P38624
Proteasome subunit beta type-2	2, i	protein	261	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P25043
Proteasome subunit beta type-3	3, j	protein	205	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P25451
Proteasome subunit beta type-4	4, k	protein	198	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P22141
Proteasome subunit beta type-5	5, l	protein	287	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P30656

8 more molecules are not listed.

Sequence of entity 1 (A, a), FASTA

>5MP9_1 Proteasome subunit alpha type-1 (chains A, a)
MSGAAAASAAGYDRHITIFSPEGRLYQVEYAFKATNQTNINSLAVRGKDCTVVISQKKVP
DKLLDPTTVSYIFCISRTIGMVVNGPIPDARNAALRAKAEAAEFRYKYGYDMPCDVLAKR
MANLSQIYTQRAYMRPLGVILTFVSVDEELGPSIYKTDPAGYYVGYKATATGPKQQEITT
NLENHFKKSKIDHINEESWEKVVEFAITHMIDALGTEFSKNDLEVGVATKDKFFTLSAEN
IEERLVAIAEQD

Sequence of entity 2 (B, b), FASTA

>5MP9_2 Proteasome subunit alpha type-2 (chains B, b)
MTDRYSFSLTTFSPSGKLGQIDYALTAVKQGVTSLGIKATNGVVIATEKKSSSPLAMSET
LSKVSLLTPDIGAVYSGMGPDYRVLVDKSRKVAHTSYKRIYGEYPPTKLLVSEVAKIMQE
ATQSGGVRPFGVSLLIAGHDEFNGFSLYQVDPSGSYFPWKATAIGKGSVAAKTFLEKRWN
DELELEDAIHIALLTLKESVEGEFNGDTIELAIIGDENPDLLGYTGIPTDKGPRFRKLTS
QEINDRLEAL

Sequence of entity 3 (C, c), FASTA

>5MP9_3 Proteasome subunit alpha type-3 (chains C, c)
MGSRRYDSRTTIFSPEGRLYQVEYALESISHAGTAIGIMASDGIVLAAERKVTSTLLEQD
TSTEKLYKLNDKIAVAVAGLTADAEILINTARIHAQNYLKTYNEDIPVEILVRRLSDIKQ
GYTQHGGLRPFGVSFIYAGYDDRYGYQLYTSNPSGNYTGWKAISVGANTSAAQTLLQMDY
KDDMKVDDAIELALKTLSKTTDSSALTYDRLEFATIRKGANDGEVYQKIFKPQEIKDILV
KTGITKKDEDEEADEDMK

Sequence of entity 4 (D, d), FASTA

>5MP9_4 Proteasome subunit alpha type-4 (chains D, d)
MSGYDRALSIFSPDGHIFQVEYALEAVKRGTCAVGVKGKNCVVLGCERRSTLKLQDTRIT
PSKVSKIDSHVVLSFSGLNADSRILIEKARVEAQSHRLTLEDPVTVEYLTRYVAGVQQRY
TQSGGVRPFGVSTLIAGFDPRDDEPKLYQTEPSGIYSSWSAQTIGRNSKTVREFLEKNYD
RKEPPATVEECVKLTVRSLLEVVQTGAKNIEITVVKPDSDIVALSSEEINQYVTQIEQEK
QEQQEQDKKKKSNH

Sequence of entity 5 (E, e), FASTA

>5MP9_5 Proteasome subunit alpha type-5 (chains E, e)
MFLTRSEYDRGVSTFSPEGRLFQVEYSLEAIKLGSTAIGIATKEGVVLGVEKRATSPLLE
SDSIEKIVEIDRHIGCAMSGLTADARSMIEHARTAAVTHNLYYDEDINVESLTQSVCDLA
LRFGEGASGEERLMSRPFGVALLIAGHDADDGYQLFHAEPSGTFYRYNAKAIGSGSEGAQ
AELLNEWHSSLTLKEAELLVLKILKQVMEEKLDENNAQLSCITKQDGFKIYDNEKTAELI
KELKEKEAAESPEEADVEMS

Sequence of entity 6 (F, f), FASTA

>5MP9_6 Proteasome subunit alpha type-6 (chains F, f)
MFRNNYDGDTVTFSPTGRLFQVEYALEAIKQGSVTVGLRSNTHAVLVALKRNADELSSYQ
KKIIKCDEHMGLSLAGLAPDARVLSNYLRQQCNYSSLVFNRKLAVERAGHLLCDKAQKNT
QSYGGRPYGVGLLIIGYDKSGAHLLEFQPSGNVTELYGTAIGARSQGAKTYLERTLDTFI
KIDGNPDELIKAGVEAISQSLRDESLTVDNLSIAIVGKDTPFTIYDGEAVAKYI

Sequence of entity 7 (G, g), FASTA

>5MP9_7 Probable proteasome subunit alpha type-7 (chains G, g)
MTSIGTGYDLSNSVFSPDGRNFQVEYAVKAVENGTTSIGIKCNDGVVFAVEKLITSKLLV
PQKNVKIQVVDRHIGCVYSGLIPDGRHLVNRGREEAASFKKLYKTPIPIPAFADRLGQYV
QAHTLYNSVRPFGVSTIFGGVDKNGAHLYMLEPSGSYWGYKGAATGKGRQSAKAELEKLV
DHHPEGLSAREAVKQAAKIIYLAHEDNKEKDFELEISWCSLSETNGLHKFVKGDLLQEAI
DFAQKEINGDDDEDEDDSDNVMSSDDENAPVATNANATTDQEGDIHLE

Sequence of entity 8 (1, h), FASTA

>5MP9_8 Proteasome subunit beta type-1 (chains 1, h)
MNGIQVDINRLKKGEVSLGTSIMAVTFKDGVILGADSRTTTGAYIANRVTDKLTRVHDKI
WCCRSGSAADTQAIADIVQYHLELYTSQYGTPSTETAASVFKELCYENKDNLTAGIIVAG
YDDKNKGEVYTIPLGGSVHKLPYAIAGSGSTFIYGYCDKNFRENMSKEETVDFIKHSLSQ
AIKWDGSSGGVIRMVVLTAAGVERLIFYPDEYEQL

Sequence of entity 9 (2, i), FASTA

>5MP9_9 Proteasome subunit beta type-2 (chains 2, i)
MAGLSFDNYQRNNFLAENSHTQPKATSTGTTIVGVKFNNGVVIAADTRSTQGPIVADKNC
AKLHRISPKIWCAGAGTAADTEAVTQLIGSNIELHSLYTSREPRVVSALQMLKQHLFKYQ
GHIGAYLIVAGVDPTGSHLFSIHAHGSTDVGYYLSLGSGSLAAMAVLESHWKQDLTKEEA
IKLASDAIQAGIWNDLGSGSNVDVCVMEIGKDAEYLRNYLTPNVREEKQKSYKFPRGTTA
VLKESIVNICDIQEEQVDITA

Sequence of entity 10 (3, j), FASTA

>5MP9_10 Proteasome subunit beta type-3 (chains 3, j)
MSDPSSINGGIVVAMTGKDCVAIACDLRLGSQSLGVSNKFEKIFHYGHVFLGITGLATDV
TTLNEMFRYKTNLYKLKEERAIEPETFTQLVSSSLYERRFGPYFVGPVVAGINSKSGKPF
IAGFDLIGCIDEAKDFIVSGTASDQLFGMCESLYEPNLEPEDLFETISQALLNAADRDAL
SGWGAVVYIIKKDEVVKRYLKMRQD

Sequence of entity 11 (4, k), FASTA

>5MP9_11 Proteasome subunit beta type-4 (chains 4, k)
MDIILGIRVQDSVILASSKAVTRGISVLKDSDDKTRQLSPHTLMSFAGEAGDTVQFAEYI
QANIQLYSIREDYELSPQAVSSFVRQELAKSIRSRRPYQVNVLIGGYDKKKNKPELYQID
YLGTKVELPYGAHGYSGFYTFSLLDHHYRPDMTTEEGLDLLKLCVQELEKRMPMDFKGVI
VKIVDKDGIRQVDDFQAQ

Sequence of entity 12 (5, l), FASTA

>5MP9_12 Proteasome subunit beta type-5 (chains 5, l)
MQAIADSFSVPNRLVKELQYDNEQNLESDFVTGASQFQRLAPSLTVPPIASPQQFLRAHT
DDSRNPDCKIKIAHGTTTLAFRFQGGIIVAVDSRATAGNWVASQTVKKVIEINPFLLGTM
AGGAADCQFWETWLGSQCRLHELREKERISVAAASKILSNLVYQYKGAGLSMGTMICGYT
RKEGPTIYYVDSDGTRLKGDIFCVGSGQTFAYGVLDSNYKWDLSVEDALYLGKRSILAAA
HRDAYSGGSVNLYHVTEDGWIYHGNHDVGELFWKVKEEEGSFNNVIG

Ligands and cofactors

ID	Name	Formula	Copies
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	1
MG	Magnesium ion	Mg	6
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	5

Primary citation

Structural insights into the functional cycle of the ATPase module of the 26S proteasome. Wehmer, M., Rudack, T., Beck, F. et al. Proc Natl Acad Sci U S A (2017) 114:1305-1310. DOI 10.1073/pnas.1621129114 · PubMed

Other PDB entries of the same protein (UniProt P21243 (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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