6EF3: Yeast 26S proteasome

Yeast 26S proteasome bound to ubiquitinated substrate (4D motor state). Determined by electron microscopy at 4.17 Å resolution. Released 17 Oct 2018.

Method: Electron microscopy
Resolution: 4.17 Å
Organisms: Saccharomyces cerevisiae S288c, Homo sapiens
Chains: 24
Atoms: 44,271
Mol. weight: 733.22 kDa
Ligands: ADP, ATP
Released: 17 Oct 2018

Explore 6EF3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6EF3 contains 227 α-helices and 289 β-strands across 23 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: 5 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	3-8	6	1
β-strand	11-18	8	1
β-strand	22	1	2
β-strand	25	1	2
β-strand	38	1	3
β-strand	41-47	7	3
α-helix	50-69	20
α-helix	76-86	11
β-strand	95-101	7	3
β-strand	109	1	3
β-strand	111-113	3	3
β-strand	120-121	2	3
β-strand	124-127	4	1
α-helix	135-139	5
α-helix	148-164	17
β-strand	172-179	8	1
β-strand	183	1	1
β-strand	186-188	3	1
α-helix	190-194	5

Chain 2: 6 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-8	6	4
β-strand	11-17	7	4
β-strand	34-35	2	5
β-strand	42-45	4	5
α-helix	49-62	14
α-helix	64-70	7
α-helix	78-81	4
α-helix	83-90	8
β-strand	98-104	7	5
β-strand	107-113	7	5
β-strand	120	1	5
β-strand	124-127	4	4
α-helix	131-139	9
α-helix	148-164	17
β-strand	173-177	5	4
β-strand	185-191	7	4
β-strand	215-218	4	6

Chain 3: 5 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	4-6	3
β-strand	11-17	7	6
β-strand	20-26	7	6
β-strand	29	1	7
β-strand	37	1	7
β-strand	43-46	4	8
β-strand	49-52	4	8
α-helix	58-78	21
α-helix	84-96	13
β-strand	108-113	6	8
β-strand	118-123	6	8
β-strand	131	1	8
β-strand	136-140	5	6
α-helix	148-151	4
α-helix	160-175	16
β-strand	185-190	6	6
β-strand	195-200	6	6

Chain 4: 5 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	9
β-strand	13-15	3	9
β-strand	22-23	2	10
β-strand	26-27	2	10
β-strand	35-39	5	11
β-strand	42-48	7	11
α-helix	54-68	15
α-helix	77-91	15
β-strand	100-107	8	11
β-strand	114-119	6	11
β-strand	126	1	11
β-strand	130-132	3	9
α-helix	137-139	3
α-helix	154-161	8
α-helix	164-169	6
β-strand	182-184	3	9
β-strand	190-191	2	9

Chain 5: 6 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	12
β-strand	12-16	5	12
β-strand	20-22	3	13
β-strand	25-28	4	13
β-strand	34-38	5	14
β-strand	41-44	4	14
β-strand	47	1	15
α-helix	49-64	16
α-helix	67-70	4
α-helix	76-88	13
β-strand	97	1	15
β-strand	98-104	7	14
β-strand	110-116	7	14
β-strand	123	1	14
β-strand	126-130	5	12
α-helix	133-143	11
α-helix	151-162	12
β-strand	174-181	8	12
β-strand	184-192	9	12
α-helix	193-204	12

Chain 6: 6 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	11-15	5	16
β-strand	16	1	17
β-strand	21	1	17
β-strand	24-25	2	16
β-strand	29-30	2	18
β-strand	35-37	3	18
β-strand	43-45	3	19
β-strand	51-56	6	19
α-helix	60-79	20
α-helix	86-98	13
β-strand	107-114	8	19
β-strand	120-124	5	19
β-strand	132-134	3	19
β-strand	136-140	5	16
α-helix	147-150	4
β-strand	160	1	20
α-helix	168	1
β-strand	169	1	20
α-helix	170	1
α-helix	177-187	11
β-strand	202-204	3	16
β-strand	207-208	2	17
β-strand	211-212	2	17
β-strand	215-217	3	16

Chain 7: 6 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	7	1	21
β-strand	11-15	5	22
β-strand	19-24	6	22
β-strand	28-29	2	23
β-strand	34-36	3	23
β-strand	42	1	24
β-strand	45	1	24
β-strand	49-52	4	24
β-strand	56	1	21
α-helix	57-75	19
α-helix	90-93	4
α-helix	95-104	10
β-strand	114-119	6	24
β-strand	125-130	6	24
β-strand	136-137	2	24
β-strand	143	1	22
α-helix	146-150	5
α-helix	152-158	7
α-helix	170-187	18
β-strand	196-201	6	22
β-strand	205-208	4	22

Chain A: 12 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	5-9	5
α-helix	28-30	3
α-helix	32-34	3
β-strand	43-45	3	25
β-strand	51-56	6	25
β-strand	64	1	26
β-strand	72-73	2	27
β-strand	79-82	4	27
α-helix	88-98	11
α-helix	101-107	7
α-helix	114-120	7
α-helix	122-125	4
α-helix	127-129	3
α-helix	135-137	3
β-strand	141-147	7	27
β-strand	151-157	7	27
β-strand	166	1	28
β-strand	168-170	3	25
α-helix	175-189	15
α-helix	199-212	14
β-strand	223-229	7	25
β-strand	232-235	4	25
α-helix	242-245	4

15 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	protein	215	Saccharomyces cerevisiae S288c	P38624 (AlphaFold model)
Proteasome subunit beta type-2	2	protein	261	Saccharomyces cerevisiae S288c	P25043 (AlphaFold model)
Proteasome subunit beta type-3	3	protein	205	Saccharomyces cerevisiae S288c	P25451 (AlphaFold model)
Proteasome subunit beta type-4	4	protein	198	Saccharomyces cerevisiae S288c	P22141 (AlphaFold model)
Proteasome subunit beta type-5	5	protein	287	Saccharomyces cerevisiae S288c	P30656
Proteasome subunit beta type-6	6	protein	241	Saccharomyces cerevisiae S288c	P23724
Proteasome subunit beta type-7	7	protein	266	Saccharomyces cerevisiae S288c	P30657
Proteasome subunit alpha type-1	A	protein	252	Saccharomyces cerevisiae S288c	P21243
Proteasome subunit alpha type-2	B	protein	250	Saccharomyces cerevisiae S288c	P23639
Proteasome subunit alpha type-3	C	protein	258	Saccharomyces cerevisiae S288c	P23638
Proteasome subunit alpha type-4	D	protein	254	Saccharomyces cerevisiae S288c	P40303
Proteasome subunit alpha type-5	E	protein	260	Saccharomyces cerevisiae S288c	P32379

12 more molecules are not listed.

Sequence of entity 1 (1), FASTA

>6EF3_1 Proteasome subunit beta type-1 (chains 1)
MNGIQVDINRLKKGEVSLGTSIMAVTFKDGVILGADSRTTTGAYIANRVTDKLTRVHDKI
WCCRSGSAADTQAIADIVQYHLELYTSQYGTPSTETAASVFKELCYENKDNLTAGIIVAG
YDDKNKGEVYTIPLGGSVHKLPYAIAGSGSTFIYGYCDKNFRENMSKEETVDFIKHSLSQ
AIKWDGSSGGVIRMVVLTAAGVERLIFYPDEYEQL

Sequence of entity 2 (2), FASTA

>6EF3_2 Proteasome subunit beta type-2 (chains 2)
MAGLSFDNYQRNNFLAENSHTQPKATSTGTTIVGVKFNNGVVIAADTRSTQGPIVADKNC
AKLHRISPKIWCAGAGTAADTEAVTQLIGSNIELHSLYTSREPRVVSALQMLKQHLFKYQ
GHIGAYLIVAGVDPTGSHLFSIHAHGSTDVGYYLSLGSGSLAAMAVLESHWKQDLTKEEA
IKLASDAIQAGIWNDLGSGSNVDVCVMEIGKDAEYLRNYLTPNVREEKQKSYKFPRGTTA
VLKESIVNICDIQEEQVDITA

Sequence of entity 3 (3), FASTA

>6EF3_3 Proteasome subunit beta type-3 (chains 3)
MSDPSSINGGIVVAMTGKDCVAIACDLRLGSQSLGVSNKFEKIFHYGHVFLGITGLATDV
TTLNEMFRYKTNLYKLKEERAIEPETFTQLVSSSLYERRFGPYFVGPVVAGINSKSGKPF
IAGFDLIGCIDEAKDFIVSGTASDQLFGMCESLYEPNLEPEDLFETISQALLNAADRDAL
SGWGAVVYIIKKDEVVKRYLKMRQD

Sequence of entity 4 (4), FASTA

>6EF3_4 Proteasome subunit beta type-4 (chains 4)
MDIILGIRVQDSVILASSKAVTRGISVLKDSDDKTRQLSPHTLMSFAGEAGDTVQFAEYI
QANIQLYSIREDYELSPQAVSSFVRQELAKSIRSRRPYQVNVLIGGYDKKKNKPELYQID
YLGTKVELPYGAHGYSGFYTFSLLDHHYRPDMTTEEGLDLLKLCVQELEKRMPMDFKGVI
VKIVDKDGIRQVDDFQAQ

Sequence of entity 5 (5), FASTA

>6EF3_5 Proteasome subunit beta type-5 (chains 5)
MQAIADSFSVPNRLVKELQYDNEQNLESDFVTGASQFQRLAPSLTVPPIASPQQFLRAHT
DDSRNPDCKIKIAHGTTTLAFRFQGGIIVAVDSRATAGNWVASQTVKKVIEINPFLLGTM
AGGAADCQFWETWLGSQCRLHELREKERISVAAASKILSNLVYQYKGAGLSMGTMICGYT
RKEGPTIYYVDSDGTRLKGDIFCVGSGQTFAYGVLDSNYKWDLSVEDALYLGKRSILAAA
HRDAYSGGSVNLYHVTEDGWIYHGNHDVGELFWKVKEEEGSFNNVIG

Sequence of entity 6 (6), FASTA

>6EF3_6 Proteasome subunit beta type-6 (chains 6)
MATIASEYSSEASNTPIEHQFNPYGDNGGTILGIAGEDFAVLAGDTRNITDYSINSRYEP
KVFDCGDNIVMSANGFAADGDALVKRFKNSVKWYHFDHNDKKLSINSAARNIQHLLYGKR
FFPYYVHTIIAGLDEDGKGAVYSFDPVGSYEREQCRAGGAAASLIMPFLDNQVNFKNQYE
PGTNGKVKKPLKYLSVEEVIKLVRDSFTSATERHIQVGDGLEILIVTKDGVRKEFYELKR
D

Sequence of entity 7 (7), FASTA

>6EF3_7 Proteasome subunit beta type-7 (chains 7)
MNHDPFSWGRPADSTYGAYNTQIANAGASPMVNTQQPIVTGTSVISMKYDNGVIIAADNL
GSYGSLLRFNGVERLIPVGDNTVVGISGDISDMQHIERLLKDLVTENAYDNPLADAEEAL
EPSYIFEYLATVMYQRRSKMNPLWNAIIVAGVQSNGDQFLRYVNLLGVTYSSPTLATGFG
AHMANPLLRKVVDRESDIPKTTVQVAEEAIVNAMRVLYYRDARSSRNFSLAIIDKNTGLT
FKKNLQVENMKWDFAKDIKGYGTQKI

Sequence of entity 8 (A), FASTA

>6EF3_8 Proteasome subunit alpha type-1 (chains A)
MSGAAAASAAGYDRHITIFSPEGRLYQVEYAFKATNQTNINSLAVRGKDCTVVISQKKVP
DKLLDPTTVSYIFCISRTIGMVVNGPIPDARNAALRAKAEAAEFRYKYGYDMPCDVLAKR
MANLSQIYTQRAYMRPLGVILTFVSVDEELGPSIYKTDPAGYYVGYKATATGPKQQEITT
NLENHFKKSKIDHINEESWEKVVEFAITHMIDALGTEFSKNDLEVGVATKDKFFTLSAEN
IEERLVAIAEQD

Sequence of entity 9 (B), FASTA

>6EF3_9 Proteasome subunit alpha type-2 (chains B)
MTDRYSFSLTTFSPSGKLGQIDYALTAVKQGVTSLGIKATNGVVIATEKKSSSPLAMSET
LSKVSLLTPDIGAVYSGMGPDYRVLVDKSRKVAHTSYKRIYGEYPPTKLLVSEVAKIMQE
ATQSGGVRPFGVSLLIAGHDEFNGFSLYQVDPSGSYFPWKATAIGKGSVAAKTFLEKRWN
DELELEDAIHIALLTLKESVEGEFNGDTIELAIIGDENPDLLGYTGIPTDKGPRFRKLTS
QEINDRLEAL

Sequence of entity 10 (C), FASTA

>6EF3_10 Proteasome subunit alpha type-3 (chains C)
MGSRRYDSRTTIFSPEGRLYQVEYALESISHAGTAIGIMASDGIVLAAERKVTSTLLEQD
TSTEKLYKLNDKIAVAVAGLTADAEILINTARIHAQNYLKTYNEDIPVEILVRRLSDIKQ
GYTQHGGLRPFGVSFIYAGYDDRYGYQLYTSNPSGNYTGWKAISVGANTSAAQTLLQMDY
KDDMKVDDAIELALKTLSKTTDSSALTYDRLEFATIRKGANDGEVYQKIFKPQEIKDILV
KTGITKKDEDEEADEDMK

Sequence of entity 11 (D), FASTA

>6EF3_11 Proteasome subunit alpha type-4 (chains D)
MSGYDRALSIFSPDGHIFQVEYALEAVKRGTCAVGVKGKNCVVLGCERRSTLKLQDTRIT
PSKVSKIDSHVVLSFSGLNADSRILIEKARVEAQSHRLTLEDPVTVEYLTRYVAGVQQRY
TQSGGVRPFGVSTLIAGFDPRDDEPKLYQTEPSGIYSSWSAQTIGRNSKTVREFLEKNYD
RKEPPATVEECVKLTVRSLLEVVQTGAKNIEITVVKPDSDIVALSSEEINQYVTQIEQEK
QEQQEQDKKKKSNH

Sequence of entity 12 (E), FASTA

>6EF3_12 Proteasome subunit alpha type-5 (chains E)
MFLTRSEYDRGVSTFSPEGRLFQVEYSLEAIKLGSTAIGIATKEGVVLGVEKRATSPLLE
SDSIEKIVEIDRHIGCAMSGLTADARSMIEHARTAAVTHNLYYDEDINVESLTQSVCDLA
LRFGEGASGEERLMSRPFGVALLIAGHDADDGYQLFHAEPSGTFYRYNAKAIGSGSEGAQ
AELLNEWHSSLTLKEAELLVLKILKQVMEEKLDENNAQLSCITKQDGFKIYDNEKTAELI
KELKEKEAAESPEEADVEMS

Ligands and cofactors

ID	Name	Formula	Copies
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	2
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	4

Primary citation

Substrate-engaged 26Sproteasome structures reveal mechanisms for ATP-hydrolysis-driven translocation. de la Pena, A.H., Goodall, E.A., Gates, S.N. et al. Science (2018) 362. DOI 10.1126/science.aav0725 · 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

Browse structure collections

About this viewer

MolViewer shows 6EF3 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.