6EPD: Substrate processing state 26S proteasome

Substrate processing state 26S proteasome (SPS1). Determined by electron microscopy at 15.4 Å resolution. Released 7 Feb 2018.

Method: Electron microscopy
Resolution: 15.4 Å
Organism: Rattus norvegicus
Chains: 32
Atoms: 82,757
Mol. weight: 1284 kDa
Released: 7 Feb 2018

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

Secondary structure: helices and β-sheets

6EPD contains 450 α-helices and 291 β-strands across 32 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: 4 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	35	1	28
β-strand	37-41	5	29
β-strand	46-51	6	29
β-strand	54-56	3	30
β-strand	59-62	4	30
β-strand	77-78	2	31
β-strand	81	1	28
α-helix	83-104	22
α-helix	110-123	14
β-strand	133-136	4	31
β-strand	144-148	5	31
β-strand	154-157	4	31
β-strand	160-162	3	29
α-helix	170-176	7
α-helix	183-200	18
β-strand	208-214	7	29
β-strand	217-223	7	29

Chain 2: 4 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	45	1	32
β-strand	47-50	4	33
β-strand	56-61	6	33
β-strand	64-66	3	34
β-strand	69-72	4	34
β-strand	79-80	2	35
β-strand	86-90	5	35
β-strand	91	1	32
α-helix	93-114	22
α-helix	120-134	15
β-strand	141-147	7	35
β-strand	152-157	6	35
β-strand	170-171	2	33
α-helix	175-185	11
α-helix	192-209	18
β-strand	217-222	6	33
β-strand	227-228	2	33
β-strand	234	1	33
β-strand	259	1	36

Chain 3: 6 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	13-17	5	36
β-strand	22-27	6	36
β-strand	45	1	37
β-strand	52-54	3	37
α-helix	59-79	21
α-helix	83-85	3
α-helix	86-98	13
β-strand	110-112	3	37
α-helix	114-115	2
β-strand	123-125	3	37
β-strand	139-141	3	36
α-helix	145-154	10
α-helix	162-179	18
β-strand	187-192	6	36
β-strand	197-202	6	36

Chain 4: 5 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	38
β-strand	15-20	6	38
β-strand	25	1	39
β-strand	28	1	39
β-strand	37-39	3	40
β-strand	44-49	6	40
α-helix	52-73	22
α-helix	79-93	15
β-strand	103-109	7	40
β-strand	115-119	5	40
β-strand	127	1	40
β-strand	132-134	3	38
α-helix	136-147	12
α-helix	155-171	17
β-strand	180-185	6	38
β-strand	190-193	4	38
α-helix	194-195	2

Chain 5: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	64-68	5	41
β-strand	73-77	5	41
α-helix	110-131	22
α-helix	134-136	3
α-helix	137-151	15
β-strand	159-165	7	42
β-strand	170-176	7	42
β-strand	181-183	3	42
β-strand	186-189	4	41
α-helix	194-197	4
α-helix	210-227	18
β-strand	234-239	6	41
β-strand	246-252	7	41
α-helix	253-259	7

Chain 6: 7 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	29-30	2
β-strand	40-45	6	43
β-strand	50-56	7	43
β-strand	58	1	44
β-strand	66	1	44
β-strand	72-74	3	45
β-strand	79-84	6	45
α-helix	87-107	21
α-helix	114-125	12
β-strand	136-142	7	45
β-strand	148-153	6	45
β-strand	159-162	4	45
β-strand	164-168	5	43
α-helix	175-178	4
α-helix	179-183	5
α-helix	194-196	3
α-helix	197-214	18
β-strand	221-227	7	43
β-strand	232-238	7	43

Chain 7: 7 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	52-54	3	46
β-strand	57	1	47
β-strand	60-62	3	47
β-strand	65-71	7	47
β-strand	74-76	3	46
β-strand	79-82	4	46
β-strand	88-89	2	48
β-strand	95-100	6	48
β-strand	101-102	2	46
α-helix	103-123	21
α-helix	127-129	3
α-helix	131-145	15
β-strand	155-162	8	48
β-strand	165-172	8	48
β-strand	178-179	2	48
β-strand	182	1	47
α-helix	187-190	4
α-helix	193-200	8
α-helix	208-225	18
β-strand	233-238	6	47
β-strand	243-244	2	47
α-helix	246-248	3
β-strand	249	1	47

Chain A: 8 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	23-35	13
β-strand	39-43	5	1
β-strand	47-53	7	1
β-strand	69-71	3	2
β-strand	77-82	6	2
α-helix	84-105	22
α-helix	108-110	3
α-helix	111-127	17
α-helix	132-134	3
β-strand	136-144	9	2
β-strand	148-154	7	2
β-strand	160-162	3	2
β-strand	165-168	4	1
α-helix	172-184	13
α-helix	191-206	16
β-strand	215-221	7	1
β-strand	228-229	2	1
α-helix	231-244	14

24 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-6	A	protein	246	Rattus norvegicus	P60901 (AlphaFold model)
Proteasome subunit alpha type-2	B	protein	234	Rattus norvegicus	P17220 (AlphaFold model)
Proteasome subunit alpha type-4	C	protein	261	Rattus norvegicus	P21670 (AlphaFold model)
Proteasome subunit alpha type-7	D	protein	254	Rattus norvegicus	P48004 (AlphaFold model)
Proteasome subunit alpha type-5	E	protein	241	Rattus norvegicus	P34064
Proteasome subunit alpha type-1	F	protein	263	Rattus norvegicus	P18420
Proteasome subunit alpha type-3	G	protein	255	Rattus norvegicus	P18422
Proteasome subunit beta type-6	1	protein	238	Rattus norvegicus	P28073
Proteasome subunit beta type-7	2	protein	277	Rattus norvegicus	Q9JHW0
Proteasome subunit beta type-3	3	protein	205	Rattus norvegicus	P40112
Proteasome subunit beta type-2	4	protein	201	Rattus norvegicus	P40307
Proteasome subunit beta type-5	5	protein	263	Rattus norvegicus	P28075

20 more molecules are not listed.

Sequence of entity 1 (A), FASTA

>6EPD_1 Proteasome subunit alpha type-6 (chains A)
MSRGSSAGFDRHITIFSPEGRLYQVEYAFKAINQGGLTSVAVRGKDCAVIVTQKKVPDKL
LDSSTVTHLFKITENIGCVMTGMTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKRIAD
ISQVYTQNAEMRPLGCCMILIGIDEEQGPQVYKCDPAGYYCGFKATAAGVKQTESTSFLE
KKVKKKFDWTFEQTVETAITCLSTVLSIDFKPSEIEVGVVTVENPKFRILTEAEIDAHLV
ALAERD

Sequence of entity 2 (B), FASTA

>6EPD_2 Proteasome subunit alpha type-2 (chains B)
MAERGYSFSLTTFSPSGKLVQIEYALAAVAGGAPSVGIKAANGVVLATEKKQKSILYDER
SVHKVEPITKHIGLVYSGMGPDYRVLVHRARKLAQQYYLVYQEPIPTAQLVQRVASVMQE
YTQSGGVRPFGVSLLICGWNEGRPYLFQSDPSGAYFAWKATAMGKNYVNGKTFLEKRYNE
DLELEDAIHTAILTLKESFEGQMTEDNIEVGICNEAGFRRLTPTEVRDYLAAIA

Sequence of entity 3 (C), FASTA

>6EPD_3 Proteasome subunit alpha type-4 (chains C)
MSRRYDSRTTIFSPEGRLYQVEYAMEAIGHAGTCLGILANDGVLLAAERRNIHKLLDEVF
FSEKIYKLNEDMACSVAGITSDANVLTNELRLIAQRYLLQYQEPIPCEQLVTALCDIKQA
YTQFGGKRPFGVSLLYIGWDKHYGFQLYQSDPSGNYGGWKATCIGNNSAAAVSMLKQDYK
EGEMTLKSALALAVKVLNKTMDVSKLSAEKVEIATLTRENGKTVIRVLKQKEVEQLIKKH
EEEEAKAEREKKEKEQREKDK

Sequence of entity 4 (D), FASTA

>6EPD_4 Proteasome subunit alpha type-7 (chains D)
MSYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVEKKSVAKLQDERTVR
KICALDDNVCMAFAVVASVSGLTADARIVINRARVECQSHRLTVGDPVTVEYITRYIASL
KQRYTQSNGRRPFGISALIVGFDFDGTPRLYQTDPSGTYHAWKANAIGRGAKSVREFLEK
NYTDDAIETDDLTIKLVIKALLEVVQSGGKNIELAVMRRDQPLKILSPEEIEKYVAEIEK
EKEENEKKKQKKAS

Sequence of entity 5 (E), FASTA

>6EPD_5 Proteasome subunit alpha type-5 (chains E)
MFLTRSEYDRGVNTFSPEGRLFQVEYAIEGHKLGSTAIGIQTSEGVCLAVEKRITSPLME
PSSIEKIVEIDAHIGCAMSGLIADAKTLIDKARVETQNHWFTYNETMTVESVTQAVSNLA
LQFGEEDADPGAMSRPFGVALLFGGVDEKGPQLFHMDPSGTFVQCDARAIGSASEGAQSS
LQEVYHKSTTLKEAIKSSLIILKQVMEEKLNATNIELATVQPGQNFHMFTKEELEEVIKD
I

Sequence of entity 6 (F), FASTA

>6EPD_6 Proteasome subunit alpha type-1 (chains F)
MFRNQYDNDVTVWSPQGRIHQIEYAMEAVKQGSATVGLKSKTHAVLVALKRAQSELAAHQ
KKILHVDNHIGISIAGLTADARLLCNFMRQECLDSRFVFDRPLPVSRLVSLIGSKTQIPT
QRYGRRPYGVGLLIAGYDDMGPHVFQTCPSANYFDCRAMSIGARSQSARTYLERHMSEFM
QCNLDELVKHGLRALRETLPAEQDLTTKNVSIGIVGKDLEFTIYDDDDVSPFLDGLEERP
QRKAQPSQAADEPAEKADEPMEH

Sequence of entity 7 (G), FASTA

>6EPD_7 Proteasome subunit alpha type-3 (chains G)
MSSIGTGYDLSASTFSPDGRVFQVEYAMKAVENSSTAIGIRCKDGVVFGVEKLVLSKLYE
EGSNKRLFNVDRHVGMAVAGLLADARSLADIAREEASNFRSNFGYNIPLKHLADRVAMYV
HAYTLYSAVRPFGCSFMLGSYSVNDGAQLYMIDPSGVSYGYWGCAIGKARQAAKTEIEKL
QMKEMTCRDVVKEVAKIIYIVHDEVKDKAFELELSWVGELTKGRHEIVPKDVREEAEKYA
KESLKEEDESDDDNM

Sequence of entity 8 (1), FASTA

>6EPD_8 Proteasome subunit beta type-6 (chains 1)
MAAALAVRGAVSAPAFGPEALTPDWENREVSTGTTIMAVQFDGGVVLGADSRTTTGSYIA
NRVTDKLTPIHDHIFCCRSGSAADTQAVADAVTYQLGFHSIELNEPPLVHTAASLFKEMC
YRYREDLMAGIIIAGWDPQEGGQVYSVPMGGMMVRQSFAIGGSGSSYIYGYVDATYREGM
TKDECLQFTANALALAMERDGSSGGVIRLAAIQQSGVERQVLLGDQIPKVTISTLPPP

Sequence of entity 9 (2), FASTA

>6EPD_9 Proteasome subunit beta type-7 (chains 2)
MAAVSVFQAPVGGFSFDNCRRNAVLEADFAKKGFKLPKARKTGTTIAGVVYKDGIVLGAD
TRATEGMVVADKNCSKIHFISPNIYCCGAGTAADTDMTTQLISSNLELHSLTTGRLPRVV
TANRMLKQMLFRYQGYIGAALVLGGVDVTGPHLYSIYPHGSTDKLPYVTMGSGSLAAMAV
FEDKFRPDMEEEEAKKLVSEAIAAGIFNDLGSGSNIDLCVISKSKLDFLRPYSVPNKKGT
RFGRYRCEKGTTAVLTEKVTPLELEVLEEIVQTMDTS

Sequence of entity 10 (3), FASTA

>6EPD_10 Proteasome subunit beta type-3 (chains 3)
MSVMSYNGGAVMAMKGKNCVAIAADRRFGIQAQMVTTDFQKIFPMGDRLYIGLAGLATDV
QTVAQRLKFRLNLYELKEGRQIKPYTLMSMVANLLYEKRFGPYYTEPVIAGLDPKTFKPF
ICSLDLIGCPMVTDDFVVSGTCSEQMYGMCESLWEPNMDPEHLFETISQAMLNAVDRDAV
SGMGVIVHIIEKDKITTRTLKARMD

Sequence of entity 11 (4), FASTA

>6EPD_11 Proteasome subunit beta type-2 (chains 4)
MEYLIGIQGPDYVLVASDRVAASNIVQMKDDHDKMFKMSEKILLLCVGEAGDTVQFAEYI
QKNVQLYKMRNGYELSPTAAANFTRRNLADCLRSRTPYHVNLLLAGYDEHEGPALYYMDY
LAALAKAPFAAHGYGAFLTLSILDRYYTPTISRERAVELLRKCLEELQKRFILNLPTFSV
RVIDKDGIHNLENITFTKRSS

Sequence of entity 12 (5), FASTA

>6EPD_12 Proteasome subunit beta type-5 (chains 5)
MALASVLQRPMPVNQHGFFGLGGRADLLDLGPGSPGDGLSLAAPSWGVPEEPRIEMLHGT
TTLAFKFQHGVIVAADSRATAGPYIASQTVKKVIEINPYLLGTMAGGAADCSFWERLLAR
QCRIYELRNKERISVAAASKLLANMVYQYKGMGLSMGTMICGWDKRGPGLYYVDSEGNRI
SGTAFSVGSGSVYAFGVMDRGYSYDLQVEEAYDLARRAIYQATYRDAYSGGAVNLYHVRE
DGWIRVSSDNVADLHDKYTSSIP

Primary citation

In Situ Structure of Neuronal C9orf72 Poly-GA Aggregates Reveals Proteasome Recruitment. Guo, Q., Lehmer, C., Martinez-Sanchez, A. et al. Cell (2018) 172:696-705.e12. DOI 10.1016/j.cell.2017.12.030 · PubMed

Other PDB entries of the same protein (UniProt P60901 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6TU3 2.7 Å, Rat 20S proteasome
6EPF 11.8 Å, Ground state 26S proteasome (GS1)
6EPC 12.3 Å, Ground state 26S proteasome (GS2)
6EPE 12.8 Å, Substrate processing state 26S proteasome (SPS2)

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