5WVI: The resting state of yeast proteasome

The resting state of yeast proteasome. Determined by electron microscopy at 6.3 Å resolution. Released 22 Mar 2017.

Method: Electron microscopy
Resolution: 6.3 Å
Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains: 47
Atoms: 105,787
Mol. weight: 1692.66 kDa
Released: 22 Mar 2017

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

Secondary structure: helices and β-sheets

5WVI contains 626 α-helices and 528 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, 12 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	34
β-strand	22-25	4	35
β-strand	31-35	5	35
β-strand	54-55	2	36
β-strand	61-62	2	36
β-strand	67	1	34
α-helix	68-71	4
α-helix	74-82	9
α-helix	94-107	14
β-strand	116-119	4	37
β-strand	129-132	4	37
β-strand	141	1	37
β-strand	144-146	3	35
α-helix	154-157	4
α-helix	167-183	17
β-strand	193-197	5	35
β-strand	202-206	5	35
α-helix	209-212	4

Chain 2: 6 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	32-37	6	31
β-strand	40-46	7	31
β-strand	49-51	3	43
β-strand	54-57	4	43
β-strand	63-67	5	44
β-strand	70-74	5	44
α-helix	78-82	5
α-helix	85-99	15
α-helix	107-118	12
β-strand	127-132	6	44
β-strand	137-142	6	44
β-strand	148-150	3	44
β-strand	153	1	31
β-strand	156	1	31
α-helix	160-169	10
α-helix	177-194	18
β-strand	202-208	7	31
β-strand	213-220	8	31
α-helix	234-235	2
β-strand	244-246	3	45

Chain 3: 6 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	4-7	4
β-strand	12-16	5	45
β-strand	21-26	6	45
β-strand	29-31	3	50
β-strand	34-37	4	50
β-strand	44-46	3	51
β-strand	49-51	3	51
β-strand	52-54	3	52
α-helix	57-60	4
α-helix	64-77	14
α-helix	84-95	12
β-strand	106-108	3	52
β-strand	109-112	4	53
β-strand	119-122	4	53
β-strand	136	1	45
β-strand	139	1	45
α-helix	143-149	7
α-helix	160-177	18
β-strand	185-190	6	45
β-strand	195-200	6	45

Chain 4: 6 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	59
β-strand	13-18	6	59
β-strand	22	1	60
β-strand	27	1	60
β-strand	35-37	3	61
β-strand	43-47	5	61
α-helix	50-54	5
α-helix	60-70	11
α-helix	77-90	14
β-strand	101-104	4	61
β-strand	107-108	2	62
β-strand	113-114	2	62
β-strand	117-119	3	61
β-strand	127	1	61
β-strand	130	1	59
α-helix	134-137	4
α-helix	141-147	7
α-helix	154-168	15
β-strand	174	1	63
β-strand	179-184	6	59
β-strand	189-192	4	59

Chain 5: 6 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	77-82	6	66
β-strand	87-91	5	66
β-strand	92	1	67
β-strand	95-97	3	68
β-strand	100-103	4	68
β-strand	110-111	2	69
β-strand	117-118	2	69
β-strand	121-122	2	70
α-helix	124-142	19
α-helix	148-150	3
α-helix	151-165	15
β-strand	172-173	2	70
β-strand	174-179	6	71
β-strand	185-190	6	71
β-strand	196	1	71
β-strand	199	1	71
β-strand	203-205	3	66
α-helix	208-217	10
α-helix	225-242	18
β-strand	243	1	32
β-strand	249	1	72
β-strand	250	1	67
β-strand	253-255	3	66
β-strand	260-262	3	66
β-strand	267	1	72
α-helix	268-278	11

Chain 6: 8 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	31-35	5	73
β-strand	40-45	6	73
β-strand	48-49	2	74
β-strand	54-56	3	74
β-strand	62-66	5	75
β-strand	69-75	7	75
α-helix	77-97	21
α-helix	101-104	4
α-helix	110-117	8
β-strand	126-131	6	75
α-helix	138-140	3
β-strand	141-142	2	76
β-strand	144	1	75
β-strand	152-153	2	76
β-strand	155-156	2	73
α-helix	160-164	5
α-helix	166-172	7
β-strand	179	1	77
β-strand	188	1	77
α-helix	189-191	3
α-helix	196-211	16
β-strand	214	1	17
β-strand	221-226	6	73
β-strand	231-236	6	73

Chain 7: 7 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	39-41	3	81
β-strand	44-48	5	82
β-strand	52-57	6	82
β-strand	61-63	3	81
β-strand	66-67	2	81
β-strand	77-78	2	83
β-strand	82-88	7	83
α-helix	90-108	19
α-helix	122-138	17
β-strand	145-152	8	83
β-strand	158-163	6	83
β-strand	169-170	2	83
β-strand	175	1	82
α-helix	178-182	5
α-helix	184-191	8
α-helix	195-197	3
α-helix	203-218	16
β-strand	221	1	84
β-strand	228-234	7	82
β-strand	239-245	7	82
α-helix	253-256	4

Chain a: 7 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	44-48	5	108
β-strand	52-58	7	108
β-strand	61-63	3	109
β-strand	66-69	4	109
β-strand	77-78	2	110
β-strand	82-88	7	110
α-helix	90-108	19
α-helix	122-138	17
β-strand	145-152	8	110
β-strand	158-163	6	110
β-strand	169-170	2	110
β-strand	175	1	108
α-helix	178-182	5
α-helix	184-191	8
α-helix	195-197	3
α-helix	208-218	11
β-strand	228-234	7	108
β-strand	239-245	7	108
α-helix	253-257	5

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
26S protease regulatory subunit 4 homolog	I	protein	437	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P40327 (AlphaFold model)
26S protease regulatory subunit 6B homolog	K	protein	428	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P33298 (AlphaFold model)
Proteasome subunit beta type-2	2, i	protein	261	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P25043 (AlphaFold model)
Proteasome subunit alpha type-1	A, c	protein	252	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P21243 (AlphaFold model)
Proteasome subunit beta type-3	3, h	protein	205	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P25451
Probable proteasome subunit alpha type-7	G, k	protein	288	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P21242
Proteasome subunit alpha type-6	F, l	protein	234	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P40302
Proteasome subunit alpha type-5	E, m	protein	260	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P32379
Proteasome subunit alpha type-4	D, n	protein	254	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P40303
26S proteasome complex subunit SEM1	Y	protein	89	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	O94742
26S proteasome regulatory subunit RPN2	N	protein	945	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P32565
26S proteasome regulatory subunit RPN3	S	protein	523	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P40016

21 more molecules are not listed.

Sequence of entity 1 (I), FASTA

>5WVI_1 26S protease regulatory subunit 4 homolog (chains I)
MGQGVSSGQDKKKKKGSNQKPKYEPPVQSKFGRKKRKGGPATAEKLPNIYPSTRCKLKLL
RMERIKDHLLLEEEFVSNSEILKPFEKKQEEEKKQLEEIRGNPLSIGTLEEIIDDDHAIV
TSPTMPDYYVSILSFVDKELLEPGCSVLLHHKTMSIVGVLQDDADPMVSVMKMDKSPTES
YSDIGGLESQIQEIKESVELPLTHPELYEEMGIKPPKGVILYGAPGTGKTLLAKAVANQT
SATFLRIVGSELIQKYLGDGPRLCRQIFKVAGENAPSIVFIDEIDAIGTKRYDSNSGGER
EIQRTMLELLNQLDGFDDRGDVKVIMATNKIETLDPALIRPGRIDRKILFENPDLSTKKK
ILGIHTSKMNLSEDVNLETLVTTKDDLSGADIQAMCTEAGLLALRERRMQVTAEDFKQAK
ERVMKNKVEENLEGLYL

Sequence of entity 2 (K), FASTA

>5WVI_2 26S protease regulatory subunit 6B homolog (chains K)
MEELGIVTPVEKAVEEKPAVKSYASLLAQLNGTVNNNSALSNVNSDIYFKLKKLEKEYEL
LTLQEDYIKDEQRHLKRELKRAQEEVKRIQSVPLVIGQFLEPIDQNTGIVSSTTGMSYVV
RILSTLDRELLKPSMSVALHRHSNALVDILPPDSDSSISVMGENEKPDVTYADVGGLDMQ
KQEIREAVELPLVQADLYEQIGIDPPRGVLLYGPPGTGKTMLVKAVANSTKAAFIRVNGS
EFVHKYLGEGPRMVRDVFRLARENAPSIIFIDEVDSIATKRFDAQTGSDREVQRILIELL
TQMDGFDQSTNVKVIMATNRADTLDPALLRPGRLDRKIEFPSLRDRRERRLIFGTIASKM
SLAPEADLDSLIIRNDSLSGAVIAAIMQEAGLRAVRKNRYVILQSDLEEAYATQVKTDNT
VDKFDFYK

Sequence of entity 3 (2, i), FASTA

>5WVI_3 Proteasome subunit beta type-2 (chains 2, i)
MAGLSFDNYQRNNFLAENSHTQPKATSTGTTIVGVKFNNGVVIAADTRSTQGPIVADKNC
AKLHRISPKIWCAGAGTAADTEAVTQLIGSNIELHSLYTSREPRVVSALQMLKQHLFKYQ
GHIGAYLIVAGVDPTGSHLFSIHAHGSTDVGYYLSLGSGSLAAMAVLESHWKQDLTKEEA
IKLASDAIQAGIWNDLGSGSNVDVCVMEIGKDAEYLRNYLTPNVREEKQKSYKFPRGTTA
VLKESIVNICDIQEEQVDITA

Sequence of entity 4 (A, c), FASTA

>5WVI_4 Proteasome subunit alpha type-1 (chains A, c)
MSGAAAASAAGYDRHITIFSPEGRLYQVEYAFKATNQTNINSLAVRGKDCTVVISQKKVP
DKLLDPTTVSYIFCISRTIGMVVNGPIPDARNAALRAKAEAAEFRYKYGYDMPCDVLAKR
MANLSQIYTQRAYMRPLGVILTFVSVDEELGPSIYKTDPAGYYVGYKATATGPKQQEITT
NLENHFKKSKIDHINEESWEKVVEFAITHMIDALGTEFSKNDLEVGVATKDKFFTLSAEN
IEERLVAIAEQD

Sequence of entity 5 (3, h), FASTA

>5WVI_5 Proteasome subunit beta type-3 (chains 3, h)
MSDPSSINGGIVVAMTGKDCVAIACDLRLGSQSLGVSNKFEKIFHYGHVFLGITGLATDV
TTLNEMFRYKTNLYKLKEERAIEPETFTQLVSSSLYERRFGPYFVGPVVAGINSKSGKPF
IAGFDLIGCIDEAKDFIVSGTASDQLFGMCESLYEPNLEPEDLFETISQALLNAADRDAL
SGWGAVVYIIKKDEVVKRYLKMRQD

Sequence of entity 6 (G, k), FASTA

>5WVI_6 Probable proteasome subunit alpha type-7 (chains G, k)
MTSIGTGYDLSNSVFSPDGRNFQVEYAVKAVENGTTSIGIKCNDGVVFAVEKLITSKLLV
PQKNVKIQVVDRHIGCVYSGLIPDGRHLVNRGREEAASFKKLYKTPIPIPAFADRLGQYV
QAHTLYNSVRPFGVSTIFGGVDKNGAHLYMLEPSGSYWGYKGAATGKGRQSAKAELEKLV
DHHPEGLSAREAVKQAAKIIYLAHEDNKEKDFELEISWCSLSETNGLHKFVKGDLLQEAI
DFAQKEINGDDDEDEDDSDNVMSSDDENAPVATNANATTDQEGDIHLE

Sequence of entity 7 (F, l), FASTA

>5WVI_7 Proteasome subunit alpha type-6 (chains F, l)
MFRNNYDGDTVTFSPTGRLFQVEYALEAIKQGSVTVGLRSNTHAVLVALKRNADELSSYQ
KKIIKCDEHMGLSLAGLAPDARVLSNYLRQQCNYSSLVFNRKLAVERAGHLLCDKAQKNT
QSYGGRPYGVGLLIIGYDKSGAHLLEFQPSGNVTELYGTAIGARSQGAKTYLERTLDTFI
KIDGNPDELIKAGVEAISQSLRDESLTVDNLSIAIVGKDTPFTIYDGEAVAKYI

Sequence of entity 8 (E, m), FASTA

>5WVI_8 Proteasome subunit alpha type-5 (chains E, m)
MFLTRSEYDRGVSTFSPEGRLFQVEYSLEAIKLGSTAIGIATKEGVVLGVEKRATSPLLE
SDSIEKIVEIDRHIGCAMSGLTADARSMIEHARTAAVTHNLYYDEDINVESLTQSVCDLA
LRFGEGASGEERLMSRPFGVALLIAGHDADDGYQLFHAEPSGTFYRYNAKAIGSGSEGAQ
AELLNEWHSSLTLKEAELLVLKILKQVMEEKLDENNAQLSCITKQDGFKIYDNEKTAELI
KELKEKEAAESPEEADVEMS

Sequence of entity 9 (D, n), FASTA

>5WVI_9 Proteasome subunit alpha type-4 (chains D, n)
MSGYDRALSIFSPDGHIFQVEYALEAVKRGTCAVGVKGKNCVVLGCERRSTLKLQDTRIT
PSKVSKIDSHVVLSFSGLNADSRILIEKARVEAQSHRLTLEDPVTVEYLTRYVAGVQQRY
TQSGGVRPFGVSTLIAGFDPRDDEPKLYQTEPSGIYSSWSAQTIGRNSKTVREFLEKNYD
RKEPPATVEECVKLTVRSLLEVVQTGAKNIEITVVKPDSDIVALSSEEINQYVTQIEQEK
QEQQEQDKKKKSNH

Sequence of entity 10 (Y), FASTA

>5WVI_10 26S proteasome complex subunit SEM1 (chains Y)
MSTDVAAAQAQSKIDLTKKKNEEINKKSLEEDDEFEDFPIDTWANGETIKSNAVTQTNIW
EENWDDVEVDDDFTNELKAELDRYKRENQ

Sequence of entity 11 (N), FASTA

>5WVI_11 26S proteasome regulatory subunit RPN2 (chains N)
MSLTTAAPLLALLRENQDSVKTYALESINNVVDQLWSEISNELPDIEALYDDDTFSDREM
AALIASKVYYNLGEYESAVKYALAAKDRFDIDEKSQFVETIVSKSIEMYVQEASKQYTKD
EQFYTKDIIDPKLTSIFERMIEKCLKASELKLALGIALEGYRLDIIESALKSKLDQDSTS
ENVKIINYLLTLAITTVTNSKFRSSILRKSFDFLMNMPNCDYLTLNKVVVNLNDAGLALQ
LFKKLKEENDEGLSAQIAFDLVSSASQQLLEILVTELTAQGYDPALLNILSGLPTCDYYN
TFLLNNKNIDIGLLNKSKSSLDGKFSLFHTAVSVANGFMHAGTTDNSFIKANLPWLGKAQ
NWAKFTATASLGVIHKGNLLEGKKVMAPYLPGSRASSRFIKGGSLYGLGLIYAGFGRDTT
DYLKNIIVENSGTSGDEDVDVLLHGASLGIGLAAMGSANIEVYEALKEVLYNDSATSGEA
AALGMGLCMLGTGKPEAIHDMFTYSQETQHGNITRGLAVGLALINYGRQELADDLITKML
ASDESLLRYGGAFTIALAYAGTGNNSAVKRLLHVAVSDSNDDVRRAAVIALGFVLLRDYT
TVPRIVQLLSKSHNAHVRCGTAFALGIACAGKGLQSAIDVLDPLTKDPVDFVRQAAMIAL
SMILIQQTEKLNPQVADINKNFLSVITNKHQEGLAKFGACVAQGIMNAGGRNVTIQLENA
DTGTLDTKSVVGLVMFSQFWYWFPLAHFLSLSFTPTTVIGIRGSDQAIPKFQMNCYAKED
AFSYPRMYEEASGKEVEKVATAVLSTTARAKARAKKTKKEKGPNEEEKKKEHEEKEKERE
TNKKGIKETKENDEEFYKNKYSSKPYKVDNMTRILPQQSRYISFIKDDRFVPVRKFKGNN
GVVVLRDREPKEPVALIETVRQMKDVNAPLPTPFKVDDNVDFPSA

Sequence of entity 12 (S), FASTA

>5WVI_12 26S proteasome regulatory subunit RPN3 (chains S)
MASTAVMMDVDSSGVNDLHHSEKKYAEEDQVQELLKVLNEISKTTLTLDPRYIWRSLKDL
SSLRNQELLNAETLCFTVNVLYPDSSSFKKNLLKFITSNHKSSVPGSAELRNSYPASFYS
VNTEKKTIEVTAEINCFMHLLVQLFLWDSKELEQLVEFNRKVVIPNLLCYYNLRSLNLIN
AKLWFYIYLSHETLARSSEEINSDNQNIILRSTMMKFLKIASLKHDNETKAMLINLILRD
FLNNGEVDSASDFISKLEYPHTDVSSSLEARYFFYLSKINAIQLDYSTANEYIIAAIRKA
PHNSKSLGFLQQSNKLHCCIQLLMGDIPELSFFHQSNMQKSLLPYYHLTKAVKLGDLKKF
TSTITKYKQLLLKDDTYQLCVRLRSNVIKTGIRIISLTYKKISLRDICLKLNLDSEQTVE
YMVSRAIRDGVIEAKINHEDGFIETTELLNIYDSEDPQQVFDERIKFANQLHDEYLVSMR
YPEDKKTQQNEKSENGENDDDTLDGDLMDDMSDISDLDDLGFL

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 P40327 (AlphaFold model), which also has an AlphaFold model), best resolution first:

35ZR 2.99 Å, yeast 26S proteasome base assembly intermediate, Hsm3-Rpt1-Rpt2 (base-Hsm3-Nas6 with…
35ZW 3.31 Å, yeast 26S proteasome base assembly intermediate, Hsm3-Rpt1-Rpt2-Rpt3-Rpt4-Rpt5…
9CGC 3.61 Å, Yeast 26S proteasome non-substrate-engaged (S1 state)
6J2Q 3.8 Å, Yeast proteasome in Ub-accepted state (C1-b)
6J2X 3.8 Å, Yeast proteasome in resting state (C1-a)
36BM 3.82 Å, yeast 26S proteasome base assembly intermediate, base-Hsm3-Nas6 with Rpt4-EQ
36BL 3.91 Å, yeast 26S proteasome base assembly intermediate, base-Rpn14-Hsm3-Nas6(2) with Rpt4-EQ
36BD 3.93 Å, yeast 26S proteasome base assembly intermediate, base-Rpn14-Hsm3-Nas6 with Rpt4-EQ
5MP9 4.1 Å, 26S proteasome in presence of ATP (s1)
6FVT 4.1 Å, 26S proteasome, s1 state
6EF3 4.17 Å, Yeast 26S proteasome bound to ubiquitinated substrate (4D motor state)
5WVK 4.2 Å, Yeast proteasome-ADP-AlFx

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