8RVL: Proteasomal late precursor complex from pre1-1

Proteasomal late precursor complex from pre1-1. Determined by electron microscopy at 2.14 Å resolution. Released 11 Sept 2024.

Method: Electron microscopy
Resolution: 2.14 Å
Organism: Saccharomyces cerevisiae
Chains: 34
Atoms: 62,379
Mol. weight: 927.1 kDa
Released: 11 Sept 2024

Explore 8RVL in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8RVL contains 319 α-helices and 445 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.

Chains 1 and M: 6 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	11-16	6	73
β-strand	21-26	6	73
β-strand	29-31	3	74
β-strand	34-37	4	74
β-strand	43-45	3	73
β-strand	50-56	7	73
α-helix	58-78	21
α-helix	82-85	4
α-helix	86-98	13
β-strand	107-114	8	73
β-strand	120-125	6	73
β-strand	131-140	10	73
α-helix	143-153	11
β-strand	155	1	75
β-strand	171	1	75
α-helix	172-174	3
α-helix	177-194	18
β-strand	195	1	76
β-strand	201-208	8	73
β-strand	211-218	8	73

Chain 2: 7 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	7-8	2	1
β-strand	11-15	5	2
β-strand	19-25	7	2
β-strand	27-30	4	3
β-strand	33-37	5	3
β-strand	42-45	4	1
β-strand	49-56	8	1
α-helix	57-74	18
α-helix	86-88	3
α-helix	89-105	17
β-strand	112-119	8	1
β-strand	125-130	6	1
β-strand	136-138	3	1
β-strand	141-143	3	2
α-helix	146-156	11
α-helix	162-167	6
α-helix	170-187	18
β-strand	188	1	4
β-strand	194-201	8	2
β-strand	205-213	9	2
α-helix	221-223	3

Chains 3 and 6: 10 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	12-13	2	77
α-helix	19-21	3
β-strand	22	1	78
β-strand	30	1	78
α-helix	32-35	4
α-helix	43-47	5
α-helix	52-58	7
α-helix	60-75	16
α-helix	79-93	15
α-helix	102-104	3
α-helix	105-110	6
α-helix	119-122	4
α-helix	138-146	9

Chain 4: 11 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	10-12	3
α-helix	18-20	3
β-strand	35-37	3	79
α-helix	44-46	3
β-strand	49-54	6	79
α-helix	55-60	6
α-helix	63-66	4
β-strand	69-78	10	79
β-strand	118-127	10	79
β-strand	130-135	6	79
α-helix	144-158	15
β-strand	164-170	7	79
β-strand	178-181	4	79
β-strand	184	1	79
β-strand	193-194	2	80
α-helix	196-206	11
β-strand	215-219	5	79
α-helix	232-246	15
α-helix	250-261	12
α-helix	266-268	3
α-helix	271-274	4
β-strand	275	1	34

Chain 5: 16 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	81
α-helix	11-13	3
α-helix	14-25	12
α-helix	27-29	3
β-strand	31-35	5	81
β-strand	41	1	82
α-helix	42-43	2
β-strand	44-45	2	80
β-strand	46	1	83
β-strand	51	1	84
α-helix	55-57	3
β-strand	67	1	83
β-strand	70-75	6	81
β-strand	80-85	6	81
β-strand	89	1	82
α-helix	92-94	3
α-helix	95-98	4
α-helix	99-103	5
α-helix	104-110	7
β-strand	114-121	8	81
α-helix	123-125	3
β-strand	131	1	85
β-strand	138-144	7	81
α-helix	149-152	4
β-strand	165	1	86
β-strand	169-170	2	81
β-strand	176	1	85
β-strand	179	1	86
α-helix	184-194	11
β-strand	204-211	8	81
α-helix	218-230	13
α-helix	237-239	3
α-helix	244-245	2
β-strand	246	1	84
α-helix	247-251	5
β-strand	266	1	87

Chain 7: 11 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	9-12	4
α-helix	18-20	3
β-strand	35-37	3	90
α-helix	44-46	3
β-strand	49-54	6	90
α-helix	55-60	6
α-helix	63-66	4
β-strand	69-78	10	90
β-strand	118-127	10	90
β-strand	130-135	6	90
α-helix	144-158	15
β-strand	164-170	7	90
β-strand	178-181	4	90
β-strand	184	1	90
β-strand	193-194	2	91
α-helix	196-206	11
β-strand	215-219	5	90
α-helix	232-246	15
α-helix	250-261	12
α-helix	266-268	3
α-helix	271-274	4
β-strand	275	1	68

Chain 8: 13 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	92
α-helix	11-13	3
α-helix	14-25	12
β-strand	31-35	5	92
β-strand	41	1	93
β-strand	44-46	3	91
β-strand	51	1	94
α-helix	55-57	3
β-strand	67-68	2	91
β-strand	70-75	6	92
β-strand	80-85	6	92
β-strand	89	1	93
α-helix	92-94	3
α-helix	95-98	4
α-helix	99-103	5
α-helix	104-110	7
β-strand	114-121	8	92
α-helix	123-125	3
β-strand	131	1	95
β-strand	138-144	7	92
β-strand	165	1	96
β-strand	169-170	2	92
β-strand	176	1	95
β-strand	179	1	96
α-helix	184-193	10
β-strand	204-211	8	92
α-helix	218-230	13
α-helix	237-239	3
α-helix	244-245	2
β-strand	246	1	94
α-helix	247-251	5
β-strand	266	1	97

Chains A and O: 11 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	12-14	3
α-helix	26-34	9
β-strand	42-46	5	9
β-strand	51-56	6	9
β-strand	64	1	10
α-helix	66-68	3
β-strand	72-74	3	11
β-strand	80-84	5	11
α-helix	87-108	22
α-helix	111-113	3
α-helix	114-130	17
β-strand	131	1	12
α-helix	135-137	3
β-strand	140-147	8	11
β-strand	151-157	7	11
β-strand	163-165	3	11
β-strand	166	1	13
β-strand	169-171	3	9
α-helix	175-189	15
α-helix	199-214	16
α-helix	220-222	3
β-strand	223-228	6	9
β-strand	233-235	3	9
α-helix	238-246	8

19 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-7	2, N	protein	266	Saccharomyces cerevisiae	P30657 (AlphaFold model)
Proteasome subunit alpha type-1	A, O	protein	252	Saccharomyces cerevisiae	P21243 (AlphaFold model)
Proteasome subunit alpha type-4	D, R	protein	254	Saccharomyces cerevisiae	P40303 (AlphaFold model)
Proteasome subunit alpha type-5	E, S	protein	260	Saccharomyces cerevisiae	P32379 (AlphaFold model)
Proteasome subunit alpha type-6	F, T	protein	234	Saccharomyces cerevisiae	P40302
Proteasome subunit beta type-1	H, V	protein	215	Saccharomyces cerevisiae	P38624
Proteasome subunit beta type-6	1, M	protein	241	Saccharomyces cerevisiae	P23724
Proteasome maturation factor UMP1	3, 6	protein	148	Saccharomyces cerevisiae	P38293
Proteasome chaperone 1	4, 7	protein	276	Saccharomyces cerevisiae	Q05778
Proteasome assembly chaperone 2	5, 8	protein	267	Saccharomyces cerevisiae	P36040
Proteasome subunit alpha type-2	B, P	protein	250	Saccharomyces cerevisiae	P23639
Proteasome subunit alpha type-3	C, Q	protein	258	Saccharomyces cerevisiae	P23638

5 more molecules are not listed.

Sequence of entity 1 (2, N), FASTA

>8RVL_1 Proteasome subunit beta type-7 (chains 2, N)
MNHDPFSWGRPADSTYGAYNTQIANAGASPMVNTQQPIVTGTSVISMKYDNGVIIAADNL
GSYGSLLRFNGVERLIPVGDNTVVGISGDISDMQHIERLLKDLVTENAYDNPLADAEEAL
EPSYIFEYLATVMYQRRSKMNPLWNAIIVAGVQSNGDQFLRYVNLLGVTYSSPTLATGFG
AHMANPLLRKVVDRESDIPKTTVQVAEEAIVNAMRVLYYRDARSSRNFSLAIIDKNTGLT
FKKNLQVENMKWDFAKDIKGYGTQKI

Sequence of entity 2 (A, O), FASTA

>8RVL_2 Proteasome subunit alpha type-1 (chains A, O)
MSGAAAASAAGYDRHITIFSPEGRLYQVEYAFKATNQTNINSLAVRGKDCTVVISQKKVP
DKLLDPTTVSYIFCISRTIGMVVNGPIPDARNAALRAKAEAAEFRYKYGYDMPCDVLAKR
MANLSQIYTQRAYMRPLGVILTFVSVDEELGPSIYKTDPAGYYVGYKATATGPKQQEITT
NLENHFKKSKIDHINEESWEKVVEFAITHMIDALGTEFSKNDLEVGVATKDKFFTLSAEN
IEERLVAIAEQD

Sequence of entity 3 (D, R), FASTA

>8RVL_3 Proteasome subunit alpha type-4 (chains D, R)
MSGYDRALSIFSPDGHIFQVEYALEAVKRGTCAVGVKGKNCVVLGCERRSTLKLQDTRIT
PSKVSKIDSHVVLSFSGLNADSRILIEKARVEAQSHRLTLEDPVTVEYLTRYVAGVQQRY
TQSGGVRPFGVSTLIAGFDPRDDEPKLYQTEPSGIYSSWSAQTIGRNSKTVREFLEKNYD
RKEPPATVEECVKLTVRSLLEVVQTGAKNIEITVVKPDSDIVALSSEEINQYVTQIEQEK
QEQQEQDKKKKSNH

Sequence of entity 4 (E, S), FASTA

>8RVL_4 Proteasome subunit alpha type-5 (chains E, S)
MFLTRSEYDRGVSTFSPEGRLFQVEYSLEAIKLGSTAIGIATKEGVVLGVEKRATSPLLE
SDSIEKIVEIDRHIGCAMSGLTADARSMIEHARTAAVTHNLYYDEDINVESLTQSVCDLA
LRFGEGASGEERLMSRPFGVALLIAGHDADDGYQLFHAEPSGTFYRYNAKAIGSGSEGAQ
AELLNEWHSSLTLKEAELLVLKILKQVMEEKLDENNAQLSCITKQDGFKIYDNEKTAELI
KELKEKEAAESPEEADVEMS

Sequence of entity 5 (F, T), FASTA

>8RVL_5 Proteasome subunit alpha type-6 (chains F, T)
MFRNNYDGDTVTFSPTGRLFQVEYALEAIKQGSVTVGLRSNTHAVLVALKRNADELSSYQ
KKIIKCDEHMGLSLAGLAPDARVLSNYLRQQCNYSSLVFNRKLAVERAGHLLCDKAQKNT
QSYGGRPYGVGLLIIGYDKSGAHLLEFQPSGNVTELYGTAIGARSQGAKTYLERTLDTFI
KIDGNPDELIKAGVEAISQSLRDESLTVDNLSIAIVGKDTPFTIYDGEAVAKYI

Sequence of entity 6 (H, V), FASTA

>8RVL_6 Proteasome subunit beta type-1 (chains H, V)
MNGIQVDINRLKKGEVSLGTSIMAVTFKDGVILGADSRTTTGAYIANRVTDKLTRVHDKI
WCCRSGSAADTQAIADIVQYHLELYTSQYGTPSTETAASVFKELCYENKDNLTAGIIVAG
YDDKNKGEVYTIPLGGSVHKLPYAIAGSGSTFIYGYCDKNFRENMSKEETVDFIKHSLSQ
AIKWDGSSGGVIRMVVLTAAGVERLIFYPDEYEQL

Sequence of entity 7 (1, M), FASTA

>8RVL_7 Proteasome subunit beta type-6 (chains 1, M)
MATIASEYSSEASNTPIEHQFNPYGDNGGTILGIAGEDFAVLAGDTRNITDYSINSRYEP
KVFDCGDNIVMSANGFAADGDALVKRFKNSVKWYHFDHNDKKLSINSAARNIQHLLYGKR
FFPYYVHTIIAGLDEDGKGAVYSFDPVGSYEREQCRAGGAAASLIMPFLDNQVNFKNQYE
PGTNGKVKKPLKYLSVEEVIKLVRDSFTSATERHIQVGDGLEILIVTKDGVRKEFYELKR
D

Sequence of entity 8 (3, 6), FASTA

>8RVL_8 Proteasome maturation factor UMP1 (chains 3, 6)
MNIVPQDTFKSQVSTDQDKSVLSSAVPSLPDTLRQQEGGAVPLSTQLNDRHPLESTLKNW
ETTQRQRQMEQYRQIFGIAEPMKRTMEMEIVNRTDFNPLSTNGSIHRDILLNKECSIDWE
DVYPGTGLQASTMVGDDVHSKIEKQLGI

Sequence of entity 9 (4, 7), FASTA

>8RVL_9 Proteasome chaperone 1 (chains 4, 7)
MLFKQWNDLPEPKHLLDLPEISKNLQSLEVCPVPKVEFPQDLDVPQYSTAVITTKIMNPL
FPKNLLQLTSIGEIKTTLTVKSPSLPQSSGKHSWNYDENFPNEVDPDQKNDTADETVYGF
SFPIYSFGKTLLFSMEENFISISPIFGNMISRSIISQLAQFSPDIIVIGTSDKIASMKVM
TENECTLQPPEFITGFIGSVLTQLIVGPSKGLKFKCLVAPSEGPNGFEKLSLSDMGSLVD
LCGQWLGFEPSRYSEECYRLWRCDSAAIGAQSGLYI

Sequence of entity 10 (5, 8), FASTA

>8RVL_10 Proteasome assembly chaperone 2 (chains 5, 8)
MSCLVLPLVSVGNIPQLSIDWLLNSQANEWEYLEALDSKYLVEFVGPLDRPEDGSDSLYK
DADMKYSSALEVFYNKKRGLFAIQQRTPLVSVNYLNNFIVEIILPFLSKYNISEICIWDS
LYAMEDENGVIVRPQEVYSLGEFYFDDEAELLSNLHLNDQESMVNNWLHFTPTSFQDKIS
VDQPIFKILFQILNASQRPKALRSIKYCSCLANEGDNSLDSQQFLQWIISQKVIKNAPPI
VKFVRPISWQGAYGMADARDKFVDLYN

Sequence of entity 11 (B, P), FASTA

>8RVL_11 Proteasome subunit alpha type-2 (chains B, P)
MTDRYSFSLTTFSPSGKLGQIDYALTAVKQGVTSLGIKATNGVVIATEKKSSSPLAMSET
LSKVSLLTPDIGAVYSGMGPDYRVLVDKSRKVAHTSYKRIYGEYPPTKLLVSEVAKIMQE
ATQSGGVRPFGVSLLIAGHDEFNGFSLYQVDPSGSYFPWKATAIGKGSVAAKTFLEKRWN
DELELEDAIHIALLTLKESVEGEFNGDTIELAIIGDENPDLLGYTGIPTDKGPRFRKLTS
QEINDRLEAL

Sequence of entity 12 (C, Q), FASTA

>8RVL_12 Proteasome subunit alpha type-3 (chains C, Q)
MGSRRYDSRTTIFSPEGRLYQVEYALESISHAGTAIGIMASDGIVLAAERKVTSTLLEQD
TSTEKLYKLNDKIAVAVAGLTADAEILINTARIHAQNYLKTYNEDIPVEILVRRLSDIKQ
GYTQHGGLRPFGVSFIYAGYDDRYGYQLYTSNPSGNYTGWKAISVGANTSAAQTLLQMDY
KDDMKVDDAIELALKTLSKTTDSSALTYDRLEFATIRKGANDGEVYQKIFKPQEIKDILV
KTGITKKDEDEEADEDMK

Primary citation

Structural roles of Ump1 and beta-subunit propeptides in proteasome biogenesis. Mark, E., Ramos, P.C., Kayser, F. et al. Life Sci Alliance (2024) 7. DOI 10.26508/lsa.202402865 · PubMed

Other PDB entries of the same protein (UniProt P30657 (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
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
3NZJ 2.4 Å, Crystal structure of yeast 20S proteasome in complex with ligand 2a

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