4CR2: Proteasome component PRE3

Deep classification of a large cryo-EM dataset defines the conformational landscape of the 26S proteasome. Determined by electron microscopy at 7.7 Å resolution. Released 2 Apr 2014.

Method: Electron microscopy
Resolution: 7.7 Å
Organism: SACCHAROMYCES CEREVISIAE
Chains: 33
Atoms: 80,139
Mol. weight: 1309.28 kDa
Released: 2 Apr 2014

Explore 4CR2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4CR2 contains 446 α-helices and 344 β-strands across 33 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, 13 β-strands

Element	Residues	Length	Sheet
β-strand	-3	1	1
β-strand	2-7	6	2
β-strand	12-17	6	2
β-strand	20-22	3	3
β-strand	25-28	4	3
β-strand	34-38	5	4
β-strand	41-47	7	4
α-helix	49-70	22
α-helix	75-88	14
β-strand	95-102	8	4
β-strand	108-113	6	4
β-strand	120-122	3	4
β-strand	124-128	5	2
α-helix	131-134	4
α-helix	135-141	7
α-helix	148-165	18
β-strand	173-179	7	2
β-strand	182-188	7	2
α-helix	190-195	6

Chain 2: 6 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	6
β-strand	11-17	7	6
β-strand	20-22	3	7
β-strand	25-28	4	7
β-strand	34-38	5	8
β-strand	41-47	7	8
α-helix	49-70	22
α-helix	73-75	3
α-helix	76-89	14
β-strand	96-100	5	8
β-strand	101-104	4	9
β-strand	107-110	4	9
β-strand	111-113	3	8
β-strand	119-121	3	8
β-strand	124-128	5	6
α-helix	131-141	11
α-helix	148-165	18
β-strand	173-179	7	6
β-strand	184	1	10
β-strand	185-191	7	6
α-helix	204-206	3
β-strand	212-218	7	11

Chain 3: 4 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	11
β-strand	12-17	6	11
β-strand	20-22	3	14
β-strand	25-28	4	14
β-strand	34-37	4	15
β-strand	40-46	7	15
α-helix	48-69	22
α-helix	75-88	14
β-strand	96-103	8	15
β-strand	110-114	5	15
β-strand	122	1	15
β-strand	127-131	5	11
α-helix	134-144	11
α-helix	151-166	16
β-strand	176-183	8	11
β-strand	185-191	7	11

Chain 4: 5 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	18
β-strand	12-17	6	18
β-strand	20-22	3	19
β-strand	25-28	4	19
β-strand	34-38	5	20
β-strand	41-47	7	20
α-helix	49-70	22
α-helix	73-75	3
α-helix	76-90	15
β-strand	99-107	9	20
β-strand	112-118	7	20
β-strand	124-125	2	20
β-strand	129-131	3	18
α-helix	135-146	12
α-helix	153-170	18
β-strand	178-184	7	18
β-strand	187-191	5	18

Chain 5: 6 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-8	6	22
β-strand	11-18	8	22
β-strand	20-22	3	23
β-strand	25-28	4	23
β-strand	34-36	3	24
β-strand	42-44	3	24
α-helix	49-69	21
α-helix	73-75	3
α-helix	76-87	12
β-strand	98-105	8	24
β-strand	109-116	8	24
β-strand	120-124	5	24
β-strand	126-129	4	22
α-helix	133-141	9
α-helix	150-167	18
β-strand	174-180	7	22
β-strand	185-192	8	22
α-helix	193-204	12

Chain 6: 5 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	28
β-strand	12-17	6	28
β-strand	20-22	3	29
β-strand	25-28	4	29
β-strand	34-36	3	30
β-strand	41-47	7	30
α-helix	49-69	21
α-helix	77-89	13
β-strand	98-105	8	30
β-strand	111-117	7	30
β-strand	120-125	6	30
β-strand	127-131	5	28
α-helix	134-141	8
α-helix	142-146	5
α-helix	168-185	18
β-strand	192-199	8	28
β-strand	202-209	8	28

Chain 7: 7 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	-2	1	31
β-strand	-1	1	32
β-strand	3-8	6	33
β-strand	11-17	7	33
β-strand	20-22	3	34
β-strand	25-28	4	34
β-strand	34-36	3	32
β-strand	41-47	7	32
α-helix	49-67	19
α-helix	81-96	16
β-strand	104-111	8	32
β-strand	117-123	7	32
β-strand	128-129	2	32
β-strand	133-136	4	33
α-helix	137-142	6
α-helix	144-147	4
α-helix	154-159	6
α-helix	162-179	18
β-strand	186-193	8	33
β-strand	197-205	9	33
α-helix	212-216	5

Chain A: 10 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	26-33	8
β-strand	42-46	5	39
β-strand	51-56	6	39
β-strand	64	1	40
β-strand	72-74	3	41
β-strand	80-84	5	41
α-helix	87-107	21
α-helix	111-113	3
α-helix	114-130	17
β-strand	134	1	42
α-helix	135-137	3
β-strand	140-146	7	41
β-strand	152-157	6	41
β-strand	163-165	3	41
β-strand	166	1	43
β-strand	169-171	3	39
α-helix	175-189	15
α-helix	199-213	15
β-strand	223-229	7	39
β-strand	232-235	4	39
α-helix	236-237	2
α-helix	238-247	10
α-helix	248-250	3

25 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 component PRE3	1	protein	215	SACCHAROMYCES CEREVISIAE	P38624 (AlphaFold model)
Proteasome component PUP1	2	protein	261	SACCHAROMYCES CEREVISIAE	P25043 (AlphaFold model)
Proteasome component PUP3	3	protein	205	SACCHAROMYCES CEREVISIAE	P25451 (AlphaFold model)
Proteasome component C11	4	protein	198	SACCHAROMYCES CEREVISIAE	P22141 (AlphaFold model)
Proteasome component PRE2	5	protein	287	SACCHAROMYCES CEREVISIAE	P30656
Proteasome component C5	6	protein	241	SACCHAROMYCES CEREVISIAE	P23724
Proteasome component PRE4	7	protein	266	SACCHAROMYCES CEREVISIAE	P30657
Proteasome component C7-alpha	A	protein	252	SACCHAROMYCES CEREVISIAE	P21243
Proteasome component Y7	B	protein	250	SACCHAROMYCES CEREVISIAE	P23639
Proteasome component Y13	C	protein	258	SACCHAROMYCES CEREVISIAE	P23638
Proteasome component PRE6	D	protein	254	SACCHAROMYCES CEREVISIAE	P40303
Proteasome component PUP2	E	protein	260	SACCHAROMYCES CEREVISIAE	P32379

21 more molecules are not listed.

Sequence of entity 1 (1), FASTA

>4CR2_1 PROTEASOME COMPONENT PRE3 (chains 1)
MNGIQVDINRLKKGEVSLGTSIMAVTFKDGVILGADSRTTTGAYIANRVTDKLTRVHDKI
WCCRSGSAADTQAIADIVQYHLELYTSQYGTPSTETAASVFKELCYENKDNLTAGIIVAG
YDDKNKGEVYTIPLGGSVHKLPYAIAGSGSTFIYGYCDKNFRENMSKEETVDFIKHSLSQ
AIKWDGSSGGVIRMVVLTAAGVERLIFYPDEYEQL

Sequence of entity 2 (2), FASTA

>4CR2_2 PROTEASOME COMPONENT PUP1 (chains 2)
MAGLSFDNYQRNNFLAENSHTQPKATSTGTTIVGVKFNNGVVIAADTRSTQGPIVADKNC
AKLHRISPKIWCAGAGTAADTEAVTQLIGSNIELHSLYTSREPRVVSALQMLKQHLFKYQ
GHIGAYLIVAGVDPTGSHLFSIHAHGSTDVGYYLSLGSGSLAAMAVLESHWKQDLTKEEA
IKLASDAIQAGIWNDLGSGSNVDVCVMEIGKDAEYLRNYLTPNVREEKQKSYKFPRGTTA
VLKESIVNICDIQEEQVDITA

Sequence of entity 3 (3), FASTA

>4CR2_3 PROTEASOME COMPONENT PUP3 (chains 3)
MSDPSSINGGIVVAMTGKDCVAIACDLRLGSQSLGVSNKFEKIFHYGHVFLGITGLATDV
TTLNEMFRYKTNLYKLKEERAIEPETFTQLVSSSLYERRFGPYFVGPVVAGINSKSGKPF
IAGFDLIGCIDEAKDFIVSGTASDQLFGMCESLYEPNLEPEDLFETISQALLNAADRDAL
SGWGAVVYIIKKDEVVKRYLKMRQD

Sequence of entity 4 (4), FASTA

>4CR2_4 PROTEASOME COMPONENT C11 (chains 4)
MDIILGIRVQDSVILASSKAVTRGISVLKDSDDKTRQLSPHTLMSFAGEAGDTVQFAEYI
QANIQLYSIREDYELSPQAVSSFVRQELAKSIRSRRPYQVNVLIGGYDKKKNKPELYQID
YLGTKVELPYGAHGYSGFYTFSLLDHHYRPDMTTEEGLDLLKLCVQELEKRMPMDFKGVI
VKIVDKDGIRQVDDFQAQ

Sequence of entity 5 (5), FASTA

>4CR2_5 PROTEASOME COMPONENT PRE2 (chains 5)
MQAIADSFSVPNRLVKELQYDNEQNLESDFVTGASQFQRLAPSLTVPPIASPQQFLRAHT
DDSRNPDCKIKIAHGTTTLAFRFQGGIIVAVDSRATAGNWVASQTVKRVIEINPFLLGTM
AGGAADCQFWETWLGSQCRLHELREKERISVAAASKILSNLVYQYKGAGLSMGTMICGYT
RKEGPTIYYVDSDGTRLKGDIFCVGSGQTFAYGVLDSNYKWDLSVEDALYLGKRSILAAA
HRDAYSGGSVNLYHVTEDGWIYHGNHDVGELFWKVKEEEGSFNNVIG

Sequence of entity 6 (6), FASTA

>4CR2_6 PROTEASOME COMPONENT C5 (chains 6)
MATIASEYSSEASNTPIEHQFNPYGDNGGTILGIAGEDFAVLAGDTRNITDYSINSRYEP
KVFDCGDNIVMSANGFAADGDALVKRFKNSVKWYHFDHNDKKLSINSAARNIQHLLYGKR
FFPYYVHTIIAGLDEDGKGAVYSFDPVGSYEREQCRAGGAAASLIMPFLDNQVNFKNQYE
PGTNGKVKKPLKYLSVEEVIKLVRDSFTSATERHIQVGDGLEILIVTKDGVRKEFYELKR
D

Sequence of entity 7 (7), FASTA

>4CR2_7 PROTEASOME COMPONENT PRE4 (chains 7)
MNHDPFSWGRPADSTYGAYNTQIANAGASPMVNTQQPIVTGTSVISMKYDNGVIIAADNL
GSYGSLLRFNGVERLIPVGDNTVVGISGDISDMQHIERLLKDLVTENAYDNPLADAEEAL
EPSYIFEYLATVMYQRRSKMNPLWNAIIVAGVQSNGDQFLRYVNLLGVTYSSPTLATGFG
AHMANPLLRKVVDRESDIPKTTVQVAEEAIVNAMRVLYYRDARSSRNFSLAIIDKNTGLT
FKKNLQVENMKWDFAKDIKGYGTQKI

Sequence of entity 8 (A), FASTA

>4CR2_8 PROTEASOME COMPONENT C7-ALPHA (chains A)
MSGAAAASAAGYDRHITIFSPEGRLYQVEYAFKATNQTNINSLAVRGKDCTVVISQKKVP
DKLLDPTTVSYIFCISRTIGMVVNGPIPDARNAALRAKAEAAEFRYKYGYDMPCDVLAKR
MANLSQIYTQRAYMRPLGVILTFVSVDEELGPSIYKTDPAGYYVGYKATATGPKQQEITT
NLENHFKKSKIDHINEESWEKVVEFAITHMIDALGTEFSKNDLEVGVATKDKFFTLSAEN
IEERLVAIAEQD

Sequence of entity 9 (B), FASTA

>4CR2_9 PROTEASOME COMPONENT Y7 (chains B)
MTDRYSFSLTTFSPSGKLGQIDYALTAVKQGVTSLGIKATNGVVIATEKKSSSPLAMSET
LSKVSLLTPDIGAVYSGMGPDYRVLVDKSRKVAHTSYKRIYGEYPPTKLLVSEVAKIMQE
ATQSGGVRPFGVSLLIAGHDEFNGFSLYQVDPSGSYFPWKATAIGKGSVAAKTFLEKRWN
DELELEDAIHIALLTLKESVEGEFNGDTIELAIIGDENPDLLGYTGIPTDKGPRFRKLTS
QEINDRLEAL

Sequence of entity 10 (C), FASTA

>4CR2_10 PROTEASOME COMPONENT Y13 (chains C)
MGSRRYDSRTTIFSPEGRLYQVEYALESISHAGTAIGIMASDGIVLAAERKVTSTLLEQD
TSTEKLYKLNDKIAVAVAGLTADAEILINTARIHAQNYLKTYNEDIPVEILVRRLSDIKQ
GYTQHGGLRPFGVSFIYAGYDDRYGYQLYTSNPSGNYTGWKAISVGANTSAAQTLLQMDY
KDDMKVDDAIELALKTLSKTTDSSALTYDRLEFATIRKGANDGEVYQKIFKPQEIKDILV
KTGITKKDEDEEADEDMK

Sequence of entity 11 (D), FASTA

>4CR2_11 PROTEASOME COMPONENT PRE6 (chains D)
MSGYDRALSIFSPDGHIFQVEYALEAVKRGTCAVGVKGKNCVVLGCERRSTLKLQDTRIT
PSKVSKIDSHVVLSFSGLNADSRILIEKARVEAQSHRLTLEDPVTVEYLTRYVAGVQQRY
TQSGGVRPFGVSTLIAGFDPRDDEPKLYQTEPSGIYSSWSAQTIGRNSKTVREFLEKNYD
RKEPPATVEECVKLTVRSLLEVVQTGAKNIEITVVKPDSDIVALSSEEINQYVTQIEQEK
QEQQEQDKKKKSNH

Sequence of entity 12 (E), FASTA

>4CR2_12 PROTEASOME COMPONENT PUP2 (chains E)
MFLTRSEYDRGVSTFSPEGRLFQVEYSLEAIKLGSTAIGIATKEGVVLGVEKRATSPLLE
SDSIEKIVEIDRHIGCAMSGLTADARSMIEHARTAAVTHNLYYDEDINVESLTQSVCDLA
LRFGEGASGEERLMSRPFGVALLIAGHDADDGYQLFHAEPSGTFYRYNAKAIGSGSEGAQ
AELLNEWHSSLTLKEAELLVLKILKQVMEEKLDENNAQLSCITKQDGFKIYDNEKTAELI
KELKEKEAAESPEEADVEMS

Primary citation

Deep Classification of a Large Cryo-Em Dataset Defines the Conformational Landscape of the 26S Proteasome. Unverdorben, P., Beck, F., Sledz, P. et al. Proc Natl Acad Sci U S A (2014) 111:5544. DOI 10.1073/PNAS.1403409111 · 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

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