4G4S: Proteasome-Pba1-Pba2 Complex

Structure of Proteasome-Pba1-Pba2 Complex. Determined by X-ray diffraction at 2.49 Å resolution. Released 5 Sept 2012.

Method: X-ray diffraction
Resolution: 2.49 Å
Organism: Saccharomyces cerevisiae
Chains: 16
Atoms: 28,531
Mol. weight: 426.63 kDa
Ligands: LDZ, MG
Released: 5 Sept 2012

Explore 4G4S in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4G4S contains 148 α-helices and 219 β-strands across 16 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 A: 9 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	26-34	9
β-strand	42-46	5	1
β-strand	47	1	2
β-strand	51-56	6	1
β-strand	64	1	3
α-helix	66-68	3
β-strand	72-74	3	4
β-strand	80-84	5	4
α-helix	87-108	22
α-helix	111-113	3
α-helix	114-128	15
β-strand	131	1	5
α-helix	135-137	3
β-strand	140-147	8	4
β-strand	151-157	7	4
β-strand	163-166	4	4
β-strand	168-171	4	1
α-helix	175-189	15
β-strand	194	1	2
α-helix	199-214	16
β-strand	223-228	6	1
β-strand	233-235	3	1
α-helix	238-247	10

Chain B: 15 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	8	1	6
β-strand	12	1	7
β-strand	18	1	7
α-helix	19-30	12
α-helix	32-33	2
β-strand	34-38	5	8
β-strand	43-48	6	8
β-strand	56-57	2	4
α-helix	58-60	3
β-strand	65-68	4	9
β-strand	71-77	7	9
α-helix	79-93	15
α-helix	94-98	5
α-helix	99-101	3
α-helix	104-106	3
α-helix	107-121	15
β-strand	125	1	6
β-strand	127	1	5
α-helix	128-130	3
β-strand	132-140	9	9
β-strand	144-150	7	9
β-strand	156-158	3	9
β-strand	159	1	10
β-strand	161-164	4	8
α-helix	168-178	11
α-helix	185-199	15
β-strand	209-214	6	8
α-helix	219-221	3
β-strand	224-225	2	11
α-helix	231-233	3
β-strand	235-237	3	8
α-helix	238-239	2
α-helix	240-248	9

Chain C: 10 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	20-29	10
α-helix	33-34	2
β-strand	35-40	6	12
β-strand	43-49	7	12
β-strand	57	1	10
β-strand	66-68	3	13
β-strand	73-79	7	13
α-helix	81-102	22
α-helix	105-107	3
α-helix	108-124	17
β-strand	125	1	14
α-helix	128-131	4
β-strand	133-141	9	13
β-strand	145-151	7	13
β-strand	157-159	3	13
β-strand	162-165	4	12
α-helix	169-178	10
α-helix	186-198	13
α-helix	208-210	3
β-strand	211-218	8	12
β-strand	225-229	5	12
α-helix	232-240	9

Chain D: 11 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	11	1	15
β-strand	17	1	15
α-helix	18-29	12
α-helix	31-32	2
β-strand	33-37	5	16
β-strand	42-47	6	16
α-helix	61-62	2
β-strand	64-68	5	17
β-strand	71-77	7	17
α-helix	79-100	22
α-helix	103-105	3
α-helix	106-119	14
β-strand	126	1	14
α-helix	127-129	3
β-strand	131-137	7	17
β-strand	146-150	5	17
β-strand	156-158	3	17
β-strand	159	1	18
β-strand	161-164	4	16
α-helix	168-178	11
β-strand	180	1	19
β-strand	183	1	19
α-helix	188-200	13
β-strand	210-216	7	16
β-strand	220-223	4	16
α-helix	224-225	2
α-helix	226-236	11

Chain E: 16 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	14-16	3
α-helix	22-29	8
α-helix	30-33	4
α-helix	35-36	2
β-strand	37-43	7	20
β-strand	45-51	7	20
β-strand	59	1	18
α-helix	61-63	3
β-strand	67-71	5	21
β-strand	74-80	7	21
α-helix	82-84	3
α-helix	85-103	19
α-helix	106-108	3
α-helix	109-120	12
α-helix	121-123	3
α-helix	130-132	3
β-strand	140-148	9	21
β-strand	152-159	8	21
β-strand	163-166	4	21
β-strand	167	1	22
β-strand	169-172	4	20
α-helix	176-186	11
α-helix	193-207	15
α-helix	211-212	2
β-strand	217-223	7	20
β-strand	227-230	4	20
α-helix	231-232	2
α-helix	233-244	12

Chain F: 12 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
α-helix	20-30	11
α-helix	33-34	2
β-strand	35-39	5	23
β-strand	43-49	7	23
α-helix	50-51	2
β-strand	52	1	24
β-strand	57	1	22
α-helix	58	1
β-strand	59	1	24
α-helix	60-61	2
β-strand	63-67	5	25
β-strand	70-76	7	25
β-strand	77	1	26
α-helix	78-99	22
α-helix	102-104	3
α-helix	105-118	14
β-strand	122	1	27
β-strand	130-138	9	25
β-strand	141-147	7	25
β-strand	153-155	3	25
β-strand	156	1	28
β-strand	158-161	4	23
α-helix	166-179	14
α-helix	186-198	13
β-strand	211-217	7	23
β-strand	220-225	6	23
α-helix	227-233	7

Chain G: 10 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	14-16	3
α-helix	22-32	11
β-strand	37-41	5	29
β-strand	45-54	10	29
β-strand	59	1	28
α-helix	60	1
β-strand	68-70	3	30
β-strand	74-80	7	30
α-helix	82-103	22
α-helix	106-108	3
α-helix	109-122	14
β-strand	129	1	27
β-strand	134-142	9	30
β-strand	145-151	7	30
β-strand	157-159	3	30
β-strand	160	1	3
β-strand	162-165	4	29
α-helix	169-182	14
α-helix	189-203	15
α-helix	204-206	3
β-strand	211-220	10	29
β-strand	228-230	3	29
α-helix	233-245	13

Chain H: 9 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-8	6	31
β-strand	11-16	6	31
β-strand	20-22	3	32
β-strand	25-28	4	32
β-strand	34-38	5	33
β-strand	41-47	7	33
α-helix	49-70	22
α-helix	73-74	2
α-helix	75-88	14
α-helix	90-92	3
β-strand	95-103	9	33
β-strand	107-113	7	33
β-strand	120-121	2	33
β-strand	124-127	4	31
α-helix	129-134	6
α-helix	135-141	7
α-helix	148-165	18
α-helix	172	1
β-strand	173-179	7	31
β-strand	182-188	7	31
α-helix	190-193	4

8 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 C7-alpha	A	protein	252	Saccharomyces cerevisiae	P21243 (AlphaFold model)
Proteasome component Y7	B	protein	250	Saccharomyces cerevisiae	P23639 (AlphaFold model)
Proteasome component Y13	C	protein	258	Saccharomyces cerevisiae	P23638 (AlphaFold model)
Proteasome component PRE6	D	protein	254	Saccharomyces cerevisiae	P40303 (AlphaFold model)
Proteasome component PUP2	E	protein	261	Saccharomyces cerevisiae	P32379
Proteasome component PRE5	F	protein	235	Saccharomyces cerevisiae	P40302
Proteasome component C1	G	protein	288	Saccharomyces cerevisiae	P21242
Proteasome component PRE3	H	protein	196	Saccharomyces cerevisiae	P38624
Proteasome component PUP1	I	protein	232	Saccharomyces cerevisiae	P25043
Proteasome component PUP3	J	protein	205	Saccharomyces cerevisiae	P25451
Proteasome component C11	K	protein	198	Saccharomyces cerevisiae	P22141
Proteasome component PRE2	L	protein	212	Saccharomyces cerevisiae	P30656

4 more molecules are not listed.

Sequence of entity 1 (A), FASTA

>4G4S_1 Proteasome component C7-alpha (chains A)
MSGAAAASAAGYDRHITIFSPEGRLYQVEYAFKATNQTNINSLAVRGKDCTVVISQKKVP
DKLLDPTTVSYIFCISRTIGMVVNGPIPDARNAALRAKAEAAEFRYKYGYDMPCDVLAKR
MANLSQIYTQRAYMRPLGVILTFVSVDEELGPSIYKTDPAGYYVGYKATATGPKQQEITT
NLENHFKKSKIDHINEESWEKVVEFAITHMIDALGTEFSKNDLEVGVATKDKFFTLSAEN
IEERLVAIAEQD

Sequence of entity 2 (B), FASTA

>4G4S_2 Proteasome component Y7 (chains B)
MTDRYSFSLTTFSPSGKLGQIDYALTAVKQGVTSLGIKATNGVVIATEKKSSSPLAMSET
LSKVSLLTPDIGAVYSGMGPDYRVLVDKSRKVAHTSYKRIYGEYPPTKLLVSEVAKIMQE
ATQSGGVRPFGVSLLIAGHDEFNGFSLYQVDPSGSYFPWKATAIGKGSVAAKTFLEKRWN
DELELEDAIHIALLTLKESVEGEFNGDTIELAIIGDENPDLLGYTGIPTDKGPRFRKLTS
QEINDRLEAL

Sequence of entity 3 (C), FASTA

>4G4S_3 Proteasome component Y13 (chains C)
MGSRRYDSRTTIFSPEGRLYQVEYALESISHAGTAIGIMASDGIVLAAERKVTSTLLEQD
TSTEKLYKLNDKIAVAVAGLTADAEILINTARIHAQNYLKTYNEDIPVEILVRRLSDIKQ
GYTQHGGLRPFGVSFIYAGYDDRYGYQLYTSNPSGNYTGWKAISVGANTSAAQTLLQMDY
KDDMKVDDAIELALKTLSKTTDSSALTYDRLEFATIRKGANDGEVYQKIFKPQEIKDILV
KTGITKKDEDEEADEDMK

Sequence of entity 4 (D), FASTA

>4G4S_4 Proteasome component PRE6 (chains D)
MSGYDRALSIFSPDGHIFQVEYALEAVKRGTCAVGVKGKNCVVLGCERRSTLKLQDTRIT
PSKVSKIDSHVVLSFSGLNADSRILIEKARVEAQSHRLTLEDPVTVEYLTRYVAGVQQRY
TQSGGVRPFGVSTLIAGFDPRDDEPKLYQTEPSGIYSSWSAQTIGRNSKTVREFLEKNYD
RKEPPATVEECVKLTVRSLLEVVQTGAKNIEITVVKPDSDIVALSSEEINQYVTQIEQEK
QEQQEQDKKKKSNH

Sequence of entity 5 (E), FASTA

>4G4S_5 Proteasome component PUP2 (chains E)
XMFLTRSEYDRGVSTFSPEGRLFQVEYSLEAIKLGSTAIGIATKEGVVLGVEKRATSPLL
ESDSIEKIVEIDRHIGCAMSGLTADARSMIEHARTAAVTHNLYYDEDINVESLTQSVCDL
ALRFGEGASGEERLMSRPFGVALLIAGHDADDGYQLFHAEPSGTFYRYNAKAIGSGSEGA
QAELLNEWHSSLTLKEAELLVLKILKQVMEEKLDENNAQLSCITKQDGFKIYDNEKTAEL
IKELKEKEAAESPEEADVEMS

Sequence of entity 6 (F), FASTA

>4G4S_6 Proteasome component PRE5 (chains F)
XMFRNNYDGDTVTFSPTGRLFQVEYALEAIKQGSVTVGLRSNTHAVLVALKRNADELSSY
QKKIIKCDEHMGLSLAGLAPDARVLSNYLRQQCNYSSLVFNRKLAVERAGHLLCDKAQKN
TQSYGGRPYGVGLLIIGYDKSGAHLLEFQPSGNVTELYGTAIGARSQGAKTYLERTLDTF
IKIDGNPDELIKAGVEAISQSLRDESLTVDNLSIAIVGKDTPFTIYDGEAVAKYI

Sequence of entity 7 (G), FASTA

>4G4S_7 Proteasome component C1 (chains G)
MTSIGTGYDLSNSVFSPDGRNFQVEYAVKAVENGTTSIGIKCNDGVVFAVEKLITSKLLV
PQKNVKIQVVDRHIGCVYSGLIPDGRHLVNRGREEAASFKKLYKTPIPIPAFADRLGQYV
QAHTLYNSVRPFGVSTIFGGVDKNGAHLYMLEPSGSYWGYKGAATGKGRQSAKAELEKLV
DHHPEGLSAREAVKQAAKIIYLAHEDNKEKDFELEISWCSLSETNGLHKFVKGDLLQEAI
DFAQKEINGDDDEDEDDSDNVMSSDDENAPVATNANATTDQEGDIHLE

Sequence of entity 8 (H), FASTA

>4G4S_8 Proteasome component PRE3 (chains H)
TSIMAVTFKDGVILGADSRTTTGAYIANRVTDKLTRVHDKIWCCRSGSAADTQAIADIVQ
YHLELYTSQYGTPSTETAASVFKELCYENKDNLTAGIIVAGYDDKNKGEVYTIPLGGSVH
KLPYAIAGSGSTFIYGYCDKNFRENMSKEETVDFIKHSLSQAIKWDGSSGGVIRMVVLTA
AGVERLIFYPDEYEQL

Sequence of entity 9 (I), FASTA

>4G4S_9 Proteasome component PUP1 (chains I)
TTIVGVKFNNGVVIAADTRSTQGPIVADKNCAKLHRISPKIWCAGAGTAADTEAVTQLIG
SNIELHSLYTSREPRVVSALQMLKQHLFKYQGHIGAYLIVAGVDPTGSHLFSIHAHGSTD
VGYYLSLGSGSLAAMAVLESHWKQDLTKEEAIKLASDAIQAGIWNDLGSGSNVDVCVMEI
GKDAEYLRNYLTPNVREEKQKSYKFPRGTTAVLKESIVNICDIQEEQVDITA

Sequence of entity 10 (J), FASTA

>4G4S_10 Proteasome component PUP3 (chains J)
MSDPSSINGGIVVAMTGKDCVAIACDLRLGSQSLGVSNKFEKIFHYGHVFLGITGLATDV
TTLNEMFRYKTNLYKLKEERAIEPETFTQLVSSSLYERRFGPYFVGPVVAGINSKSGKPF
IAGFDLIGCIDEAKDFIVSGTASDQLFGMCESLYEPNLEPEDLFETISQALLNAADRDAL
SGWGAVVYIIKKDEVVKRYLKMRQD

Sequence of entity 11 (K), FASTA

>4G4S_11 Proteasome component C11 (chains K)
MDIILGIRVQDSVILASSKAVTRGISVLKDSDDKTRQLSPHTLMSFAGEAGDTVQFAEYI
QANIQLYSIREDYELSPQAVSSFVRQELAKSIRSRRPYQVNVLIGGYDKKKNKPELYQID
YLGTKVELPYGAHGYSGFYTFSLLDHHYRPDMTTEEGLDLLKLCVQELEKRMPMDFKGVI
VKIVDKDGIRQVDDFQAQ

Sequence of entity 12 (L), FASTA

>4G4S_12 Proteasome component PRE2 (chains L)
TTTLAFRFQGGIIVAVDSRATAGNWVASQTVKKVIEINPFLLGTMAGGAADCQFWETWLG
SQCRLHELREKERISVAAASKILSNLVYQYKGAGLSMGTMICGYTRKEGPTIYYVDSDGT
RLKGDIFCVGSGQTFAYGVLDSNYKWDLSVEDALYLGKRSILAAAHRDAYSGGSVNLYHV
TEDGWIYHGNHDVGELFWKVKEEEGSFNNVIG

Ligands and cofactors

ID	Name	Formula	Copies
LDZ	N-[(benzyloxy)carbonyl]-L-leucyl-N-[(2S)-4-methyl-1-oxopentan-2-yl]-L-leucinami…	C26 H41 N3 O5	1
MG	Magnesium ion	Mg	8

Primary citation

Structure of a Proteasome Pba1-Pba2 Complex: IMPLICATIONS FOR PROTEASOME ASSEMBLY, ACTIVATION, AND BIOLOGICAL FUNCTION. Stadtmueller, B.M., Kish-Trier, E., Ferrell, K. et al. J Biol Chem (2012) 287:37371-37382. DOI 10.1074/jbc.M112.367003 · PubMed

Other PDB entries of the same protein (UniProt P21243 (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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