6OPC: Cell division control protein 48

Cdc48 Hexamer in a complex with substrate and Shp1(Ubx Domain). Determined by electron microscopy at 3.7 Å resolution. Released 10 Jul 2019.

Method: Electron microscopy
Resolution: 3.7 Å
Organism: Saccharomyces cerevisiae
Chains: 8
Atoms: 30,015
Mol. weight: 606.57 kDa
Ligands: MG, BEF, ADP
Released: 10 Jul 2019

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

Secondary structure: helices and β-sheets

6OPC contains 203 α-helices and 177 β-strands across 8 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: 33 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	35-39	5	1
β-strand	49-51	3	1
α-helix	53-56	4
β-strand	66-70	5	1
β-strand	76-83	8	1
β-strand	91-94	4	1
α-helix	96-101	6
β-strand	109-114	6	1
β-strand	120	1	2
β-strand	123-128	6	3
β-strand	129	1	4
α-helix	130-132	3
α-helix	140	1
α-helix	141-145	5
α-helix	146-149	4
β-strand	155-157	3	2
β-strand	161-165	5	3
β-strand	170-178	9	3
β-strand	183-185	3	2
β-strand	191-194	4	3
β-strand	199	1	4
α-helix	201-209	9
α-helix	220-235	16
α-helix	238-243	6
α-helix	246-248	3
β-strand	251-254	4	5
α-helix	261-270	10
β-strand	276-280	5	5
α-helix	292-305	14
β-strand	310-314	5	5
α-helix	330-343	14
β-strand	352-356	5	5
β-strand	375-378	4	5
α-helix	384-394	11
α-helix	395-397	3
α-helix	406-412	7
α-helix	420-435	16
α-helix	459-467	9
α-helix	478-481	4
α-helix	493-508	16
α-helix	511-516	6
α-helix	519-521	3
β-strand	523-527	5	6
α-helix	534-543	10
β-strand	550-552	3	6
α-helix	555-557	3
β-strand	561	1	7
α-helix	564-578	15
β-strand	583-587	5	6
β-strand	594	1	8
α-helix	606-618	13
β-strand	628-632	5	6
α-helix	636-638	3
β-strand	639	1	8
β-strand	653-654	2	6
α-helix	660-670	11
β-strand	676	1	9
α-helix	683-688	6
α-helix	694-724	31
β-strand	753	1	9
α-helix	755-761	7
α-helix	762-764	3
α-helix	771-783	13

Chain B: 33 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	35-39	5	10
β-strand	49-51	3	10
α-helix	53-56	4
β-strand	66-70	5	10
β-strand	76-83	8	10
β-strand	91-94	4	10
α-helix	96-101	6
β-strand	109-114	6	10
β-strand	120	1	11
β-strand	123-128	6	12
α-helix	130-132	3
α-helix	140	1
α-helix	141-145	5
α-helix	146-149	4
β-strand	155-157	3	11
β-strand	161-165	5	12
β-strand	170-178	9	12
β-strand	183-185	3	11
β-strand	191-194	4	12
α-helix	202-208	7
α-helix	220-235	16
α-helix	238-243	6
α-helix	246-248	3
β-strand	251-254	4	13
α-helix	261-271	11
β-strand	276-279	4	13
α-helix	282-284	3
α-helix	292-305	14
β-strand	310-314	5	13
α-helix	316-318	3
α-helix	330-342	13
β-strand	352-357	6	13
β-strand	375-378	4	13
α-helix	384-394	11
α-helix	406-412	7
α-helix	419-435	17
α-helix	449-452	4
α-helix	459-467	9
α-helix	478-480	3
α-helix	493-504	12
α-helix	510-515	6
α-helix	519-521	3
β-strand	524-527	4	14
α-helix	534-544	11
β-strand	548-552	5	14
α-helix	555-557	3
β-strand	561	1	15
α-helix	564-578	15
β-strand	582-587	6	14
α-helix	607-618	12
β-strand	627-633	7	14
β-strand	651-654	4	14
α-helix	660-670	11
β-strand	676	1	16
α-helix	683-688	6
α-helix	694-721	28
β-strand	753	1	16
α-helix	755-761	7
α-helix	771-786	16

Chain C: 34 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	35-39	5	17
β-strand	49-51	3	17
α-helix	53-56	4
β-strand	66-70	5	17
β-strand	76-83	8	17
β-strand	91-94	4	17
α-helix	96-101	6
β-strand	109-114	6	17
β-strand	120	1	18
β-strand	123-128	6	19
β-strand	129	1	20
α-helix	130-132	3
α-helix	140	1
α-helix	141-145	5
α-helix	146-149	4
β-strand	155-157	3	18
β-strand	161-165	5	19
β-strand	170-178	9	19
β-strand	183-185	3	18
β-strand	191-194	4	19
β-strand	199	1	20
α-helix	202-209	8
α-helix	213-215	3
α-helix	220-235	16
α-helix	238-243	6
α-helix	245-248	4
β-strand	250-253	4	21
β-strand	254	1	22
α-helix	261-271	11
β-strand	275-279	5	21
α-helix	281-283	3
α-helix	292-306	15
β-strand	309-314	6	21
α-helix	330-342	13
β-strand	352-356	5	21
β-strand	375	1	21
β-strand	378	1	22
α-helix	384-394	11
α-helix	407-412	6
α-helix	420-439	20
α-helix	459-467	9
α-helix	478-480	3
α-helix	486-488	3
α-helix	493-508	16
α-helix	510-516	7
α-helix	519-521	3
β-strand	524-527	4	23
α-helix	534-544	11
β-strand	548-552	5	23
β-strand	561	1	24
α-helix	564-578	15
β-strand	582-587	6	23
α-helix	589-592	4
α-helix	607-618	12
β-strand	627-633	7	23
α-helix	636-638	3
β-strand	651-654	4	23
α-helix	660-670	11
β-strand	676	1	25
α-helix	683-689	7
α-helix	694-721	28
β-strand	753	1	25
α-helix	755-761	7
α-helix	773-786	14

Chain D: 36 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	35-39	5	26
β-strand	49-51	3	26
α-helix	53-56	4
β-strand	66-70	5	26
β-strand	76-83	8	26
β-strand	91-94	4	26
α-helix	96-101	6
β-strand	109-114	6	26
β-strand	120	1	27
β-strand	123-128	6	28
β-strand	129	1	29
α-helix	130-132	3
α-helix	140	1
α-helix	141-145	5
α-helix	146-149	4
β-strand	155-157	3	27
β-strand	161-165	5	28
β-strand	170-178	9	28
β-strand	183-185	3	27
β-strand	191-194	4	28
β-strand	199	1	29
α-helix	202-209	8
α-helix	213-215	3
α-helix	220-235	16
α-helix	238-243	6
α-helix	246-248	3
β-strand	250-253	4	30
β-strand	254	1	31
α-helix	261-271	11
β-strand	275-279	5	30
β-strand	288	1	32
α-helix	292-305	14
β-strand	309-314	6	30
α-helix	316-318	3
α-helix	329-342	14
β-strand	352-356	5	30
β-strand	375	1	30
β-strand	378	1	31
α-helix	384-394	11
α-helix	407-412	6
α-helix	419-435	17
α-helix	449-452	4
α-helix	459-467	9
α-helix	478-480	3
α-helix	486-488	3
α-helix	493-504	12
α-helix	510-516	7
α-helix	519-521	3
β-strand	524-527	4	33
α-helix	534-544	11
β-strand	548-552	5	33
α-helix	555-557	3
β-strand	561	1	34
α-helix	564-578	15
β-strand	582-587	6	33
α-helix	589-592	4
α-helix	602-618	17
β-strand	627-633	7	33
α-helix	636-638	3
β-strand	651-654	4	33
α-helix	660-670	11
β-strand	676	1	35
α-helix	683-687	5
α-helix	694-721	28
β-strand	753	1	35
α-helix	755-762	8
α-helix	773-786	14

Chain E: 31 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	35-39	5	36
β-strand	49-51	3	36
α-helix	53-56	4
β-strand	66-70	5	36
β-strand	76-83	8	36
β-strand	91-94	4	36
α-helix	96-101	6
β-strand	109-114	6	36
β-strand	120	1	37
β-strand	123-128	6	38
α-helix	130-132	3
α-helix	140	1
α-helix	141-145	5
α-helix	146-149	4
β-strand	155-157	3	37
β-strand	161-165	5	38
β-strand	170-178	9	38
β-strand	183-185	3	37
β-strand	191-194	4	38
α-helix	202-208	7
α-helix	213-215	3
α-helix	220-235	16
α-helix	238-243	6
α-helix	246-248	3
β-strand	250-254	5	39
α-helix	261-271	11
β-strand	276-279	4	39
α-helix	281-284	4
α-helix	292-305	14
β-strand	310-314	5	39
α-helix	329-342	14
β-strand	352-357	6	39
β-strand	375-378	4	39
α-helix	384-394	11
α-helix	406-412	7
α-helix	419-435	17
α-helix	459-467	9
α-helix	493-508	16
α-helix	510-516	7
β-strand	524-527	4	40
α-helix	534-542	9
β-strand	548-552	5	40
α-helix	564-577	14
β-strand	582-587	6	40
α-helix	589-592	4
α-helix	602-618	17
β-strand	628-632	5	40
α-helix	636-638	3
β-strand	651-654	4	40
α-helix	660-670	11
α-helix	682-687	6
α-helix	694-712	19
α-helix	755-761	7
α-helix	772-787	16

Chain F: 33 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	35-39	5	41
β-strand	49-51	3	41
α-helix	53-56	4
β-strand	66-70	5	41
β-strand	76-83	8	41
β-strand	91-94	4	41
α-helix	96-101	6
β-strand	109-114	6	41
β-strand	120	1	42
β-strand	123-128	6	43
α-helix	130-132	3
α-helix	140	1
α-helix	141-145	5
α-helix	146-149	4
β-strand	155-157	3	42
β-strand	161-165	5	43
β-strand	170-178	9	43
β-strand	183-185	3	42
β-strand	191-194	4	43
α-helix	220-235	16
α-helix	237-243	7
β-strand	250-254	5	44
α-helix	261-271	11
β-strand	276-280	5	44
α-helix	282-284	3
α-helix	292-306	15
β-strand	310-314	5	44
α-helix	316-319	4
α-helix	330-343	14
β-strand	352-356	5	44
β-strand	375-378	4	44
α-helix	384-394	11
α-helix	395-397	3
α-helix	406-412	7
α-helix	420-435	16
α-helix	450-453	4
α-helix	459-467	9
α-helix	486-488	3
α-helix	493-507	15
α-helix	511-515	5
β-strand	524-527	4	45
α-helix	534-543	10
β-strand	550-552	3	45
α-helix	555-557	3
α-helix	564-578	15
β-strand	582-587	6	45
α-helix	589-593	5
α-helix	602-618	17
β-strand	627-633	7	45
β-strand	653-654	2	45
α-helix	660-670	11
β-strand	676	1	46
α-helix	683-688	6
α-helix	694-724	31
β-strand	753	1	46
α-helix	755-761	7
α-helix	762-764	3
α-helix	771-783	13

Chain G: 0 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	7	1	32
β-strand	13	1	7
β-strand	15	1	15
β-strand	17	1	24
β-strand	19	1	34

Chain Z: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	325-336	12
α-helix	343-346	4
β-strand	351-355	5	47
β-strand	360-364	5	47
β-strand	370	1	48
α-helix	371-381	11
β-strand	391-394	4	47
β-strand	399-401	3	47
β-strand	407	1	48
β-strand	417-421	5	47

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cell division control protein 48	A, B, C, D, E, F	protein	835	Saccharomyces cerevisiae	P25694 (AlphaFold model)
Substrate bound to the central pore of the Cdc48 hexamer	G	protein	22	Saccharomyces cerevisiae
UBX domain-containing protein 1	Z	protein	423	Saccharomyces cerevisiae	P34223 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F), FASTA

>6OPC_1 Cell division control protein 48 (chains A, B, C, D, E, F)
MGEEHKPLLDASGVDPREEDKTATAILRRKKKDNMLLVDDAINDDNSVIAINSNTMDKLE
LFRGDTVLVKGKKRKDTVLIVLIDDELEDGACRINRVVRNNLRIRLGDLVTIHPCPDIKY
ATRISVLPIADTIEGITGNLFDVFLKPYFVEAYRPVRKGDHFVVRGGMRQVEFKVVDVEP
EEYAVVAQDTIIHWEGEPINREDEENNMNEVGYDDIGGCRKQMAQIREMVELPLRHPQLF
KAIGIKPPRGVLMYGPPGTGKTLMARAVANETGAFFFLINGPEVMSKMAGESESNLRKAF
EEAEKNAPAIIFIDEIDSIAPKRDKTNGEVERRVVSQLLTLMDGMKARSNVVVIAATNRP
NSIDPALRRFGRFDREVDIGIPDATGRLEVLRIHTKNMKLADDVDLEALAAETHGYVGAD
IASLCSEAAMQQIREKMDLIDLDEDEIDAEVLDSLGVTMDNFRFALGNSNPSALRETVVE
SVNVTWDDVGGLDEIKEELKETVEYPVLHPDQYTKFGLSPSKGVLFYGPPGTGKTLLAKA
VATEVSANFISVKGPELLSMWYGESESNIRDIFDKARAAAPTVVFLDELDSIAKARGGSL
GDAGGASDRVVNQLLTEMDGMNAKKNVFVIGATNRPDQIDPAILRPGRLDQLIYVPLPDE
NARLSILNAQLRKTPLEPGLELTAIAKATQGFSGADLLYIVQRAAKYAIKDSIEAHRQHE
AEKEVKVEGEDVEMTDEGAKAEQEPEVDPVPYITKEHFAEAMKTAKRSVSDAELRRYEAY
SQQMKASRGQFSNFNFNDAPLGTTATDNANSNNSAPSGAGAAFGSNAEEDDDLYS

Sequence of entity 2 (G), FASTA

>6OPC_2 Substrate bound to the central pore of the Cdc48 hexamer (chains G)
XXXXXXXXXXXXXXXXXXXXXX

Sequence of entity 3 (Z), FASTA

>6OPC_3 UBX domain-containing protein 1 (chains Z)
MAEIPDETIQQFMALTNVSHNIAVQYLSEFGDLNEALNSYYASQTDDQKDRREEAHWNRQ
QEKALKQEAFSTNSSNKAINTEHVGGLCPKPGSSQGSNEYLKRKGSTSPEPTKGSSRSGS
GNNSRFMSFSDMVRGQADDDDEDQPRNTFAGGETSGLEVTDPSDPNSLLKDLLEKARRGG
QMGAENGFRDDEDHEMGANRFTGRGFRLGSTIDAADEVVEDNTSQSQRRPEKVTREITFW
KEGFQVADGPLYRYDDPANSFYLSELNQGRAPLKLLDVQFGQEVEVNVYKKLDESYKAPT
RKLGGFSGQGQRLGSPIPGESSPAEVPKNETPAAQEQPMPDNEPKQGDTSIQIRYANGKR
EVLHCNSTDTVKFLYEHVTSNANTDPSRNFTLNYAFPIKPISNDETTLKDADLLNSVVVQ
RWA

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	8
BEF	Beryllium trifluoride ion	Be F3	8
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	10

Primary citation

Structure of the Cdc48 segregase in the act of unfolding an authentic substrate. Cooney, I., Han, H., Stewart, M.G. et al. Science (2019) 365:502-505. DOI 10.1126/science.aax0486 · PubMed

Other PDB entries of the same protein (UniProt P25694 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8UB4 2.9 Å, Cdc48-Shp1 unfolding native substrate, consensus structure
8DAR 3.0 Å, Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex unbound but in the presence of…
9OFV 3.16 Å, Consensus reconstruction of the eukaryotic Ribosome-associated Quality Control complex
8U9P 3.2 Å, Cdc48-Shp1 unfolding native substrate, Class 2
8U7T 3.3 Å, Substrate-bound Cdc48, Class 1
8UA1 3.4 Å, Cdc48-Shp1 unfolding native substrate, Class 9
8UAA 3.4 Å, Cdc48-Shp1 unfolding native substrate, Class 3
8DAS 3.5 Å, Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex bound to two ubiquitin moieties in…
8DAV 3.5 Å, Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex bound to two ubiquitin moieties and one…
8U8I 3.5 Å, Cdc48-Shp1 unfolding native substrate, Class 4
8UA0 3.5 Å, Cdc48-Shp1 unfolding native substrate, Class 8
6OAB 3.6 Å, Cdc48-Npl4 complex processing poly-ubiquitinated substrate in the presence of ADP-BeFx,…

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