9OFV: Cell division control protein 48

Consensus reconstruction of the eukaryotic Ribosome-associated Quality Control complex. Determined by electron microscopy at 3.16 Å resolution. Released 11 Jun 2025.

Method: Electron microscopy
Resolution: 3.16 Å
Organism: Saccharomyces cerevisiae
Chains: 64
Atoms: 183,852
Mol. weight: 3104.23 kDa
Ligands: ATP, ADP, ZN, MG
Released: 11 Jun 2025

Explore 9OFV in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9OFV contains 695 α-helices and 514 β-strands across 58 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 0: 6 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	4-21	18
β-strand	24-29	6	33
α-helix	35-44	10
β-strand	49-53	5	33
α-helix	56-65	10
α-helix	71-75	5
α-helix	76-79	4
β-strand	85-89	5	33
α-helix	94-102	9
β-strand	186-192	7	33
β-strand	195-197	3	33

Chain 2: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	63
β-strand	11	1	53
β-strand	12-16	5	63
β-strand	22	1	64
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	63
β-strand	48-49	2	63
α-helix	50-51	2
β-strand	55	1	64
α-helix	57-59	3
β-strand	66-71	6	63
α-helix	72-73	2

Chain 3: 8 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	11-13	3
β-strand	14-22	9	65
α-helix	26-36	11
β-strand	40	1	65
α-helix	41-52	12
β-strand	58-59	2	66
α-helix	67-68	2
β-strand	69	1	67
α-helix	71-73	3
β-strand	80	1	67
β-strand	81-82	2	66
α-helix	85-105	21
β-strand	112-121	10	65
α-helix	122-124	3
β-strand	125-131	7	68
β-strand	135-141	7	68
β-strand	144-152	9	65
α-helix	170-182	13

Chain 4: 8 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	24-39	16
α-helix	43-52	10
β-strand	62-63	2	73
α-helix	64-71	8
α-helix	79	1
β-strand	80-88	9	73
β-strand	100-106	7	73
α-helix	108-116	9
β-strand	120-122	3	73
α-helix	124-130	7
β-strand	137-139	3	73
α-helix	144-146	3
α-helix	149-151	3
β-strand	177-178	2	74
β-strand	185	1	74

Chain 5: 12 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	5-15	11
α-helix	19-21	3
β-strand	22-24	3	76
α-helix	26-28	3
α-helix	29-34	6
α-helix	38-46	9
β-strand	50-52	3	76
α-helix	53-57	5
α-helix	61-72	12
α-helix	78-80	3
α-helix	85-88	4
α-helix	91-112	22
α-helix	117-128	12
α-helix	135-156	22

Chain 6: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	5-13	9	83
α-helix	14-15	2
β-strand	25-31	7	83
α-helix	34-48	15
β-strand	56-63	8	83
β-strand	73-82	10	84
β-strand	87-96	10	84
α-helix	99-113	15
β-strand	121-128	8	84
α-helix	138-141	4
α-helix	142-144	3
β-strand	150	1	85
α-helix	157-159	3
β-strand	164	1	86

Chain 7: 9 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	25-26	2
α-helix	28-31	4
β-strand	39-42	4	92
α-helix	52-54	3
α-helix	55-57	3
β-strand	61-67	7	92
β-strand	71-80	10	92
β-strand	83-92	10	92
α-helix	93-95	3
β-strand	96-98	3	92
α-helix	100-119	20
α-helix	134-136	3
β-strand	139-141	3	93
α-helix	147-148	2
β-strand	149-150	2	83
α-helix	153-156	4

Chain 8: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	13-18	6	98
α-helix	20-23	4
α-helix	30-40	11
β-strand	42-43	2	99
β-strand	46-47	2	99
β-strand	54-58	5	98
β-strand	62-67	6	98
α-helix	73-86	14
β-strand	94-97	4	98
β-strand	102-106	5	98

50 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
Cell division control protein 48	A, B, C, D, E, F	protein	835	Saccharomyces cerevisiae	P25694 (AlphaFold model)
Ubiquitin	H, J, K	protein	76	Saccharomyces cerevisiae	P0CG63 (AlphaFold model)
Nuclear protein localization protein 4	G	protein	580	Saccharomyces cerevisiae	P33755 (AlphaFold model)
60S ribosomal protein L17-A	3	protein	184	Saccharomyces cerevisiae	P05740 (AlphaFold model)
60S ribosomal protein L18-A	4	protein	186	Saccharomyces cerevisiae	P0CX49
60S ribosomal protein L19-A	5	protein	189	Saccharomyces cerevisiae	P0CX82
60S ribosomal protein L20-A	6	protein	172	Saccharomyces cerevisiae	P0CX23
60S ribosomal protein L21-A	7	protein	160	Saccharomyces cerevisiae	Q02753
60S ribosomal protein L22-A	8	protein	121	Saccharomyces cerevisiae	P05749
60S ribosomal protein L23-A	I	protein	137	Saccharomyces cerevisiae	P0CX41
Large ribosomal subunit protein eL24A	9	protein	155	Saccharomyces cerevisiae	P04449
60S ribosomal protein L26-A	L	protein	127	Saccharomyces cerevisiae	P05743

44 more molecules are not listed.

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

>9OFV_1 Cell division control protein 48 (chains A, B, C, D, E, F)
MGEEHKPLLDASGVDPREEDKTATAILRRKKKDNMLLVDDAINDDNSVIAINSNTMDKLE
LFRGDTVLVKGKKRKDTVLIVLIDDELEDGACRINRVVRNNLRIRLGDLVTIHPCPDIKY
ATRISVLPIADTIEGITGNLFDVFLKPYFVEAYRPVRKGDHFVVRGGMRQVEFKVVDVEP
EEYAVVAQDTIIHWEGEPINREDEENNMNEVGYDDIGGCRKQMAQIREMVELPLRHPQLF
KAIGIKPPRGVLMYGPPGTGKTLMARAVANETGAFFFLINGPEVMSKMAGESESNLRKAF
EEAEKNAPAIIFIDEIDSIAPKRDKTNGEVERRVVSQLLTLMDGMKARSNVVVIAATNRP
NSIDPALRRFGRFDREVDIGIPDATGRLEVLRIHTKNMKLADDVDLEALAAETHGYVGAD
IASLCSEAAMQQIREKMDLIDLDEDEIDAEVLDSLGVTMDNFRFALGNSNPSALRETVVE
SVNVTWDDVGGLDEIKEELKETVEYPVLHPDQYTKFGLSPSKGVLFYGPPGTGKTLLAKA
VATEVSANFISVKGPELLSMWYGESESNIRDIFDKARAAAPTVVFLDQLDSIAKARGGSL
GDAGGASDRVVNQLLTEMDGMNAKKNVFVIGATNRPDQIDPAILRPGRLDQLIYVPLPDE
NARLSILNAQLRKTPLEPGLELTAIAKATQGFSGADLLYIVQRAAKYAIKDSIEAHRQHE
AEKEVKVEGEDVEMTDEGAKAEQEPEVDPVPYITKEHFAEAMKTAKRSVSDAELRRYEAY
SQQMKASRGQFSNFNFNDAPLGTTATDNANSNNSAPSGAGAAFGSNAEEDDDLYS

Sequence of entity 2 (H, J, K), FASTA

>9OFV_2 Ubiquitin (chains H, J, K)
MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Sequence of entity 3 (G), FASTA

>9OFV_3 Nuclear protein localization protein 4 (chains G)
MLIRFRSKNGTHRVSCQENDLFGTVIEKLVGNLDPNADVDTFTVCEKPGQGIHAVSELAD
RTVMDLGLKHGDMLILNYSDKPANEKDGVNVEIGSVGIDSKGIRQHRYGPLRIKELAVDE
ELEKEDGLIPRQKSKLCKHGDRGMCEYCSPLPPWDKEYHEKNKIKHISFHSYLKKLNENA
NKKENGSSYISPLSEPDFRINKRCHNGHEPWPRGICSKCQPSAITLQQQEFRMVDHVEFQ
KSEIINEFIQAWRYTGMQRFGYMYGSYSKYDNTPLGIKAVVEAIYEPPQHDEQDGLTMDV
EQVKNEMLQIDRQAQEMGLSRIGLIFTDLSDAGAGDGSVFCKRHKDSFFLSSLEVIMAAR
HQTRHPNVSKYSEQGFFSSKFVTCVISGNLEGEIDISSYQVSTEAEALVTADMISGSTFP
SMAYINDTTDERYVPEIFYMKSNEYGITVKENAKPAFPVDYLLVTLTHGFPNTDTETNSK
FVSSTGFPWSNRQAMGQSQDYQELKKYLFNVASSGDFNLLHEKISNFHLLLYINSLQILS
PDEWKLLIESAVKNEWEESLLKLVSSAGWQTLVMILQESG

Sequence of entity 4 (3), FASTA

>9OFV_4 60S ribosomal protein L17-A (chains 3)
MARYGATSTNPAKSASARGSYLRVSFKNTRETAQAINGWELTKAQKYLEQVLDHQRAIPF
RRFNSSIGRTAQGKEFGVTKARWPAKSVKFVQGLLQNAAANAEAKGLDATKLYVSHIQVN
QAPKQRRRTYRAHGRINKYESSPSHIELVVTEKEEAVAKAAEKKVVRLTSRQRGRIAAQK
RIAA

Sequence of entity 5 (4), FASTA

>9OFV_5 60S ribosomal protein L18-A (chains 4)
MGIDHTSKQHKRSGHRTAPKSDNVYLKLLVKLYTFLARRTDAPFNKVVLKALFLSKINRP
PVSVSRIARALKQEGAANKTVVVVGTVTDDARIFEFPKTTVAALRFTAGARAKIVKAGGE
CITLDQLAVRAPKGQNTLILRGPRNSREAVRHFGMGPHKGKAPRILSTGRKFERARGRRR
SKGFKV

Sequence of entity 6 (5), FASTA

>9OFV_6 60S ribosomal protein L19-A (chains 5)
MANLRTQKRLAASVVGVGKRKVWLDPNETSEIAQANSRNAIRKLVKNGTIVKKAVTVHSK
SRTRAHAQSKREGRHSGYGKRKGTREARLPSQVVWIRRLRVLRRLLAKYRDAGKIDKHLY
HVLYKESKGNAFKHKRALVEHIIQAKADAQREKALNEEAEARRLKNRAARDRRAQRVAEK
RDALLKEDA

Sequence of entity 7 (6), FASTA

>9OFV_7 60S ribosomal protein L20-A (chains 6)
MAHFKEYQVIGRRLPTESVPEPKLFRMRIFASNEVIAKSRYWYFLQKLHKVKKASGEIVS
INQINEAHPTKVKNFGVWVRYDSRSGTHNMYKEIRDVSRVAAVETLYQDMAARHRARFRS
IHILKVAEIEKTADVKRQYVKQFLTKDLKFPLPHRVQKSTKTFSYKRPSTFY

Sequence of entity 8 (7), FASTA

>9OFV_8 60S ribosomal protein L21-A (chains 7)
MGKSHGYRSRTRYMFQRDFRKHGAVHLSTYLKVYKVGDIVDIKANGSIQKGMPHKFYQGK
TGVVYNVTKSSVGVIINKMVGNRYLEKRLNLRVEHIKHSKCRQEFLERVKANAAKRAEAK
AQGVAVQLKRQPAQPRESRIVSTEGNVPQTLAPVPYETFI

Sequence of entity 9 (8), FASTA

>9OFV_9 60S ribosomal protein L22-A (chains 8)
MAPNTSRKQKIAKTFTVDVSSPTENGVFDPASYAKYLIDHIKVEGAVGNLGNAVTVTEDG
TVVTVVSTAKFSGKYLKYLTKKYLKKNQLRDWIRFVSTKTNEYRLAFYQVTPEEDEEEDE
E

Sequence of entity 10 (I), FASTA

>9OFV_10 60S ribosomal protein L23-A (chains I)
MSGNGAQGTKFRISLGLPVGAIMNCADNSGARNLYIIAVKGSGSRLNRLPAASLGDMVMA
TVKKGKPELRKKVMPAIVVRQAKSWRRRDGVFLYFEDNAGVIANPKGEMKGSAITGPVGK
ECADLWPRVASNSGVVV

Sequence of entity 11 (9), FASTA

>9OFV_11 Large ribosomal subunit protein eL24A (chains 9)
MKVEIDSFSGAKIYPGRGTLFVRGDSKIFRFQNSKSASLFKQRKNPRRIAWTVLFRKHHK
KGITEEVAKKRSRKTVKAQRPITGASLDLIKERRSLKPEVRKANREEKLKANKEKKKAEK
AARKAEKAKSAGTQSSKFSKQQAKGAFQKVAATSR

Sequence of entity 12 (L), FASTA

>9OFV_12 60S ribosomal protein L26-A (chains L)
MAKQSLDVSSDRRKARKAYFTAPSSQRRVLLSAPLSKELRAQYGIKALPIRRDDEVLVVR
GSKKGQEGKISSVYRLKFAVQVDKVTKEKVNGASVPINLHPSKLVITKLHLDKDRKALIQ
RKGGKLE

Ligands and cofactors

ID	Name	Formula	Copies
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	9
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	1
ZN	Zinc ion	Zn	7
MG	Magnesium ion	Mg	12
SPD	Spermidine	C7 H19 N3	1

Primary citation

Mechanism of nascent chain removal by the ribosome-associated quality control complex. Li, W., Scheel, T., Shen, P.S. Nat Commun (2025) 16:5792-5792. DOI 10.1038/s41467-025-61235-w · 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…
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,…
8DAW 3.6 Å, Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex bound to three ubiquitin moieties and…

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