8DAR: Cell division control protein 48

Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex unbound but in the presence of SUMO-ubiquitin(K48polyUb)-mEOS and ATP. Determined by electron microscopy at 3.0 Å resolution. Released 30 Nov 2022.

Method
Electron microscopy
Resolution
3.0 Å
Organism
Saccharomyces cerevisiae
Chains
8
Atoms
30,157
Mol. weight
666.22 kDa
Ligands
ATP, ADP, ZN
Released
30 Nov 2022

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

Secondary structure: helices and β-sheets

8DAR contains 235 α-helices and 129 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: 37 helices, 18 β-strands

ElementResiduesLengthSheet
α-helix97-1026
α-helix213-2153
α-helix221-23515
α-helix239-2435
β-strand251-25441
α-helix261-27212
β-strand275-27841
α-helix281-2844
α-helix292-30413
β-strand309-31461
α-helix316-3194
β-strand32112
α-helix323-3253
α-helix330-34314
β-strand351-35771
α-helix360-3623
β-strand36312
α-helix365-3673
β-strand36913
β-strand37213
β-strand375-37841
α-helix384-39411
β-strand40014
α-helix406-4127
α-helix418-43619
α-helix437-4393
α-helix449-4524
β-strand45714
α-helix459-4679
α-helix473-4753
β-strand48015
α-helix493-4997
α-helix500-5045
α-helix505-5084
α-helix510-5156
α-helix519-5213
β-strand523-52756
α-helix535-54410
β-strand54915
β-strand550-55236
α-helix554-5629
α-helix569-57810
β-strand582-58656
α-helix589-5913
α-helix609-61911
β-strand627-63376
α-helix636-6383
α-helix641-6444
β-strand651-65446
α-helix656-6583
α-helix660-67011
α-helix683-6886
α-helix694-71825
α-helix755-7639
α-helix771-78818
Chain B: 35 helices, 15 β-strands
ElementResiduesLengthSheet
α-helix213-2153
α-helix220-23516
α-helix238-2436
β-strand251-25447
α-helix261-27212
β-strand275-28067
α-helix281-2855
α-helix291-30515
β-strand309-31467
α-helix316-3194
β-strand32118
α-helix323-3253
α-helix330-34314
β-strand351-35777
α-helix360-3623
β-strand36318
α-helix365-3673
β-strand375-37847
α-helix384-39411
β-strand40019
α-helix406-4127
α-helix418-43619
α-helix437-4393
α-helix449-4535
β-strand45719
α-helix459-46810
α-helix473-4753
β-strand480110
α-helix493-4997
α-helix500-5045
α-helix505-5084
α-helix510-5167
α-helix519-5213
β-strand523-527510
α-helix534-54411
β-strand548-552510
α-helix554-5618
α-helix569-57810
β-strand582-586510
α-helix589-5913
α-helix609-61911
β-strand627-633710
α-helix636-6383
α-helix641-6444
β-strand651-654410
α-helix660-67112
α-helix683-6886
α-helix694-71825
α-helix755-7639
α-helix771-78717
Chain C: 36 helices, 15 β-strands
ElementResiduesLengthSheet
α-helix72-743
α-helix208-2103
α-helix213-2153
α-helix220-23516
α-helix238-2436
β-strand250-254511
α-helix261-27212
β-strand275-276211
β-strand279-280211
α-helix281-2855
α-helix292-30514
β-strand309-314611
α-helix316-3183
α-helix323-3264
α-helix329-34416
β-strand351-357711
α-helix360-3623
α-helix365-3673
β-strand376-378311
α-helix384-39411
β-strand400112
α-helix406-4127
α-helix418-43619
α-helix437-4393
α-helix449-4535
β-strand457112
α-helix459-4679
α-helix473-4753
β-strand480113
α-helix493-4997
α-helix500-5045
α-helix505-5084
α-helix510-5167
α-helix519-5213
β-strand523-527514
α-helix534-54411
β-strand549113
β-strand550-552314
α-helix554-5629
α-helix569-57810
β-strand582-586514
α-helix609-62012
β-strand627-633714
α-helix641-6444
β-strand651-654414
α-helix660-67011
α-helix676-6772
α-helix683-6886
α-helix694-71825
α-helix755-7639
α-helix771-78717
Chain D: 37 helices, 15 β-strands
ElementResiduesLengthSheet
α-helix213-2153
α-helix220-23516
α-helix237-2437
α-helix246-2483
β-strand250-254515
α-helix261-27212
β-strand275-280615
α-helix281-2855
α-helix292-30514
β-strand309-314615
α-helix316-3183
β-strand321116
α-helix323-3253
α-helix329-34315
β-strand351-357715
α-helix360-3623
β-strand363116
α-helix365-3673
β-strand375-378415
α-helix384-39411
β-strand400117
α-helix406-4127
α-helix418-43619
α-helix437-4393
α-helix449-4535
β-strand457117
α-helix459-4679
α-helix473-4753
β-strand480118
α-helix493-4997
α-helix500-5045
α-helix505-5084
α-helix510-5167
α-helix519-5213
β-strand523-527518
α-helix534-54411
β-strand548-552518
α-helix554-5629
α-helix569-57810
β-strand582-586518
α-helix589-5913
α-helix609-61911
β-strand627-633718
α-helix636-6383
α-helix641-6444
β-strand651-654418
α-helix656-6583
α-helix660-67011
α-helix683-6886
α-helix694-71825
α-helix755-7639
α-helix771-78818
Chain E: 35 helices, 20 β-strands
ElementResiduesLengthSheet
α-helix213-2153
α-helix220-23516
α-helix237-2437
α-helix246-2483
β-strand250-254519
α-helix261-27212
β-strand275120
β-strand278119
α-helix281-2855
α-helix2881
α-helix291-30515
β-strand309120
β-strand312-313219
α-helix316-3183
β-strand321121
α-helix330-34314
β-strand351120
β-strand353-357519
β-strand363121
α-helix365-3673
β-strand376-378319
α-helix384-39411
β-strand400122
α-helix406-4127
α-helix418-43619
α-helix437-4393
α-helix449-4535
β-strand457122
α-helix459-4679
α-helix473-4753
β-strand480123
α-helix493-4997
α-helix500-5045
α-helix505-5084
α-helix510-5167
α-helix518-5214
β-strand523-527523
α-helix534-54411
β-strand548-552523
α-helix554-5618
α-helix569-57810
β-strand582-586523
α-helix589-5913
α-helix609-62012
β-strand627-633723
α-helix636-6383
α-helix641-6444
β-strand652-654323
α-helix660-67011
β-strand676124
α-helix683-6886
α-helix694-71825
β-strand753124
α-helix755-7639
α-helix771-78616
Chain F: 35 helices, 18 β-strands
ElementResiduesLengthSheet
α-helix213-2153
α-helix220-23516
α-helix238-2436
β-strand250-254525
α-helix261-27212
β-strand275-280625
α-helix281-2855
α-helix2881
α-helix292-30514
β-strand309-314625
α-helix316-3183
β-strand321126
α-helix329-34315
β-strand351-357725
β-strand363126
α-helix365-3673
β-strand375-378425
α-helix384-39411
β-strand400127
α-helix406-4127
α-helix418-43619
α-helix437-4393
α-helix449-4535
β-strand457127
α-helix459-4679
α-helix473-4753
β-strand480128
α-helix493-4997
α-helix500-5045
α-helix505-5084
α-helix510-5167
α-helix518-5214
β-strand524-527429
α-helix534-54411
β-strand549128
β-strand550-552329
α-helix554-5618
α-helix569-57810
β-strand582-586529
α-helix589-5913
α-helix609-61911
β-strand627-633729
α-helix636-6383
α-helix641-6444
β-strand651-654429
α-helix656-6583
α-helix660-67011
β-strand676130
α-helix683-6875
α-helix694-71825
β-strand753130
α-helix755-7628
α-helix771-78616
Chain G: 18 helices, 26 β-strands
ElementResiduesLengthSheet
α-helix117-1248
β-strand129131
α-helix1501
β-strand151131
α-helix1521
α-helix156-1627
α-helix169-17911
β-strand193132
α-helix211-2133
β-strand215-21627
α-helix221-2233
β-strand224-226333
β-strand236-239434
α-helix243-25513
β-strand260-2701134
β-strand276-2851034
β-strand290-291235
β-strand295-297335
α-helix300-31718
β-strand320-327834
β-strand331136
β-strand339136
α-helix352-36312
β-strand368137
β-strand372132
β-strand376137
β-strand382-386534
β-strand396-401634
α-helix403-4097
β-strand415-416238
β-strand417139
β-strand422-424338
β-strand437-442633
β-strand448-452533
β-strand456-458338
α-helix459-4624
β-strand463-465334
β-strand467-469334
α-helix501-5077
α-helix517-5248
α-helix527-53610
α-helix541-55212
α-helix557-5659
α-helix567-57812
Chain H: 2 helices, 2 β-strands
ElementResiduesLengthSheet
α-helix244-2529
β-strand291139
β-strand298-300335
α-helix304-3052

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Cell division control protein 48A, B, C, D, E, Fprotein838Saccharomyces cerevisiaeP25694 (AlphaFold model)
Nuclear protein localization protein 4Gprotein583Saccharomyces cerevisiaeP33755 (AlphaFold model)
Ubiquitin fusion degradation protein 1Hprotein363Saccharomyces cerevisiaeP53044 (AlphaFold model)
Sequence of entity 1 (A, B, C, D, E, F), FASTA
>8DAR_1 Cell division control protein 48 (chains A, B, C, D, E, F)
GSHMGEEHKPLLDASGVDPREEDKTATAILRRKKKDNMLLVDDAINDDNSVIAINSNTMD
KLELFRGDTVLVKGKKRKDTVLIVLIDDELEDGACRINRVVRNNLRIRLGDLVTIHPCPD
IKYATRISVLPIADTIEGITGNLFDVFLKPYFVEAYRPVRKGDHFVVRGGMRQVEFKVVD
VEPEEYAVVAQDTIIHWEGEPINREDEENNMNEVGYDDIGGCRKQMAQIREMVELPLRHP
QLFKAIGIKPPRGVLMYGPPGTGKTLMARAVANETGAFFFLINGPEVMSKMAGESESNLR
KAFEEAEKNAPAIIFIDEIDSIAPKRDKTNGEVERRVVSQLLTLMDGMKARSNVVVIAAT
NRPNSIDPALRRFGRFDREVDIGIPDATGRLEVLRIHTKNMKLADDVDLEALAAETHGYV
GADIASLCSEAAMQQIREKMDLIDLDEDEIDAEVLDSLGVTMDNFRFALGNSNPSALRET
VVESVNVTWDDVGGLDEIKEELKETVEYPVLHPDQYTKFGLSPSKGVLFYGPPGTGKTLL
AKAVATEVSANFISVKGPELLSMWYGESESNIRDIFDKARAAAPTVVFLDELDSIAKARG
GSLGDAGGASDRVVNQLLTEMDGMNAKKNVFVIGATNRPDQIDPAILRPGRLDQLIYVPL
PDENARLSILNAQLRKTPLEPGLELTAIAKATQGFSGADLLYIVQRAAKYAIKDSIEAHR
QHEAEKEVKVEGEDVEMTDEGAKAEQEPEVDPVPYITKEHFAEAMKTAKRSVSDAELRRY
EAYSQQMKASRGQFSNFNFNDAPLGTTATDNANSNNSAPSGAGAAFGSNAEEDDDLYS
Sequence of entity 2 (G), FASTA
>8DAR_2 Nuclear protein localization protein 4 (chains G)
GSHMLIRFRSKNGTHRVSCQENDLFGTVIEKLVGNLDPNADVDTFTVCEKPGQGIHAVSE
LADRTVMDLGLKHGDMLILNYSDKPANEKDGVNVEIGSVGIDSKGIRQHRYGPLRIKELA
VDEELEKEDGLIPRQKSKLCKHGDRGMCEYCSPLPPWDKEYHEKNKIKHISFHSYLKKLN
ENANKKENGSSYISPLSEPDFRINKRCHNGHEPWPRGICSKCQPSAITLQQQEFRMVDHV
EFQKSEIINEFIQAWRYTGMQRFGYMYGSYSKYDNTPLGIKAVVEAIYEPPQHDEQDGLT
MDVEQVKNEMLQIDRQAQEMGLSRIGLIFTDLSDAGAGDGSVFCKRHKDSFFLSSLEVIM
AARHQTRHPNVSKYSEQGFFSSKFVTCVISGNLEGEIDISSYQVSTEAEALVTADMISGS
TFPSMAYINDTTDERYVPEIFYMKSNEYGITVKENAKPAFPVDYLLVTLTHGFPNTDTET
NSKFVSSTGFPWSNRQAMGQSQDYQELKKYLFNVASSGDFNLLHEKISNFHLLLYINSLQ
ILSPDEWKLLIESAVKNEWEESLLKLVSSAGWQTLVMILQESG
Sequence of entity 3 (H), FASTA
>8DAR_3 Ubiquitin fusion degradation protein 1 (chains H)
GSMFSGFSSFGGGNGFVNMPQTFEEFFRCYPIAMMNDRIRKDDANFGGKIFLPPSALSKL
SMLNIRYPMLFKLTANETGRVTHGGVLEFIAEEGRVYLPQWMMETLGIQPGSLLQISSTD
VPLGQFVKLEPQSVDFLDISDPKAVLENVLRNFSTLTVDDVIEISYNGKTFKIKILEVKP
ESSSKSICVIETDLVTDFAPPVGYVEPDYKALKAQQDKEKKNSFGKGQVLDPSVLGQGSM
STRIDYAGIANSSRNKLSKFVGQGQNISGKAPKAEPKQDIKDMKITFDGEPAKLDLPEGQ
LFFGFPMVLPKEDEESAAGSKSSEQNFQGQGISLRKSNKRKTKSDHDSSKSKAPKSPEVI
EID

Ligands and cofactors

IDNameFormulaCopies
ATPAdenosine-5'-triphosphateC10 H16 N5 O13 P36
ADPAdenosine-5'-diphosphateC10 H15 N5 O10 P26
ZNZinc ionZn2

Primary citation

SUMO enhances unfolding of SUMO-polyubiquitin-modified substrates by the Ufd1/Npl4/Cdc48 complex. Lee, H.G., Lemmon, A.A., Lima, C.D. Proc Natl Acad Sci U S A (2023) 120:e2213703120-e2213703120. DOI 10.1073/pnas.2213703120 · PubMed

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

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