8CDJ: Cullin-1

Name: PDB 8CDJ: CAND1 b-hairpin++-SCF-SKP2 CAND1 rolling SCF engaged
Published: 2023-04-19
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

CAND1 b-hairpin++-SCF-SKP2 CAND1 rolling SCF engaged. Determined by electron microscopy at 3.4 Å resolution. Released 19 Apr 2023.

Method: Electron microscopy
Resolution: 3.4 Å
Organism: Homo sapiens
Chains: 5
Atoms: 13,623
Mol. weight: 306 kDa
Released: 19 Apr 2023

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

Secondary structure: helices and β-sheets

8CDJ contains 114 α-helices and 33 β-strands across 5 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 C: 38 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	18-32	15
α-helix	39-53	15
α-helix	88-107	20
α-helix	112-136	25
α-helix	138-150	13
α-helix	159-167	9
α-helix	168-172	5
α-helix	173-191	19
α-helix	198-210	13
α-helix	226-228	3
α-helix	229-233	5
α-helix	234-254	21
α-helix	257-278	22
α-helix	284-295	12
α-helix	297-299	3
α-helix	300-312	13
α-helix	316-328	13
α-helix	334-355	22
α-helix	358-361	4
α-helix	363-383	21
α-helix	389-404	16
α-helix	407-412	6
α-helix	417-429	13
β-strand	435	1	1
α-helix	436-438	3
α-helix	439-454	16
α-helix	459-476	18
α-helix	482-495	14
α-helix	498-524	27
β-strand	536-541	6	2
α-helix	557-559	3
α-helix	560-573	14
β-strand	578-588	11	2
β-strand	589	1	3
β-strand	600-602	3	3
α-helix	605-613	9
β-strand	620-621	2	4
α-helix	622-629	8
α-helix	633-645	13
β-strand	650	1	5
β-strand	668-669	2	4
β-strand	670	1	5
β-strand	681-683	3	3
α-helix	686-688	3
α-helix	691-721	31
β-strand	724-726	3	6
α-helix	727-737	11
α-helix	746-758	13
β-strand	762-763	2	6
α-helix	764-765	2
β-strand	771-774	4	6

Chain D: 54 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	6-14	9
α-helix	20-33	14
α-helix	45-55	11
α-helix	56-58	3
α-helix	62-70	9
α-helix	72-77	6
α-helix	81-95	15
α-helix	100-115	16
α-helix	128-143	16
α-helix	148-163	16
α-helix	167-172	6
α-helix	173-180	8
α-helix	181-185	5
α-helix	189-204	16
α-helix	208-223	16
α-helix	228-245	18
α-helix	247-252	6
α-helix	253-264	12
α-helix	269-285	17
α-helix	287-290	4
α-helix	291-293	3
α-helix	294-304	11
β-strand	344	1	1
α-helix	346-361	16
α-helix	368-370	3
α-helix	371-375	5
α-helix	376-381	6
α-helix	382-384	3
α-helix	388-405	18
α-helix	424-442	19
α-helix	448-464	17
α-helix	473-484	12
α-helix	491-506	16
α-helix	517-528	12
α-helix	533-550	18
α-helix	562-576	15
α-helix	583-599	17
α-helix	605-607	3
α-helix	608-618	11
α-helix	625-635	11
α-helix	645-657	13
α-helix	664-680	17
α-helix	687-700	14
α-helix	706-722	17
α-helix	724-730	7
α-helix	733-742	10
α-helix	750-765	16
β-strand	767	1	7
β-strand	770	1	7
α-helix	772-785	14
α-helix	793-809	17
α-helix	814-822	9
α-helix	834-845	12
α-helix	857-865	9
α-helix	870-884	15
α-helix	892-901	10
α-helix	907-918	12

Chain F: 14 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	102-109	8
α-helix	114-120	7
α-helix	125-131	7
β-strand	139-141	3	8
α-helix	149-157	9
β-strand	162-164	3	8
β-strand	169	1	9
α-helix	179-181	3
β-strand	185-187	3	8
β-strand	192	1	9
α-helix	195-202	8
β-strand	210-212	3	8
α-helix	220-226	7
β-strand	234	1	8
α-helix	245-254	10
β-strand	260-262	3	8
α-helix	271-279	9
β-strand	287-289	3	8
α-helix	299-308	10
β-strand	314-316	3	8
α-helix	325-333	9
β-strand	339-341	3	8
α-helix	350-358	9
β-strand	364-366	3	8
α-helix	372	1
α-helix	375-382	8
β-strand	387-388	2	8

Chain R: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	27-34	8	2

Chain S: 8 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	10
β-strand	13-17	5	10
α-helix	21-23	3
α-helix	25-32	8
β-strand	45-46	2	10
α-helix	52-64	13
α-helix	87-93	7
α-helix	97-110	14
α-helix	113-127	15
α-helix	132-138	7
α-helix	147-156	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cullin-1	C	protein	776	Homo sapiens	Q13616 (AlphaFold model)
E3 ubiquitin-protein ligase RBX1, N-terminally processed	R	protein	106	Homo sapiens	P62877 (AlphaFold model)
Cullin-associated NEDD8-dissociated protein 1	D	protein	1238	Homo sapiens	Q86VP6 (AlphaFold model)
S-phase kinase-associated protein 2	F	protein	426	Homo sapiens	Q13309 (AlphaFold model)
S-phase kinase-associated protein 1	S	protein	163	Homo sapiens	P63208

Sequence of entity 1 (C), FASTA

>8CDJ_1 Cullin-1 (chains C)
MSSTRSQNPHGLKQIGLDQIWDDLRAGIQQVYTRQSMAKSRYMELYTHVYNYCTSVHQSN
QARGAGVPPSKSKKGQTPGGAQFVGLELYKRLKEFLKNYLTNLLKDGEDLMDESVLKFYT
QQWEDYRFSSKVLNGICAYLNRHWVRRECDEGRKGIYEIYSLALVTWRDCLFRPLNKQVT
NAVLKLIEKERNGETINTRLISGVVQSYVELGLNEDDAFAKGPTLTVYKESFESQFLADT
ERFYTRESTEFLQQNPVTEYMKKAEARLLEEQRRVQVYLHESTQDELARKCEQVLIEKHL
EIFHTEFQNLLDADKNEDLGRMYNLVSRIQDGLGELKKLLETHIHNQGLAAIEKCGEAAL
NDPKMYVQTVLDVHKKYNALVMSAFNNDAGFVAALDKACGRFINNNAVTKMAQSSSKSPE
LLARYCDSLLKKSSKNPEEAELEDTLNQVMVVFKYIEDKDVFQKFYAKMLAKRLVHQNSA
SDDAEASMISKLKQACGFEYTSKLQRMFQDIGVSKDLNEQFKKHLTNSEPLDLDFSIQVL
SSGSWPFQQSCTFALPSELERSYQRFTAFYASRHSGRKLTWLYQLSKGELVTNCFKNRYT
LQASTFQMAILLQYNTEDAYTVQQLTDSTQIKMDILAQVLQILLKSKLLVLEDENANVDE
VELKPDTLIKLYLGYKNKKLRVNINVPMKTEQKQEQETTHKNIEEDRKLLIQAAIVRIMK
MRKVLKHQQLLGEVLTQLSSRFKPRVPVIKKCIDILIEKEYLERVDGEKDTYSYLA

Sequence of entity 2 (R), FASTA

>8CDJ_2 E3 ubiquitin-protein ligase RBX1, N-terminally processed (chains R)
GSMDVDTPSGTNSGAGKKRFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQAS
ATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEFQKYGH

Sequence of entity 3 (D), FASTA

>8CDJ_3 Cullin-associated NEDD8-dissociated protein 1 (chains D)
GSPEFPGRMASASYHISNLLEKMTSSDKDFRFMATNDLMTELQKDSIKLDDDSERKVVKM
ILKLLEDKNGEVQNLAVKCLGPLVSKVKEYQVETIVDTLCTNMLSDKEQLRDISSIGLKT
VIGELPPASSGSALAANVCKKITGRLTSAIAKQEDVSVQLEALDIMADMLSRQGGLLVNF
HPSILTCLLPQLTSPRLAVRKRTIIALGHLVMSCGNIVFVDLIEHLLSELSKNDSMSTTR
TYIQCIAAISRQAGHRIGEYLEKIIPLVVKFCNVDDDELREYCIQAFESFVRRCPKEVYP
HVSTIINICLKYLTYDPNYNYDDEDEDENAMDADGGDDDDQGSDDEYSDDDDMSWKVRRA
AAKCLDAVVSTRHEMLPEFYKTVSPALISRFKEREENVKADVFHAYLSLLKQTRPVQSWL
CDPDAMEQGETPLTMLQSQVPNIVKALHKQMKEKSVKTRQCCFNMLTELVNVLPGALTQH
IPVLVPGIIFSLNDKSSSSNLKIDALSCLYVILCNHSPQVFHPHVQALVPPVVACVGDPF
YKITSEALLVTQQLVKVIRPLDQPSSFDATPYIKDLFTCTIKRLKAADIDQEVKERAISC
MGQIICNLGDNLGSDLPNTLQIFLERLKNEITRLTTVKALTLIAGSPLKIDLRPVLGEGV
PILASFLRKNQRALKLGTLSALDILIKNYSDSLTAAMIDAVLDELPPLISESDMHVSQMA
ISFLTTLAKVYPSSLSKISGSILNELIGLVRSPLLQGGALSAMLDFFQALVVTGTNNLGY
MDLLRMLTGPVYSQSTALTHKQSYYSIAKCVAALTRACPKEGPAVVGQFIQDVKNSRSTD
SIRLLALLSLGEVGHHIDLSGQLELKSVILEAFSSPSEEVKSAASYALGSISVGNLPEYL
PFVLQEITSQPKRQYLLLHSLKEIISSASVVGLKPYVENIWALLLKHCECAEEGTRNVVV
ECLGKLTLIDPETLLPRLKGYLISGSSYARSSVVTAVKFTISDHPQPIDPLLKNCIGDFL
KTLEDPDLNVRRVALVTFNSAAHNKPSLIRDLLDTVLPHLYNETKVRKELIREVEWGQFK
HTVDDGLDIRKAAFECMYTLLDSCLDRLDIFEFLNHVEDGLKDHYDIKMLTFLMLVRLST
LCPSAVLQRLDRLVEPLRATCTTKVKANSVKQEFEKQDELKRSAMRAVAALLTIPEAEKS
PLMSEFQSQISSNPELAAIFESIQKDSSSTNLESMDTS

Sequence of entity 4 (F), FASTA

>8CDJ_4 S-phase kinase-associated protein 2 (chains F)
GSMHRKHLQEIPDLSSNVATSFTWGWDSSKTSELLSGMGVSALEKEEPDSENIPQELLSN
LGHPESPPRKRLKSKGSDKDFVIVRRPKLNRENFPGVSWDSLPDELLLGIFSCLCLPELL
KVSGVCKRWYRLASDESLWQTLDLTGKNLHPDVTGRLLSQGVIAFRCPRSFMDQPLAEHF
SPFRVQHMDLSNSVIEVSTLHGILSQCSKLQNLSLEGLRLSDPIVNTLAKNSNLVRLNLS
GCSGFSEFALQTLLSSCSRLDELNLSWCFDFTEKHVQVAVAHVSETITQLNLSGYRKNLQ
KSDLSTLVRRCPNLVHLDLSDSVMLKNDCFQEFFQLNYLQHLSLSRCYDIIPETLLELGE
IPTLKTLQVFGIVPDGTLQLLKEALPHLQINCSHFTTIARPTIGNKKNQEIWGIKCRLTL
QKPSCL

Sequence of entity 5 (S), FASTA

>8CDJ_5 S-phase kinase-associated protein 1 (chains S)
MPSIKLQSSDGEIFEVDVEIAKQSVTIKTMLEDLGMDDEGDDDPVPLPNVNAAILKKVIQ
WCTHHKDDPPPPEDDENKEKRTDDIPVWDQEFLKVDQGTLFELILAANYLDIKGLLDVTC
KTVANMIKGKTPEEIRKTFNIKNDFTEEEEAQVRKENQWCEEK

Primary citation

Systemwide disassembly and assembly of SCF ubiquitin ligase complexes. Baek, K., Scott, D.C., Henneberg, L.T. et al. Cell (2023) 186:1895. DOI 10.1016/j.cell.2023.02.035 · PubMed

Other PDB entries of the same protein (UniProt Q13616 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3TDU 1.5 Å, N-terminal acetylation acts as an avidity enhancer within an interconnected multiprotein…
5V89 1.55 Å, Structure of DCN4 PONY domain bound to CUL1 WHB
3TDZ 2.0 Å, N-terminal acetylation acts as an avidity enhancer within an interconnected multiprotein…
8CAF 2.66 Å, N8C_Fab3b in complex with NEDD8-CUL1(WHB)
7Z8R 2.7 Å, CAND1-CUL1-RBX1
7Z8V 2.7 Å, CAND1-SCF-SKP2 (SKP1deldel) CAND1 engaged SCF rocked
8OR3 2.9 Å, CAND1-CUL1-RBX1-SKP1-SKP2-DCNL1
9QO4 2.95 Å, Dissociation-state-3 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex
1LDJ 3.0 Å, Structure of the Cul1-Rbx1-Skp1-F boxSkp2 SCF Ubiquitin Ligase Complex
4F52 3.0 Å, Structure of a Glomulin-RBX1-CUL1 complex
7Z8T 3.0 Å, CAND1-SCF-SKP2 CAND1 engaged SCF rocked
9XZL 3.0 Å, Cryo-EM structure of F-box helicase 1 (FBH1) bound to an SCF ubiquitin ligase complex…

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