7Z8V: Cullin-1

Name: PDB 7Z8V: CAND1-SCF-SKP2 (SKP1deldel) CAND1 engaged SCF rocked
Published: 2023-04-19
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

CAND1-SCF-SKP2 (SKP1deldel) CAND1 engaged SCF rocked. Determined by electron microscopy at 2.7 Å resolution. Released 19 Apr 2023.

Method: Electron microscopy
Resolution: 2.7 Å
Organism: Homo sapiens
Chains: 5
Atoms: 18,313
Mol. weight: 304.29 kDa
Ligands: ZN
Released: 19 Apr 2023

Explore 7Z8V in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7Z8V contains 142 α-helices and 37 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: 39 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	21-31	11
β-strand	37	1	1
α-helix	39-53	15
α-helix	88-104	17
α-helix	114-136	23
α-helix	138-151	14
α-helix	159-167	9
α-helix	168-172	5
α-helix	176-191	16
α-helix	199-210	12
α-helix	226-228	3
α-helix	229-233	5
α-helix	234-254	21
α-helix	257-278	22
α-helix	281-283	3
α-helix	284-296	13
α-helix	297-299	3
α-helix	300-312	13
α-helix	316-326	11
α-helix	334-353	20
α-helix	356-361	6
α-helix	363-384	22
α-helix	389-404	16
α-helix	407-412	6
α-helix	417-430	14
α-helix	442-453	12
α-helix	459-476	18
α-helix	482-495	14
α-helix	499-526	28
α-helix	529-531	3
β-strand	534-541	8	2
α-helix	554-556	3
α-helix	560-573	14
β-strand	577-592	16	2
β-strand	599-604	6	2
α-helix	605-612	8
β-strand	619-621	3	3
α-helix	622-629	8
α-helix	633-645	13
β-strand	649-650	2	3
β-strand	668-671	4	3
β-strand	681-683	3	2
α-helix	686-688	3
α-helix	689-721	33
β-strand	724-726	3	4
α-helix	727-738	12
α-helix	746-758	13
β-strand	762-764	3	4
α-helix	765	1
β-strand	771-774	4	4

Chain D: 76 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	6-14	9
α-helix	20-35	16
α-helix	43-56	14
α-helix	62-77	16
α-helix	81-95	15
α-helix	100-116	17
α-helix	128-143	16
α-helix	149-163	15
α-helix	170-172	3
α-helix	173-180	8
α-helix	181-185	5
α-helix	189-204	16
α-helix	208-223	16
α-helix	228-244	17
α-helix	247-252	6
α-helix	253-264	12
α-helix	269-285	17
α-helix	288-293	6
α-helix	294-305	12
α-helix	347-363	17
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	510-516	7
α-helix	517-528	12
α-helix	533-550	18
α-helix	562-564	3
α-helix	565-576	12
α-helix	583-600	18
α-helix	607-618	12
α-helix	626-636	11
α-helix	645-657	13
α-helix	664-680	17
α-helix	682-684	3
α-helix	687-694	8
α-helix	698-700	3
α-helix	706-722	17
α-helix	724-730	7
α-helix	733-742	10
α-helix	750-765	16
α-helix	772-785	14
α-helix	789-790	2
α-helix	794-809	16
α-helix	811-813	3
α-helix	814-825	12
α-helix	832-848	17
α-helix	857-863	7
α-helix	870-886	17
α-helix	892-901	10
α-helix	909-918	10
α-helix	922-925	4
α-helix	929-939	11
α-helix	947-960	14
α-helix	967-975	9
α-helix	979-990	12
α-helix	1001-1012	12
α-helix	1013-1016	4
α-helix	1020-1036	17
α-helix	1038-1040	3
α-helix	1042-1044	3
α-helix	1045-1054	10
α-helix	1060-1062	3
β-strand	1063-1068	6	1
β-strand	1071-1076	6	1
α-helix	1079-1094	16
α-helix	1102-1112	11
α-helix	1117-1132	16
α-helix	1135-1140	6
α-helix	1142-1154	13
α-helix	1163-1184	22
α-helix	1193-1204	12
α-helix	1206-1214	9

Chain F: 13 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	102-109	8
α-helix	114-120	7
α-helix	125-130	6
β-strand	139-141	3	8
α-helix	149-157	9
β-strand	162-164	3	8
β-strand	169-170	2	9
α-helix	179-181	3
β-strand	185-187	3	8
β-strand	192-193	2	9
α-helix	195-202	8
β-strand	210-212	3	8
α-helix	220-226	7
β-strand	234	1	10
α-helix	245-254	10
β-strand	260-262	3	10
α-helix	271-279	9
β-strand	287-289	3	10
α-helix	299-308	10
β-strand	314-316	3	10
α-helix	325-333	9
β-strand	339-341	3	10
α-helix	350-358	9
β-strand	364-366	3	10
α-helix	375-382	8
β-strand	387-388	2	10

Chain R: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	22-35	14	2
β-strand	41	1	5
β-strand	48	1	5
α-helix	54-58	5
α-helix	60-61	2
α-helix	63-66	4
β-strand	70-73	4	6
β-strand	78-80	3	6
α-helix	81-87	7
β-strand	93	1	7
β-strand	100	1	7
α-helix	101	1
β-strand	103-105	3	6

Chain S: 9 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	11
β-strand	13-17	5	11
α-helix	18-21	4
α-helix	25-28	4
α-helix	44	1
β-strand	45-46	2	11
α-helix	52-64	13
α-helix	87-93	7
α-helix	97-110	14
α-helix	113-126	14
α-helix	132-139	8
α-helix	147-156	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cullin-1	C	protein	776	Homo sapiens	Q13616 (AlphaFold model)
Cullin-associated NEDD8-dissociated protein 1	D	protein	1238	Homo sapiens	Q86VP6 (AlphaFold model)
E3 ubiquitin-protein ligase RBX1, N-terminally processed	R	protein	106	Homo sapiens	P62877 (AlphaFold model)
S-phase kinase-associated protein 2	F	protein	426	Homo sapiens	Q13309 (AlphaFold model)
S-phase kinase-associated protein 1	S	protein	149	Homo sapiens	P63208

Sequence of entity 1 (C), FASTA

>7Z8V_1 Cullin-1 (chains C)
MSSTRSQNPHGLKQIGLDQIWDDLRAGIQQVYTRQSMAKSRYMELYTHVYNYCTSVHQSN
QARGAGVPPSKSKKGQTPGGAQFVGLELYKRLKEFLKNYLTNLLKDGEDLMDESVLKFYT
QQWEDYRFSSKVLNGICAYLNRHWVRRECDEGRKGIYEIYSLALVTWRDCLFRPLNKQVT
NAVLKLIEKERNGETINTRLISGVVQSYVELGLNEDDAFAKGPTLTVYKESFESQFLADT
ERFYTRESTEFLQQNPVTEYMKKAEARLLEEQRRVQVYLHESTQDELARKCEQVLIEKHL
EIFHTEFQNLLDADKNEDLGRMYNLVSRIQDGLGELKKLLETHIHNQGLAAIEKCGEAAL
NDPKMYVQTVLDVHKKYNALVMSAFNNDAGFVAALDKACGRFINNNAVTKMAQSSSKSPE
LLARYCDSLLKKSSKNPEEAELEDTLNQVMVVFKYIEDKDVFQKFYAKMLAKRLVHQNSA
SDDAEASMISKLKQACGFEYTSKLQRMFQDIGVSKDLNEQFKKHLTNSEPLDLDFSIQVL
SSGSWPFQQSCTFALPSELERSYQRFTAFYASRHSGRKLTWLYQLSKGELVTNCFKNRYT
LQASTFQMAILLQYNTEDAYTVQQLTDSTQIKMDILAQVLQILLKSKLLVLEDENANVDE
VELKPDTLIKLYLGYKNKKLRVNINVPMKTEQKQEQETTHKNIEEDRKLLIQAAIVRIMK
MRKVLKHQQLLGEVLTQLSSRFKPRVPVIKKCIDILIEKEYLERVDGEKDTYSYLA

Sequence of entity 2 (D), FASTA

>7Z8V_2 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
KTLEDPDLNVRRVALVTFNSAAHNKPSLIRDLLDTVLPHLYNETKVRKELIREVEMGPFK
HTVDDGLDIRKAAFECMYTLLDSCLDRLDIFEFLNHVEDGLKDHYDIKMLTFLMLVRLST
LCPSAVLQRLDRLVEPLRATCTTKVKANSVKQEFEKQDELKRSAMRAVAALLTIPEAEKS
PLMSEFQSQISSNPELAAIFESIQKDSSSTNLESMDTS

Sequence of entity 3 (R), FASTA

>7Z8V_3 E3 ubiquitin-protein ligase RBX1, N-terminally processed (chains R)
GSMDVDTPSGTNSGAGKKRFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQAS
ATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEFQKYGH

Sequence of entity 4 (F), FASTA

>7Z8V_4 S-phase kinase-associated protein 2 (chains F)
GSMHRKHLQEIPDLSSNVATSFTWGWDSSKTSELLSGMGVSALEKEEPDSENIPQELLSN
LGHPESPPRKRLKSKGSDKDFVIVRRPKLNRENFPGVSWDSLPDELLLGIFSCLCLPELL
KVSGVCKRWYRLASDESLWQTLDLTGKNLHPDVTGRLLSQGVIAFRCPRSFMDQPLAEHF
SPFRVQHMDLSNSVIEVSTLHGILSQCSKLQNLSLEGLRLSDPIVNTLAKNSNLVRLNLS
GCSGFSEFALQTLLSSCSRLDELNLSWCFDFTEKHVQVAVAHVSETITQLNLSGYRKNLQ
KSDLSTLVRRCPNLVHLDLSDSVMLKNDCFQEFFQLNYLQHLSLSRCYDIIPETLLELGE
IPTLKTLQVFGIVPDGTLQLLKEALPHLQINCSHFTTIARPTIGNKKNQEIWGIKCRLTL
QKPSCL

Sequence of entity 5 (S), FASTA

>7Z8V_5 S-phase kinase-associated protein 1 (chains S)
MPSIKLQSSDGEIFEVDVEIAKQSVTIKTMLEDLGMDPVPLPNVNAAILKKVIQWCTHHK
DDPGGSGTDDIPVWDQEFLKVDQGTLFELILAANYLDIKGLLDVTCKTVANMIKGKTPEE
IRKTFNIKNDFTEEEEAQVRKENQWCEEK

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	3

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
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…
9EFV 3.03 Å, Cryo-EM structure of CSN-N8CUL1 in complex with CSN5i-3

Browse structure collections

About this viewer

MolViewer shows 7Z8V directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.