7B5S: Cullin-1

Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 super-assembly: CUL1-RBX1-ARIH1 Ariadne. Transition State 1. Determined by electron microscopy at 3.6 Å resolution. Released 10 Feb 2021.

Method: Electron microscopy
Resolution: 3.6 Å
Organism: Homo sapiens
Chains: 3
Atoms: 7,671
Mol. weight: 166.62 kDa
Ligands: ZN
Released: 10 Feb 2021

Explore 7B5S in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7B5S contains 39 α-helices and 19 β-strands across 3 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: 31 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	21-31	11
α-helix	39-52	14
α-helix	86-104	19
α-helix	115-136	22
α-helix	140-143	4
α-helix	159-171	13
α-helix	175-187	13
α-helix	188-190	3
α-helix	199-210	12
α-helix	226-228	3
α-helix	229-233	5
α-helix	234-252	19
α-helix	257-274	18
α-helix	284-294	11
α-helix	300-312	13
α-helix	318-327	10
α-helix	334-353	20
α-helix	356-361	6
α-helix	363-383	21
α-helix	389-404	16
α-helix	407-411	5
α-helix	418-430	13
α-helix	439-454	16
α-helix	459-475	17
α-helix	482-496	15
α-helix	502-524	23
α-helix	525-527	3
β-strand	534-540	7	1
α-helix	560-573	14
β-strand	580-589	10	1
β-strand	590	1	2
β-strand	601-602	2	2
β-strand	604	1	1
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	682-683	2	2

Chain H: 6 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	101-104	4	4
β-strand	273-275	3	4
β-strand	284-287	4	4
β-strand	294-296	3	5
β-strand	302-304	3	5
α-helix	317-325	9
α-helix	409-429	21
α-helix	431-447	17
α-helix	453-480	28
α-helix	486-512	27
α-helix	518-549	32

Chain R: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	26-32	7	1
α-helix	54-57	4
β-strand	70-72	3	6
β-strand	73	1	7
β-strand	78-80	3	6
α-helix	81-90	10
β-strand	103	1	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cullin-1	C	protein	776	Homo sapiens	Q13616 (AlphaFold model)
E3 ubiquitin-protein ligase ARIH1	H	protein	557	Homo sapiens	Q9Y4X5 (AlphaFold model)
E3 ubiquitin-protein ligase RBX1	R	protein	108	Homo sapiens	P62877 (AlphaFold model)

Sequence of entity 1 (C), FASTA

>7B5S_1 Cullin-1 (chains C)
MSSTRSQNPHGLKQIGLDQIWDDLRAGIQQVYTRQSMAKSRYMELYTHVYNYCTSVHQSN
QARGAGVPPSKSKKGQTPGGAQFVGLELYKRLKEFLKNYLTNLLKDGEDLMDESVLKFYT
QQWEDYRFSSKVLNGICAYLNRHWVRRECDEGRKGIYEIYSLALVTWRDCLFRPLNKQVT
NAVLKLIEKERNGETINTRLISGVVQSYVELGLNEDDAFAKGPTLTVYKESFESQFLADT
ERFYTRESTEFLQQNPVTEYMKKAEARLLEEQRRVQVYLHESTQDELARKCEQVLIEKHL
EIFHTEFQNLLDADKNEDLGRMYNLVSRIQDGLGELKKLLETHIHNQGLAAIEKCGEAAL
NDPKMYVQTVLDVHKKYNALVMSAFNNDAGFVAALDKACGRFINNNAVTKMAQSSSKSPE
LLARYCDSLLKKSSKNPEEAELEDTLNQVMVVFKYIEDKDVFQKFYAKMLAKRLVHQNSA
SDDAEASMISKLKQACGFEYTSKLQRMFQDIGVSKDLNEQFKKHLTNSEPLDLDFSIQVL
SSGSWPFQQSCTFALPSELERSYQRFTAFYASRHSGRKLTWLYQLSKGELVTNCFKNRYT
LQASTFQMAILLQYNTEDAYTVQQLTDSTQIKMDILAQVLQILLKSKLLVLEDENANVDE
VELKPDTLIKLYLGYKNKKLRVNINVPMKTEQKQEQETTHKNIEEDRKLLIQAAIVRIMK
MRKVLKHQQLLGEVLTQLSSRFKPRVPVIKKCIDILIEKEYLERVDGEKDTYSYLA

Sequence of entity 2 (H), FASTA

>7B5S_2 E3 ubiquitin-protein ligase ARIH1 (chains H)
MDSDEGYNYEFDEDEECSEEDSGAEEEEDEDDDEPDDDTLDLGEVELVEPGLGVGGERDG
LLCGETGGGGGSALGPGGGGGGGGGGGGGGPGHEQEEDYRYEVLTAEQILQHMVECIREV
NEVIQNPATITRILLSHFNWDKEKLMERYFDGNLEKLFAECHVINPSKKSRTRQMNTRSS
AQDMPCQICYLNYPNSYFTGLECGHKFCMQCWSEYLTTKIMEEGMGQTISCPAHGCDILV
DDNTVMRLITDSKVKLKYQHLITNSFVECNRLLKWCPAPDCHHVVKVQYPDAKPVRCKCG
RQFCFNCGENWHDPVKCKWLKKWIKKCDDDSETSNWIAANTKECPKCHVTIEKDGGCNHM
VCRNQNCKAEFCWVCLGPWEPHGSAWYNCNRYNEDDAKAARDAQERSRAALQRYLFYCNR
YMNHMQSLRFEHKLYAQVKQKMEEMQQHNMSWIEVQFLKKAVDVLCQCRATLMYTYVFAF
YLKKNNQSIIFENNQADLENATEVLSGYLERDISQDSLQDIKQKVQDKYRYCESRRRVLL
QHVHEGYEKDLWEYIED

Sequence of entity 3 (R), FASTA

>7B5S_3 E3 ubiquitin-protein ligase RBX1 (chains R)
MAAAMDVDTPSGTNSGAGKKRFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQ
ASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEFQKYGH

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	5

Primary citation

Ubiquitin ligation to F-box protein targets by SCF-RBR E3-E3 super-assembly. Horn-Ghetko, D., Krist, D.T., Prabu, J.R. et al. Nature (2021) 590:671-676. DOI 10.1038/s41586-021-03197-9 · 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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