1LDJ: Cullin homolog 1

Name: PDB 1LDJ: Structure of the Cul1-Rbx1-Skp1-F boxSkp2 SCF Ubiquitin Ligase Complex
Published: 2002-05-08
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Structure of the Cul1-Rbx1-Skp1-F boxSkp2 SCF Ubiquitin Ligase Complex. Determined by X-ray diffraction at 3.0 Å resolution. Released 8 May 2002.

Method: X-ray diffraction
Resolution: 3.0 Å
Organism: Homo sapiens
Chains: 2
Atoms: 6,668
Mol. weight: 98.93 kDa
Ligands: ZN
Released: 8 May 2002

Explore 1LDJ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1LDJ contains 39 α-helices and 19 β-strands across 2 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, 13 β-strands

Element	Residues	Length	Sheet
α-helix	18-31	14
α-helix	39-52	14
α-helix	87-105	19
α-helix	115-136	22
α-helix	138-143	6
α-helix	159-165	7
α-helix	168-171	4
α-helix	178-187	10
α-helix	199-210	12
α-helix	226-227	2
α-helix	228-233	6
α-helix	234-254	21
α-helix	261-273	13
α-helix	285-295	11
α-helix	301-312	12
α-helix	318-328	11
α-helix	333-355	23
α-helix	359-361	3
α-helix	363-382	20
α-helix	389-404	16
α-helix	407-412	6
α-helix	417-430	14
β-strand	431	1	1
α-helix	439-453	15
α-helix	459-475	17
β-strand	479	1	1
α-helix	482-525	44
β-strand	534-541	8	2
α-helix	557-559	3
α-helix	560-569	10
β-strand	579-581	3	2
α-helix	583-585	3
β-strand	589-592	4	3
β-strand	600-602	3	3
α-helix	605-612	8
α-helix	613-615	3
β-strand	619-621	3	4
α-helix	622-628	7
α-helix	633-645	13
β-strand	649-650	2	4
α-helix	661-663	3
β-strand	668-671	4	4
α-helix	672	1
β-strand	682	1	3
α-helix	691-721	31
β-strand	724-726	3	5
α-helix	727-738	12
α-helix	746-758	13
β-strand	762-764	3	5
β-strand	771-774	4	5

Chain B: 2 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	22-24	3	3
β-strand	26-33	8	2
α-helix	55-58	4
β-strand	70-71	2	6
β-strand	79-80	2	6
α-helix	82-88	7
β-strand	93-94	2	7
β-strand	98-100	3	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cullin homolog 1	A	protein	760	Homo sapiens	Q13616 (AlphaFold model)
ring-box protein 1	B	protein	90	Homo sapiens	P62877 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>1LDJ_1 Cullin homolog 1 (chains A)
LDQIWDDLRAGIQQVYTRQSMAKSRYMELYTHVYNYCTSVHQSNQARGAGVPPSKSKKGQ
TPGGAQFVGLELYKRLKEFLKNYLTNLLKDGEDLMDESVLKFYTQQWEDYRFSSKVLNGI
CAYLNRHWVRRECDEGRKGIYEIYSLALVTWRDCLFRPLNKQVTNAVLKLIEKERNGETI
NTRLISGVVQSYVELGLNEDDAFAKGPTLTVYKESFESQFLADTERFYTRESTEFLQQNP
VTEYMKKAEARLLEEQRRVQVYLHESTQDELARKCEQVLIEKHLEIFHTEFQNLLDADKN
EDLGRMYNLVSRIQDGLGELKKLLETHIHNQGLAAIEKCGEAALNDPKMYVQTVLDVHKK
YNALVMSAFNNDAGFVAALDKACGRFINNNAVTKMAQSSSKSPELLARYCDSLLKKSSKN
PEEAELEDTLNQVMVVFKYIEDKDVFQKFYAKMLAKRLVHQNSASDDAEASMISKLKQAC
GFEYTSKLQRMFQDIGVSKDLNEQFKKHLTNSEPLDLDFSIQVLSSGSWPFQQSCTFALP
SELERSYQRFTAFYASRHSGRKLTWLYQLSKGELVTNCFKNRYTLQASTFQMAILLQYNT
EDAYTVQQLTDSTQIKMDILAQVLQILLKSKLLVLEDENANVDEVELKPDTLIKLYLGYK
NKKLRVNINVPMKTEQKQEQETTHKNIEEDRKLLIQAAIVRIMKMRKVLKHQQLLGEVLT
QLSSRFKPRVPVIKKCIDILIEKEYLERVDGEKDTYSYLA

Sequence of entity 2 (B), FASTA

>1LDJ_2 ring-box protein 1 (chains B)
KKRFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHA
FHFHCISRWLKTRQVCPLDNREWEFQKYGH

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	3

Primary citation

Structure of the Cul1-Rbx1-Skp1-F boxSkp2 SCF ubiquitin ligase complex. Zheng, N., Schulman, B.A., Song, L. et al. Nature (2002) 416:703-709. DOI 10.1038/416703a · 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
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

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