1NEX: ScSkp1-ScCdc4-CPD peptide complex

Crystal Structure of ScSkp1-ScCdc4-CPD peptide complex. Determined by X-ray diffraction at 2.7 Å resolution. Released 18 Feb 2003.

Method: X-ray diffraction
Resolution: 2.7 Å
Organism: Saccharomyces cerevisiae
Chains: 6
Atoms: 9,435
Mol. weight: 147.66 kDa
Released: 18 Feb 2003

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

Secondary structure: helices and β-sheets

1NEX contains 32 α-helices and 72 β-strands across 4 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: 8 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	5-9	5	1
β-strand	15-19	5	1
α-helix	20-23	4
α-helix	27-31	5
β-strand	76-78	3	1
α-helix	84-96	13
α-helix	118-123	6
α-helix	128-141	14
α-helix	144-158	15
α-helix	163-170	8
α-helix	178-182	5

Chain B: 7 helices, 33 β-strands

Element	Residues	Length	Sheet
α-helix	274-277	4
α-helix	280-287	8
α-helix	292-298	7
α-helix	303-310	8
α-helix	314-322	9
α-helix	328-341	14
α-helix	347-366	20
β-strand	373-378	6	2
β-strand	385-391	7	3
β-strand	394-399	6	3
β-strand	403-408	6	3
β-strand	413-419	7	3
β-strand	425-431	7	4
β-strand	435-440	6	4
β-strand	445-449	5	4
β-strand	454-459	6	4
β-strand	466-474	9	5
β-strand	477-484	8	5
β-strand	488-493	6	5
β-strand	511-513	3	4
β-strand	522-527	6	5
β-strand	533-539	7	6
β-strand	542-547	6	6
β-strand	552-556	5	6
β-strand	561-566	6	6
β-strand	573-579	7	7
β-strand	584-589	6	7
β-strand	594-598	5	7
β-strand	608-628	5	7
β-strand	637-640	4	8
β-strand	644-648	5	8
β-strand	653-658	6	8
β-strand	664-669	6	8
β-strand	678-681	4	9
β-strand	685-690	6	9
β-strand	693-698	6	9
β-strand	704	1	9
β-strand	715-722	8	2
β-strand	725-731	7	2
β-strand	736-742	7	2

Chain C: 8 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	5-9	5	10
β-strand	15-19	5	10
α-helix	20-23	4
α-helix	27-32	6
β-strand	76-78	3	10
α-helix	84-96	13
α-helix	119-123	5
α-helix	128-141	14
α-helix	144-158	15
α-helix	163-170	8
α-helix	178-182	5

Chain D: 9 helices, 33 β-strands

Element	Residues	Length	Sheet
α-helix	274-277	4
α-helix	280-287	8
α-helix	292-298	7
α-helix	303-309	7
α-helix	313-322	10
α-helix	331-341	11
α-helix	347-366	20
β-strand	373-378	6	11
β-strand	385-391	7	12
β-strand	394-399	6	12
β-strand	403-408	6	12
β-strand	413-419	7	12
β-strand	425-431	7	13
β-strand	435-440	6	13
β-strand	445-449	5	13
β-strand	454-459	6	13
β-strand	466-474	9	14
β-strand	477-484	8	14
β-strand	488-493	6	14
α-helix	494-495	2
β-strand	511-513	3	13
β-strand	522-527	6	14
β-strand	533-539	7	15
β-strand	542-547	6	15
β-strand	552-556	5	15
β-strand	561-566	6	15
β-strand	573-579	7	16
β-strand	584-589	6	16
β-strand	593-598	6	16
β-strand	608-629	6	16
β-strand	635-640	6	17
β-strand	644-649	6	17
β-strand	653-658	6	17
β-strand	664-669	6	17
α-helix	674-675	2
β-strand	676-681	6	18
β-strand	685-690	6	18
β-strand	693-698	6	18
β-strand	704-706	3	18
β-strand	715-722	8	11
β-strand	725-731	7	11
β-strand	736-742	7	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Centromere DNA-binding protein complex CBF3 subunit D	A, C	protein	169	Saccharomyces cerevisiae	P52286 (AlphaFold model)
CDC4 protein	B, D	protein	464	Saccharomyces cerevisiae	P07834 (AlphaFold model)
Gll(tpo)ppqsg	E, F	protein	9

Sequence of entity 1 (A, C), FASTA

>1NEX_1 Centromere DNA-binding protein complex CBF3 subunit D (chains A, C)
GAHMVTSNVVLVSGEGERFTVDKKIAERSLLLKNYLNDMGDDDDEDDDEIVMPVPNVRSS
VLQKVIEWAEHHRDSNFPDEDDDDSRKSAPVDSWDREFLKVDQEMLYEIILAANYLNIKP
LLDAGCKVVAEMIRGRSPEEIRRTFNIVNDFTPEEEAAIRRENEWAEDR

Sequence of entity 2 (B, D), FASTA

>1NEX_2 CDC4 protein (chains B, D)
GAGTLIKDNLKRDLITSLPFEISLKIFNYLQFEDIINSLGVSQNWNKIIRKSTSLWKKLL
ISENFVSPKGFNSLNLKLSQKYPKLSQQDRLRLSFLENIFILKNWYNPKFVPQRTTLRGH
MTSVITCLQFEDNYVITGADDKMIRVYDSINKKFLLQLSGHDGGVWALKYAHGGILVSGS
TDRTVRVWDIKKGCCTHVFEGHNSTVRCLDIVEYKNIKYIVTGSRDNTLHVWKLPKESSV
PDHGEEHDYPLVFHTPEENPYFVGVLRGHMASVRTVSGHGNIVVSGSYDNTLIVWDVAQM
KCLYILSGHTDRIYSTIYDHERKRCISASMDTTIRIWDLENGELMYTLQGHTALVGLLRL
SDKFLVSAAADGSIRGWDANDYSRKFSYHHTNLSAITTFYVSDNILVSGSENQFNIYNLR
SGKLVHANILKDADQIWSVNFKGKTLVAAVEKDGQSFLEILDFS

Sequence of entity 3 (E, F), FASTA

>1NEX_3 GLL(TPO)PPQSG (chains E, F)
GLLTPPQSG

Primary citation

Structural Basis for Phosphodependent Substrate Selection and Orientation by the SCFCdc4 Ubiquitin Ligase. Orlicky, S., Tang, X., Willems, A. et al. Cell (2003) 112:243-256. DOI 10.1016/S0092-8674(03)00034-5 · PubMed

Other PDB entries of the same protein (UniProt P52286 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8GRE 2.3 Å, F-box protein in complex with skp1(FL) and substrate
3V7D 2.31 Å, Crystal Structure of ScSkp1-ScCdc4-pSic1 peptide complex
8GRF 2.53 Å, Crystal structure of F-box protein in the ternary complex with adaptor protein Skp1(DL)…
3MKS 2.6 Å, Crystal Structure of yeast Cdc4/Skp1 in complex with an allosteric inhibitor SCF-I2
9COP 2.7 Å, Yeast RAVE bound to V-ATPase V1 complex
5AN3 2.82 Å, Structure of an Sgt1-Skp1 Complex
6GYU 3.0 Å, Cryo-EM structure of the CBF3-msk complex of the budding yeast kinetochore
7PMK 3.2 Å, S. cerevisiae replisome-SCF(Dia2) complex bound to double-stranded DNA (conformation I)
7PMN 3.2 Å, S. cerevisiae replisome-SCF(Dia2) complex bound to double-stranded DNA (conformation II)
10EH 3.5 Å, De novo assembled CBF3-CEN complex
6F07 3.6 Å, CBF3 Core Complex
6GYP 3.6 Å, Cryo-EM structure of the CBF3-core-Ndc10-DBD complex of the budding yeast kinetochore

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