3V7D: ScSkp1-ScCdc4-pSic1 peptide complex

Crystal Structure of ScSkp1-ScCdc4-pSic1 peptide complex. Determined by X-ray diffraction at 2.31 Å resolution. Released 2 May 2012.

Method: X-ray diffraction
Resolution: 2.31 Å
Organism: Saccharomyces cerevisiae
Chains: 5
Atoms: 9,899
Mol. weight: 147.05 kDa
Released: 2 May 2012

Explore 3V7D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3V7D contains 38 α-helices and 72 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 A: 9 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	27-34	8
β-strand	76-78	3	1
α-helix	84-96	13
α-helix	114-117	4
α-helix	118-123	6
α-helix	128-140	13
α-helix	144-158	15
α-helix	163-170	8
α-helix	178-185	8

Chain B: 10 helices, 33 β-strands

Element	Residues	Length	Sheet
α-helix	274-277	4
α-helix	280-287	8
α-helix	292-299	8
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	2
β-strand	385-391	7	3
β-strand	394-399	6	3
β-strand	404-408	5	3
β-strand	413-418	6	3
β-strand	425-430	6	4
β-strand	435-440	6	4
β-strand	445-449	5	4
β-strand	454-459	6	4
β-strand	466-473	8	5
β-strand	478-484	7	5
β-strand	489-493	5	5
α-helix	494-498	5
β-strand	511-513	3	4
α-helix	516-518	3
β-strand	522-526	5	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	607-628	6	7
β-strand	635-640	6	8
β-strand	644-649	6	8
β-strand	653-658	6	8
β-strand	664-669	6	8
α-helix	674-675	2
β-strand	676-681	6	9
β-strand	685-690	6	9
β-strand	693-698	6	9
β-strand	704-706	3	9
β-strand	715-722	8	2
β-strand	725-732	8	2
β-strand	735-742	8	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	75-78	4	10
α-helix	84-96	13
α-helix	118-123	6
α-helix	128-140	13
α-helix	144-158	15
α-helix	163-170	8
α-helix	178-186	9

Chain D: 10 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	404-408	5	12
β-strand	413-418	6	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	489-493	5	14
α-helix	494-495	2
β-strand	511-513	3	13
α-helix	516-518	3
β-strand	522-526	5	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	607-629	7	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	674-676	3
β-strand	678-681	4	18
β-strand	685-690	6	18
β-strand	693-698	6	18
β-strand	703-706	4	18
β-strand	715-722	8	11
β-strand	725-732	8	11
β-strand	735-742	8	11

Chain E: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	77-79	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Suppressor of kinetochore protein 1	A, C	protein	169	Saccharomyces cerevisiae	P52286 (AlphaFold model)
Cell division control protein 4	B, D	protein	464	Saccharomyces cerevisiae	P07834 (AlphaFold model)
Protein SIC1	E	protein	19	Saccharomyces cerevisiae	P38634 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>3V7D_1 Suppressor of kinetochore protein 1 (chains A, C)
GAHMVTSNVVLVSGEGERFTVDKKIAERSLLLKNYLNDMGDDDDEDDDEIVMPVPNVRSS
VLQKVIEWAEHHRDSNFPDEDDDDSRKSAPVDSWDREFLKVDQEMLYEIILAANYLNIKP
LLDAGCKVVAEMIRGRSPEEIRRTFNIVNDFTPEEEAAIRRENEWAEDR

Sequence of entity 2 (B, D), FASTA

>3V7D_2 Cell division control protein 4 (chains B, D)
GAGTLIKDNLKRDLITSLPFEISLKIFNYLQFEDIINSLGVSQNWNKIIRKSTSLWKKLL
ISENFVSPKGFNSLNLKLSQKYPKLSQQDRLRLSFLENIFILKNWYNPKFVPQRTTLRGH
MTSVITCLQFEDNYVITGADDKMIRVYDSINKKFLLQLSGHDGGVWALKYAHGGILVSGS
TDRTVRVWDIKKGCCTHVFEGHNSTVRCLDIVEYKNIKYIVTGSRDNTLHVWKLPKESSV
PDHGEEHDYPLVFHTPEENPYFVGVLRGHMASVRTVSGHGNIVVSGSYDNTLIVWDVAQM
KCLYILSGHTDRIYSTIYDHERKRCISASMDTTIRIWDLENGELMYTLQGHTALVGLLRL
SDKFLVSAAADGSIRGWDANDYSRKFSYHHTNLSAITTFYVSDNILVSGSENQFNIYNLR
SGKLVHANILKDADQIWSVNFKGKTLVAAVEKDGQSFLEILDFS

Sequence of entity 3 (E), FASTA

>3V7D_3 Protein SIC1 (chains E)
MTSPFNGLTSPQRSPFPKS

Primary citation

Composite low affinity interactions dictate recognition of the cyclin-dependent kinase inhibitor Sic1 by the SCFCdc4 ubiquitin ligase. Tang, X., Orlicky, S., Mittag, T. et al. Proc Natl Acad Sci U S A (2012) 109:3287-3292. DOI 10.1073/pnas.1116455109 · 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
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
1NEX 2.7 Å, Crystal Structure of ScSkp1-ScCdc4-CPD peptide complex
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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