3MKS: Yeast Cdc4/Skp1

Crystal Structure of yeast Cdc4/Skp1 in complex with an allosteric inhibitor SCF-I2. Determined by X-ray diffraction at 2.6 Å resolution. Released 21 Jul 2010.

Method: X-ray diffraction
Resolution: 2.6 Å
Organism: Saccharomyces cerevisiae
Chains: 4
Atoms: 9,456
Mol. weight: 146.22 kDa
Ligands: C1C
Released: 21 Jul 2010

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

Secondary structure: helices and β-sheets

3MKS contains 35 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: 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	27-30	4
β-strand	76-78	3	1
α-helix	84-96	13
α-helix	115-117	3
α-helix	118-123	6
α-helix	128-141	14
α-helix	144-158	15
α-helix	163-170	8
α-helix	178-181	4

Chain B: 8 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	303-310	8
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	425-431	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
α-helix	516-518	3
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	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
β-strand	676-681	6	9
β-strand	685-690	6	9
β-strand	693-698	6	9
β-strand	703-706	4	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	5-10	6	10
β-strand	15-19	5	10
α-helix	20-23	4
α-helix	27-31	5
β-strand	76-79	4	10
α-helix	84-96	13
α-helix	120-123	4
α-helix	128-141	14
α-helix	144-158	15
α-helix	163-170	8
α-helix	178-185	8

Chain D: 10 helices, 33 β-strands

Element	Residues	Length	Sheet
α-helix	274-277	4
α-helix	280-288	9
α-helix	292-299	8
α-helix	303-311	9
α-helix	313-322	10
α-helix	328-330	3
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	594-598	5	16
β-strand	607-628	6	16
β-strand	634-640	7	17
β-strand	644-649	6	17
β-strand	653-658	6	17
β-strand	664-669	6	17
β-strand	676-681	6	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	725-731	7	11
β-strand	736-742	7	11

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)

Sequence of entity 1 (A, C), FASTA

>3MKS_1 Suppressor of kinetochore protein 1 (chains A, C)
GAHMVTSNVVLVSGEGERFTVDKKIAERSLLLKNYLNDMGDDDDEDDDEIVMPVPNVRSS
VLQKVIEWAEHHRDSNFPDEDDDDSRKSAPVDSWDREFLKVDQEMLYEIILAANYLNIKP
LLDAGCKVVAEMIRGRSPEEIRRTFNIVNDFTPEEEAAIRRENEWAEDR

Sequence of entity 2 (B, D), FASTA

>3MKS_2 Cell division control protein 4 (chains B, D)
GAGTLIKDNLKRDLITSLPFEISLKIFNYLQFEDIINSLGVSQNWNKIIRKSTSLWKKLL
ISENFVSPKGFNSLNLKLSQKYPKLSQQDRLRLSFLENIFILKNWYNPKFVPQRTTLRGH
MTSVITCLQFEDNYVITGADDKMIRVYDSINKKFLLQLSGHDGGVWALKYAHGGILVSGS
TDRTVRVWDIKKGCCTHVFEGHNSTVRCLDIVEYKNIKYIVTGSRDNTLHVWKLPKESSV
PDHGEEHDYPLVFHTPEENPYFVGVLRGHMASVRTVSGHGNIVVSGSYDNTLIVWDVAQM
KCLYILSGHTDRIYSTIYDHERKRCISASMDTTIRIWDLENGELMYTLQGHTALVGLLRL
SDKFLVSAAADGSIRGWDANDYSRKFSYHHTNLSAITTFYVSDNILVSGSENQFNIYNLR
SGKLVHANILKDADQIWSVNFKGKTLVAAVEKDGQSFLEILDFS

Ligands and cofactors

ID	Name	Formula	Copies
C1C	1,1'-binaphthalene-2,2'-dicarboxylic acid	C22 H14 O4	1

Water and common crystallization additives (GOL, SO4) are not listed.

Primary citation

An allosteric inhibitor of substrate recognition by the SCF(Cdc4) ubiquitin ligase. Orlicky, S., Tang, X., Neduva, V. et al. Nat Biotechnol (2010) 28:733-737. DOI 10.1038/nbt.1646 · 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)…
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

Browse structure collections

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