7CQ4: Slx1-Slx4

Crystal structure of Slx1-Slx4 in complex with 5'flap DNA. Determined by X-ray diffraction at 3.29 Å resolution. Released 16 Jun 2021.

Method: X-ray diffraction
Resolution: 3.29 Å
Organisms: Saccharomyces cerevisiae, Saccharomyces cerevisiae (strain YJM789)
Chains: 5
Atoms: 4,485
Mol. weight: 70.02 kDa
Ligands: ZN
Released: 16 Jun 2021

Explore 7CQ4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7CQ4 contains 19 α-helices and 15 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: 11 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	15-21	7	1
β-strand	28-33	6	1
α-helix	36-43	8
α-helix	61	1
β-strand	63-70	8	1
α-helix	75-86	12
α-helix	96-98	3
α-helix	110-122	13
α-helix	124-127	4
β-strand	132-137	6	1
α-helix	138-146	9
β-strand	159-167	9	1
α-helix	168-170	3
α-helix	175-211	37
β-strand	216-217	2	2
β-strand	224-225	2	2
β-strand	238-240	3	3
β-strand	249-251	3	3
α-helix	252-267	16
β-strand	276-278	3	4
β-strand	285-287	3	4
α-helix	288-301	14

Chain B: 8 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	630-640	11
β-strand	642	1	5
α-helix	643-645	3
α-helix	648-664	17
α-helix	681-692	12
α-helix	696-703	8
β-strand	708-709	2	6
α-helix	710-720	11
α-helix	722-726	5
β-strand	727	1	5
α-helix	729-739	11
β-strand	743-744	2	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA (5'-d(gpgpaptptpapcpapapcpapgpapt)-3')	H	DNA	14	Saccharomyces cerevisiae
DNA (5'-d(apgpgpapcpaptpcptptptpgpcpc)-3')	K	DNA	14	Saccharomyces cerevisiae
DNA (27-mer)	L	DNA	27	Saccharomyces cerevisiae
Structure-specific endonuclease subunit SLX1	A	protein	304	Saccharomyces cerevisiae (strain YJM789)	P38324 (AlphaFold model)
SLX4 isoform 1	B	protein	151	Saccharomyces cerevisiae	Q12098 (AlphaFold model)

Sequence of entity 1 (H), FASTA

>7CQ4_1 DNA (5'-D(*GP*GP*AP*TP*TP*AP*CP*AP*AP*CP*AP*GP*AP*T)-3') (chains H)
GGATTACAACAGAT

Sequence of entity 2 (K), FASTA

>7CQ4_2 DNA (5'-D(*AP*GP*GP*AP*CP*AP*TP*CP*TP*TP*TP*GP*CP*C)-3') (chains K)
AGGACATCTTTGCC

Sequence of entity 3 (L), FASTA

>7CQ4_3 DNA (27-MER) (chains L)
CGGCAAAGATGTCCATCTGTTGTAATC

Sequence of entity 4 (A), FASTA

>7CQ4_4 Structure-specific endonuclease subunit SLX1 (chains A)
MSQKIQQHQFPDFYCCFLLQSINKRQSFYVGSTPNPVRRLRQHNGKLAVGGAYRTKRDGS
RPWEMIMIVRGFPSKIAALQFEHAWQHGYQTHYIAEKDRVVKHKAGGRTLHHKVALMKLL
LKHEFFQRMNLIVEVFNIKAWEVWKQDKFFIERDRFPINIQINENALEEPKEKTVDVLMD
HSDENLKVVEAVYTKVIENERNIFETFEKKLTTGVVRCEICEKEIDYTSEEQNLKPFVAL
CNNKDCGCVNHLKCLHRYFLDDEQLIVGRRNLIPRGGKCPKCDMFCDWTTLVKFSTRMKL
AHGK

Sequence of entity 5 (B), FASTA

>7CQ4_5 SLX4 isoform 1 (chains B)
MGSSHHHHHHSQSAASSIASPEKFCEIMMSQSMKELRQSLKTVGLKPMRTKVEIIQSLQT
ASQILSTANPDNKGEHGGVANFSKIEIFDHLTELIEAFPDFLERIYTFEPIPLNELIEKL
FSAEPFVSQIDEMTIREWADVQGICLRNDKK

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

Primary citation

Structure specific DNA recognition by the SLX1-SLX4 endonuclease complex. Xu, X., Wang, M., Sun, J. et al. Nucleic Acids Res (2021) 49:7740-7752. DOI 10.1093/nar/gkab542 · PubMed

Other PDB entries of the same protein (UniProt P38324 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7CQ3 1.45 Å, Crystal structure of Slx1-Slx4
7CQ2 2.5 Å, Crystal structure of Slx1-Slx4

Browse structure collections

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