6J0Y: Yeast Rtt107 and Slx4

Crystal Structure of Yeast Rtt107 and Slx4. Determined by X-ray diffraction at 1.8 Å resolution. Released 14 Aug 2019.

Method: X-ray diffraction
Resolution: 1.8 Å
Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains: 4
Atoms: 9,530
Mol. weight: 131.75 kDa
Released: 14 Aug 2019

Explore 6J0Y in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6J0Y contains 65 α-helices and 57 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: 32 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	8	1	1
β-strand	11-16	6	2
α-helix	19-21	3
α-helix	22-34	13
β-strand	37	1	1
β-strand	39-44	6	2
α-helix	45-47	3
α-helix	50-52	3
α-helix	57-64	8
β-strand	71-73	3	2
α-helix	82-83	2
α-helix	84-88	5
β-strand	93-94	2	2
α-helix	96-105	10
α-helix	112-114	3
β-strand	126-129	4	3
α-helix	130	1
α-helix	136-148	13
β-strand	152-154	3	3
β-strand	157	1	4
β-strand	163-165	3	3
α-helix	173-178	6
β-strand	181-182	2	5
β-strand	196-197	2	5
β-strand	203-204	2	3
α-helix	207-215	9
α-helix	221-226	6
β-strand	228	1	3
α-helix	236-247	12
α-helix	256-259	4
β-strand	270-273	4	6
α-helix	274	1
α-helix	281-293	13
β-strand	297-300	4	6
α-helix	307-313	7
β-strand	319-321	3	6
β-strand	324	1	7
α-helix	328-336	9
β-strand	341-343	3	6
α-helix	345-354	10
α-helix	360-362	3
α-helix	365-367	3
α-helix	369	1
β-strand	370	1	7
α-helix	371-373	3
β-strand	381-385	5	8
α-helix	390-402	13
β-strand	405-407	3	8
β-strand	410	1	9
β-strand	416-419	4	8
α-helix	425-434	10
α-helix	441	1
β-strand	442-444	3	8
α-helix	446-455	10
α-helix	464-466	3
α-helix	471-473	3
α-helix	475-477	3

Chain B: 27 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	11-16	6	10
α-helix	19-21	3
α-helix	22-34	13
β-strand	39-44	6	10
α-helix	45-47	3
α-helix	57-64	8
β-strand	71-73	3	10
α-helix	82-83	2
α-helix	84-88	5
β-strand	93-94	2	10
α-helix	96-105	10
α-helix	112-114	3
β-strand	126-129	4	11
α-helix	136-148	13
β-strand	152-154	3	11
β-strand	157	1	4
β-strand	163-165	3	11
α-helix	173-178	6
β-strand	181	1	12
β-strand	197	1	12
β-strand	203-204	2	11
α-helix	207-215	9
α-helix	221-226	6
β-strand	228	1	11
α-helix	236-247	12
β-strand	270-273	4	13
α-helix	281-293	13
β-strand	297-300	4	13
α-helix	307-313	7
β-strand	319-321	3	13
β-strand	324	1	14
α-helix	328-336	9
β-strand	341-343	3	13
α-helix	345-354	10
α-helix	360-362	3
α-helix	365-367	3
α-helix	369	1
β-strand	370	1	14
α-helix	371-373	3
β-strand	381-385	5	15
α-helix	390-402	13
β-strand	405-407	3	15
β-strand	410-411	2	16
β-strand	416-419	4	15
α-helix	425-434	10
β-strand	442-444	3	15
α-helix	446-455	10
α-helix	464-466	3
α-helix	471-473	3
α-helix	475-477	3

Chain C: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	537-543	7	4
α-helix	544-547	4
β-strand	550	1	5
α-helix	555	1
β-strand	556-561	6	4
β-strand	563	1	9
β-strand	578-584	7	4
α-helix	585-586	2

Chain D: 3 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	537-543	7	4
α-helix	544-546	3
α-helix	555	1
β-strand	556-561	6	4
β-strand	562-563	2	16
β-strand	578-584	7	4
α-helix	585-586	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Regulator of Ty1 transposition protein 107	A, B	protein	513	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P38850 (AlphaFold model)
Peptide from Structure-specific endonuclease subunit SLX4	C, D	protein	58	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Q12098 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6J0Y_1 Regulator of Ty1 transposition protein 107 (chains A, B)
SSTSLLFEQLNFLILVAAEAELPIAHSTRKLLMDNSCNNCQIYELYNENLKDVKTDKDWF
MNKFGPQTVHFVISNTINFPFYKIVYFDLLIPVVSHTWVQDSVKTKRHLRTNMYSPNPFH
LLRDCQVYISKSSFNKCEYILYSDLLHLLGGTLVNYISNRTTHVIVQSPQDPIIATVSKL
TFGSFSSSSTNKHTEKPLREWKFVYPIWILYHFKMAKPLKGELATLCELDMQDTSEEQLF
AKWEEVIGDKQTSSSQLTLHPNKTLFKNHHFAISPDLNFFTPLYWFLKGFIEDLDGKVTP
LSFSDDLKSVYQAFPDIDCYIGHSANSPILEKTKSIKPEIHVGNVSWLFYMFALQKFTPV
SQCKLIHQPFHAKLFTSKELTVAYTNYFGSQRFYIQRLVEILGGLSTPELTRKNTHLITK
STIGKKFKVAKKWSLDPQNAIIVTNHMWLEQCYMNNSKLNPKDSRFQNFKLDDNMGWNIG
QIGMDHSSLPTPKNLSMVTYDTQSISEKPPPTN

Sequence of entity 2 (C, D), FASTA

>6J0Y_2 Peptide from Structure-specific endonuclease subunit SLX4 (chains C, D)
GPLGSGSSIRVKLLQESVVKLNPKLVKHNFYRVEANDSEEEETEFDDQFCIADIQLVD

Primary citation

Molecular Basis for Control of Diverse Genome Stability Factors by the Multi-BRCT Scaffold Rtt107. Wan, B., Wu, J., Meng, X. et al. Mol Cell (2019) 75:238-251.e5. DOI 10.1016/j.molcel.2019.05.035 · PubMed

Other PDB entries of the same protein (UniProt P38850 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3T7K 2.03 Å, Complex structure of Rtt107p and phosphorylated histone H2A
3T7J 2.04 Å, Crystal structure of Rtt107p (residues 820-1070)
3T7I 2.3 Å, Crystal structure of Se-Met Rtt107p (residues 820-1070)
6J0X 2.31 Å, Crystal Structure of Yeast Rtt107 and Mms22
6J0V 2.31 Å, Crystal Structure of Yeast Rtt107
6J0W 2.4 Å, Crystal Structure of Yeast Rtt107 and Nse6

Browse structure collections

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