6LYV: SAUGI/KSHVUDG complex

The crystal structure of SAUGI/KSHVUDG complex. Determined by X-ray diffraction at 2.7 Å resolution. Released 24 Jun 2020.

Method: X-ray diffraction
Resolution: 2.7 Å
Organisms: Human herpesvirus 8, Staphylococcus aureus
Chains: 16
Atoms: 22,519
Mol. weight: 339.3 kDa
Released: 24 Jun 2020

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

Secondary structure: helices and β-sheets

6LYV contains 160 α-helices and 106 β-strands across 16 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.

Chains A and C: 15 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	5-8	4
α-helix	12-18	7
α-helix	22-41	20
β-strand	44-45	2	1
α-helix	48-50	3
α-helix	53-57	5
α-helix	60-62	3
β-strand	65-69	5	2
α-helix	90-92	3
α-helix	93-105	13
α-helix	118-122	5
β-strand	125-129	5	2
β-strand	134-135	2	1
β-strand	138	1	1
α-helix	148-161	14
β-strand	166-170	5	2
α-helix	171-175	5
α-helix	178-180	3
β-strand	187-191	5	2
α-helix	196-198	3
α-helix	215-225	11
α-helix	229-231	3

Chains B and P: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	2-15	14
α-helix	21-23	3
β-strand	24-31	8	3
α-helix	32-35	4
α-helix	38-43	6
β-strand	50-57	8	3
α-helix	59-63	5
β-strand	67-73	7	3
β-strand	76-83	8	3
β-strand	89-94	6	3

Chain D: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	2-15	14
α-helix	21-23	3
β-strand	24-31	8	6
α-helix	32-34	3
α-helix	38-43	6
β-strand	50-57	8	6
α-helix	59-63	5
β-strand	67-73	7	6
β-strand	76-83	8	6
β-strand	89-94	6	6

Chain E: 15 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	5-8	4
α-helix	12-18	7
α-helix	22-41	20
β-strand	44-45	2	7
α-helix	48-50	3
α-helix	53-57	5
α-helix	60-62	3
β-strand	65-69	5	8
α-helix	90-92	3
α-helix	93-105	13
α-helix	118-123	6
β-strand	125-129	5	8
β-strand	134-135	2	7
β-strand	138	1	7
α-helix	148-161	14
β-strand	166-170	5	8
α-helix	171-175	5
α-helix	178-180	3
β-strand	187-191	5	8
α-helix	196-198	3
α-helix	215-225	11
α-helix	229-231	3

Chain F: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	3-15	13
α-helix	22-23	2
β-strand	24-31	8	9
α-helix	32-34	3
α-helix	38-43	6
β-strand	50-57	8	9
α-helix	59-63	5
β-strand	67-73	7	9
β-strand	76-83	8	9
β-strand	89-94	6	9

Chains G, K and M: 15 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	6-8	3
α-helix	12-18	7
α-helix	22-41	20
β-strand	44-45	2	10
α-helix	48-50	3
α-helix	53-57	5
α-helix	60-62	3
β-strand	65-69	5	11
β-strand	78	1	12
β-strand	85	1	12
α-helix	90-92	3
α-helix	93-105	13
α-helix	118-122	5
β-strand	125-129	5	11
β-strand	134-135	2	10
β-strand	138	1	10
α-helix	148-161	14
β-strand	166-170	5	11
α-helix	171-175	5
α-helix	178-180	3
β-strand	187-191	5	11
α-helix	196-198	3
α-helix	215-225	11
α-helix	229-231	3

Chains H and N: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	3-14	12
α-helix	22-23	2
β-strand	24-31	8	13
α-helix	32-35	4
α-helix	38-43	6
β-strand	50-57	8	13
α-helix	59-63	5
β-strand	67-73	7	13
β-strand	76-83	8	13
β-strand	89-94	6	13

Chains I and O: 15 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	5-8	4
α-helix	12-18	7
α-helix	22-41	20
β-strand	44-45	2	14
α-helix	48-50	3
α-helix	53-57	5
α-helix	60-62	3
β-strand	65-69	5	15
β-strand	78	1	16
β-strand	85	1	16
α-helix	90-92	3
α-helix	93-105	13
α-helix	118-122	5
β-strand	125-129	5	15
β-strand	134-135	2	14
β-strand	138	1	14
α-helix	148-161	14
β-strand	166-170	5	15
α-helix	171-175	5
α-helix	178-180	3
β-strand	187-191	5	15
α-helix	196-198	3
α-helix	215-225	11
α-helix	229-231	3

2 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Uracil-DNA glycosylase	A, C, E, G, I, K, M, O	protein	255	Human herpesvirus 8	F5HFA1 (AlphaFold model)
Saugi	B, D, F, H, J, L, N, P	protein	112	Staphylococcus aureus	Q936H5 (AlphaFold model)

Sequence of entity 1 (A, C, E, G, I, K, M, O), FASTA

>6LYV_1 Uracil-DNA glycosylase (chains A, C, E, G, I, K, M, O)
MDAWLQQTVFRGTLSISQGVDDRDLLLAPKWISFLSLSSFLKQKLLSLLRQIRELRLTTT
VYPPQDKLMWWSHCCDPEDIKVVILGQDPYHKGQATGLAFSVDPQCQVPPSLRSIFRELE
ASVPNFSTPSHGCLDSWARQGVLLLNTVLTVEKGRAGSHEGLGWDWFTSFIISSISSKLE
HCVFLLWGRKAIDRTPLINAQKHLVLTAQHPSPLASLGGRHSRWPRFQGCNHFNLANDYL
TRHRRETVDWGLLEQ

Sequence of entity 2 (B, D, F, H, J, L, N, P), FASTA

>6LYV_2 SAUGI (chains B, D, F, H, J, L, N, P)
MTLELQLKHYITNLFNLPKDEKWECESIEEIADDILPDQYVRLGALSNKILQTYTYYSDT
LHESNIYPFILYYQKQLIAIGYIDENHDMDFLYLHNTIMPLLDQRYLLTGGQ

Primary citation

Structural insight into the differential interactions between the DNA mimic protein SAUGI and two gamma herpesvirus uracil-DNA glycosylases. Liao, Y.T., Lin, S.J., Ko, T.P. et al. Int J Biol Macromol (2020) 160:903-914. DOI 10.1016/j.ijbiomac.2020.05.267 · PubMed

Other PDB entries of the same protein (UniProt F5HFA1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5NNH 2.2 Å, KSHV uracil-DNA glycosylase, apo form
5NN7 2.5 Å, KSHV uracil-DNA glycosylase, apo form
5NNU 2.97 Å, KSHV uracil-DNA glycosylase, product complex with dsDNA exhibiting duplex nucleotide…

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