7AM1: Yeast Ssd1, a pseudonuclease

Structure of yeast Ssd1, a pseudonuclease. Determined by X-ray diffraction at 1.9 Å resolution. Released 11 Aug 2021.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Saccharomyces cerevisiae S288C
Chains: 2
Atoms: 13,015
Mol. weight: 207.61 kDa
Released: 11 Aug 2021

Explore 7AM1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7AM1 contains 72 α-helices and 76 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: 36 helices, 38 β-strands

Element	Residues	Length	Sheet
α-helix	341-346	6
α-helix	349-356	8
β-strand	360-366	7	1
β-strand	373-377	5	1
α-helix	385	1
β-strand	386-389	4	1
α-helix	390-394	5
β-strand	402-407	6	1
α-helix	410-413	4
β-strand	501-502	2	2
α-helix	509-520	12
β-strand	540-548	9	1
β-strand	555-560	6	3
β-strand	581-586	6	3
β-strand	594-597	4	3
α-helix	603-605	3
α-helix	609-612	4
β-strand	615-623	9	3
β-strand	632-641	10	3
α-helix	645-655	11
β-strand	664	1	4
β-strand	672	1	4
α-helix	678-682	5
α-helix	683-688	6
β-strand	690-692	3	5
β-strand	701-704	4	5
β-strand	712-718	7	5
β-strand	723-731	9	5
α-helix	733-736	4
α-helix	742-750	9
β-strand	752	1	6
β-strand	754-755	2	7
β-strand	760-761	2	7
α-helix	766-772	7
β-strand	780-790	11	5
β-strand	796-806	11	5
β-strand	810-813	4	5
α-helix	814-822	9
α-helix	829-844	16
α-helix	857-863	7
α-helix	878-902	25
α-helix	903-905	3
β-strand	907-910	4	8
β-strand	911	1	9
α-helix	912-915	4
α-helix	916-929	14
α-helix	938-946	9
α-helix	951-963	13
α-helix	966-968	3
β-strand	969-972	4	8
α-helix	973-975	3
α-helix	978-980	3
β-strand	983	1	9
α-helix	984-986	3
β-strand	988	1	9
β-strand	1000	1	6
α-helix	1002-1015	14
α-helix	1023-1059	37
β-strand	1066-1075	10	10
β-strand	1079-1084	6	10
β-strand	1089-1094	6	10
α-helix	1095-1097	3
β-strand	1100-1106	7	2
β-strand	1111-1116	6	2
α-helix	1128-1130	3
α-helix	1136-1139	4
α-helix	1148-1161	14
α-helix	1168-1176	9
α-helix	1181-1184	4
α-helix	1196-1201	6
β-strand	1206-1209	4	2
β-strand	1212-1218	7	2
β-strand	1222-1230	9	10
β-strand	1237-1242	6	10

Chain B: 36 helices, 38 β-strands

Element	Residues	Length	Sheet
α-helix	341-346	6
α-helix	347-349	3
α-helix	350-356	7
β-strand	360-366	7	11
β-strand	374-377	4	11
α-helix	385	1
β-strand	386-388	3	11
α-helix	390-394	5
β-strand	402-408	7	11
α-helix	410-415	6
β-strand	501-502	2	12
α-helix	509-520	12
β-strand	539-548	10	11
β-strand	555-560	6	13
β-strand	581-586	6	13
β-strand	594-597	4	13
α-helix	598-600	3
α-helix	609-612	4
β-strand	615-623	9	13
β-strand	632-641	10	13
α-helix	645-655	11
β-strand	664	1	14
β-strand	672	1	14
α-helix	678-682	5
α-helix	683-688	6
β-strand	690-692	3	15
β-strand	701-704	4	15
β-strand	712-718	7	15
β-strand	723-731	9	15
α-helix	733-736	4
α-helix	742-750	9
β-strand	752	1	16
β-strand	754-755	2	17
β-strand	760-761	2	17
α-helix	766-772	7
β-strand	780-790	11	15
β-strand	796-806	11	15
β-strand	810-813	4	15
α-helix	814-822	9
α-helix	829-844	16
α-helix	857-863	7
α-helix	878-902	25
α-helix	903-905	3
β-strand	907-910	4	18
β-strand	911	1	19
α-helix	912-915	4
α-helix	916-929	14
α-helix	938-946	9
α-helix	951-962	12
α-helix	966-968	3
β-strand	969-972	4	18
α-helix	973-975	3
α-helix	978-980	3
β-strand	983	1	19
β-strand	988	1	19
β-strand	1000	1	16
α-helix	1002-1014	13
α-helix	1023-1059	37
β-strand	1066-1075	10	20
β-strand	1079-1084	6	20
β-strand	1089-1094	6	20
α-helix	1095-1097	3
β-strand	1100-1106	7	12
β-strand	1111-1116	6	12
α-helix	1128-1130	3
α-helix	1136-1139	4
α-helix	1148-1160	13
α-helix	1168-1176	9
α-helix	1181-1184	4
α-helix	1196-1201	6
β-strand	1206-1209	4	12
β-strand	1212-1218	7	12
β-strand	1222-1230	9	20
β-strand	1237-1242	6	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein SSD1	A, B	protein	916	Saccharomyces cerevisiae S288C	P24276 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>7AM1_1 Protein SSD1 (chains A, B)
GPDSSLFAPYLPQANIPELIQEGRLVAGILRVNKKNRSDAWVSTDGALDADIYICGSKDR
NRALEGDLVAVELLVVDDVWESKKEKEEKKRRKDASMQHDLIPLNSSDDYHNDASVTAAT
SNNFLSSPSSSDSLSKDDLSVRRKRSSTINNDSDSLSSPTKSGVRRRSSLKQRPTQKKND
DVEVEGQSLLLVEEEEINDKYKPLYAGHVVAVLDRIPGQLFSGTLGLLRPSQQANSDNNK
PPQSPKIAWFKPTDKKVPLIAIPTELAPKDFVENADKYSEKLFVASIKRWPITSLHPFGI
LVSELGDIHDPDTEIDSILRDNNFLSNEYLDQKNPQKEKPSFQPLPLTAESLEYRRNFTD
TNEYNIFAISELGWVSEFALHVRNNGNGTLELGCHVVDVTSHIEEGSSVDRRARKRSSAV
FMPQKLVNLLPQSFNDELSLAPGKESATLSVVYTLDSSTLRIKSTWVGESTISPSNILSL
EQLDEKLSTGSPTSYLSTVQEIARSFYARRINDPEATLLPTLSLLESLDDEKVKVDLNIL
DRTLGFVVINEIKRKVNSTVAEKIYTKLGDLALLRRQMQPIATKMASFRKKIQNFGYNFD
TNTADELIKGVLKIKDDDVRVGIEILLFKTMPRARYFIAGKVDPDQYGHYALNLPIYTHF
TAPMRRYADHVVHRQLKAVIHDTPYTEDMEALKITSEYCNFKKDCAYQAQEQAIHLLLCK
TINDMGNTTGQLLTMATVLQVYESSFDVFIPEFGIEKRVHGDQLPLIKAEFDGTNRVLEL
HWQPGVDSATFIPADEKNPKSYRNSIKNKFRSTAAEIANIELDKEAESEPLISDPLSKEL
SDLHLTVPNLRLPSASDNKQNALEKFISTTETRIENDNYIQEIHELQKIPILLRAEVGMA
LPCLTVRALNPFMKRV

Primary citation

Yeast Ssd1 is a non-enzymatic member of the RNase II family with an alternative RNA recognition site. Bayne, R.A., Jayachandran, U., Kasprowicz, A. et al. Nucleic Acids Res (2022) 50:2923-2937. DOI 10.1093/nar/gkab615 · PubMed

Other PDB entries of the same protein (UniProt P24276 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5NCL 3.15 Å, Crystal structure of the Cbk1-Mob2 kinase-coactivator complex with an SSD1 peptide

Browse structure collections

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