8CAS: 40S ribosomal protein S0-A

Name: PDB 8CAS: Cryo-EM structure of native Otu2-bound ubiquitinated 48S initiation complex (partial)
Published: 2023-05-24
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Cryo-EM structure of native Otu2-bound ubiquitinated 48S initiation complex (partial). Determined by electron microscopy at 3.3 Å resolution. Released 24 May 2023.

Method: Electron microscopy
Resolution: 3.3 Å
Organisms: Saccharomyces cerevisiae W303, Saccharomyces cerevisiae
Chains: 50
Atoms: 86,738
Mol. weight: 1861.56 kDa
Ligands: GCP, MET, SF4, ATP
Released: 24 May 2023

Explore 8CAS in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8CAS contains 347 α-helices and 416 β-strands across 47 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: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	52
β-strand	8	1	52
α-helix	14-15	2
β-strand	16	1	53
α-helix	17	1
β-strand	23	1	53
β-strand	32-39	8	54
β-strand	45-55	11	54
α-helix	57-61	5
α-helix	65-74	10

Chain A: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	24-26	3
β-strand	33-40	8	77
β-strand	47-51	5	77
β-strand	55-61	7	77
α-helix	62	1
β-strand	76-81	6	77
α-helix	82	1
β-strand	88-95	8	77
α-helix	97-105	9

Chain b: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	6-19	14
β-strand	24-27	4	70
α-helix	32-43	12
β-strand	50-53	4	70
β-strand	60-64	5	70
β-strand	72-74	3	71
β-strand	80	1	71
α-helix	84-93	10
β-strand	101-106	6	71
β-strand	109-111	3	71
α-helix	113-119	7
β-strand	123-129	7	71

Chain B: 9 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	7-28	22
β-strand	37-42	6	98
β-strand	45-52	8	98
α-helix	55-59	5
α-helix	61-63	3
α-helix	64-76	13
β-strand	84-90	7	98
α-helix	98-111	14
α-helix	115-128	14
β-strand	133-140	8	99
β-strand	148-155	8	99
α-helix	162-167	6
β-strand	168-177	10	99
β-strand	180-189	10	99
α-helix	190-191	2
β-strand	206-208	3	100
α-helix	209-211	3
β-strand	221-223	3	25

Chain c: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	12-23	12
α-helix	27-33	7
β-strand	49-57	9	74
α-helix	59	1
β-strand	60	1	75
α-helix	61-62	2
β-strand	68	1	75
β-strand	71-76	6	74
β-strand	82-86	5	74
α-helix	93-95	3
β-strand	101-106	6	74
β-strand	122-127	6	74
β-strand	130-131	2	74
α-helix	133-136	4

Chain C: 9 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	31-38	8
β-strand	63	1	92
α-helix	83-86	4
β-strand	88	1	92
α-helix	89-96	8
α-helix	107-123	17
α-helix	129-139	11
β-strand	144-149	6	32
β-strand	156-161	6	32
α-helix	162-163	2
α-helix	164-182	19
α-helix	190-203	14
α-helix	209-223	15

Chain d: 7 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	7-15	9	76
β-strand	20-28	9	76
α-helix	37-48	12
β-strand	55-62	8	76
α-helix	63	1
β-strand	68-76	9	76
α-helix	79-85	7
α-helix	88-93	6
α-helix	99-101	3
α-helix	105-115	11
α-helix	123-133	11

Chain D: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	5-17	13
β-strand	20-22	3	101
α-helix	39-51	13
β-strand	55-58	4	101
β-strand	65-68	4	101
α-helix	70-79	10
α-helix	82-83	2

39 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
40S ribosomal protein S0-A	P	protein	252	Saccharomyces cerevisiae W303	P32905 (AlphaFold model)
40S ribosomal protein S1-A	Q	protein	255	Saccharomyces cerevisiae W303	P33442 (AlphaFold model)
40S ribosomal protein S2	R	protein	254	Saccharomyces cerevisiae W303	P25443 (AlphaFold model)
40S ribosomal protein S4-B	S	protein	261	Saccharomyces cerevisiae W303	P0CX36 (AlphaFold model)
40S ribosomal protein S6-B	T	protein	236	Saccharomyces cerevisiae W303	P0CX38
40S ribosomal protein S8-A	V	protein	200	Saccharomyces cerevisiae W303	P0CX39
40S ribosomal protein S9-A	W	protein	197	Saccharomyces cerevisiae W303	O13516
40S ribosomal protein S11-A	X	protein	156	Saccharomyces cerevisiae W303	P0CX47
40S ribosomal protein S13	Y	protein	151	Saccharomyces cerevisiae W303	P05756
40S ribosomal protein S14-A	Z	protein	137	Saccharomyces cerevisiae W303	P06367
40S ribosomal protein S21-A	a	protein	87	Saccharomyces cerevisiae W303	P0C0V8
40S ribosomal protein S22-A	b	protein	130	Saccharomyces cerevisiae W303	P0C0W1

38 more molecules are not listed.

Sequence of entity 1 (P), FASTA

>8CAS_1 40S ribosomal protein S0-A (chains P)
MSLPATFDLTPEDAQLLLAANTHLGARNVQVHQEPYVFNARPDGVHVINVGKTWEKLVLA
ARIIAAIPNPEDVVAISSRTFGQRAVLKFAAHTGATPIAGRFTPGSFTNYITRSFKEPRL
VIVTDPRSDAQAIKEASYVNIPVIALTDLDSPSEFVDVAIPCNNRGKHSIGLIWYLLARE
VLRLRGALVDRTQPWSIMPDLYFYRDPEEVEQQVAEEATTEEAGEEEAKEEVTEEQAEAT
EWAEENADNVEW

Sequence of entity 2 (Q), FASTA

>8CAS_2 40S ribosomal protein S1-A (chains Q)
MAVGKNKRLSKGKKGQKKRVVDPFTRKEWFDIKAPSTFENRNVGKTLVNKSTGLKSASDA
LKGRVVEVCLADLQGSEDHSFRKIKLRVDEVQGKNLLTNFHGMDFTTDKLRSMVRKWQTL
IEANVTVKTSDDYVLRIFAIAFTRKQANQVKRHSYAQSSHIRAIRKVISEILTKEVQGST
LAQLTSKLIPEVINKEIENATKDIFPLQNIHVRKVKLLKQPKFDVGALMALHGEGSGEEK
GKKVTGFKDEVLETV

Sequence of entity 3 (R), FASTA

>8CAS_3 40S ribosomal protein S2 (chains R)
MSAPEAQQQKRGGFGGRNRGRPNRRGPRNTEEKGWVPVTKLGRLVKAGKITTIEEIFLHS
LPVKEFQIIDTLLPGLQDEVMNIKPVQKQTRAGQRTRFKAVVVVGDSNGHVGLGIKTAKE
VAGAIRAGIIIAKLSVIPIRRGYWGTNLGQPHSLATKTTGKCGSVTVRLIPAPRGSGIVA
SPAVKKLLQLAGVEDVYTQSNGKTRTLENTLKAAFVAIGNTYGFLTPNLWAEQPLPVSPL
DIYSDEASAQKKRF

Sequence of entity 4 (S), FASTA

>8CAS_4 40S ribosomal protein S4-B (chains S)
MARGPKKHLKRLAAPHHWLLDKLSGCYAPRPSAGPHKLRESLPLIVFLRNRLKYALNGRE
VKAILMQRHVKVDGKVRTDTTYPAGFMDVITLDATNENFRLVYDVKGRFAVHRITDEEAS
YKLGKVKKVQLGKKGVPYVVTHDGRTIRYPDPNIKVNDTVKIDLASGKITDFIKFDAGKL
VYVTGGRNLGRIGTIVHKERHDGGFDLVHIKDSLDNTFVTRLNNVFVIGEQGKPYISLPK
GKGIKLSIAEERDRRRAQQGL

Sequence of entity 5 (T), FASTA

>8CAS_5 40S ribosomal protein S6-B (chains T)
MKLNISYPVNGSQKTFEIDDEHRIRVFFDKRIGQEVDGEAVGDEFKGYVFKISGGNDKQG
FPMKQGVLLPTRIKLLLTKNVSCYRPRRDGERKRKSVRGAIVGPDLAVLALVIVKKGEQE
LEGLTDTTVPKRLGPKRANNIRKFFGLSKEDDVRDFVIRREVTKGEKTYTKAPKIQRLVT
PQRLQRKRHQRALKVRNAQAQREAAAEYAQLLAKRLSERKAEKAEIRKRRASSLKA

Sequence of entity 6 (V), FASTA

>8CAS_6 40S ribosomal protein S8-A (chains V)
MGISRDSRHKRSATGAKRAQFRKKRKFELGRQPANTKIGAKRIHSVRTRGGNKKYRALRI
ETGNFSWASEGISKKTRIAGVVYHPSNNELVRTNTLTKAAIVQIDATPFRQWFEAHYGQT
LGKKKNVKEEETVAKSKNAERKWAARAASAKIESSVESQFSAGRLYACISSRPGQSGRCD
GYILEGEELAFYLRRLTAKK

Sequence of entity 7 (W), FASTA

>8CAS_7 40S ribosomal protein S9-A (chains W)
MPRAPRTYSKTYSTPKRPYESSRLDAELKLAGEFGLKNKKEIYRISFQLSKIRRAARDLL
TRDEKDPKRLFEGNALIRRLVRVGVLSEDKKKLDYVLALKVEDFLERRLQTQVYKLGLAK
SVHHARVLITQRHIAVGKQIVNIPSFMVRLDSEKHIDFAPTSPFGGARPGRVARRNAARK
AEASGEAADEADEADEE

Sequence of entity 8 (X), FASTA

>8CAS_8 40S ribosomal protein S11-A (chains X)
MSTELTVQSERAFQKQPHIFNNPKVKTSKRTKRWYKNAGLGFKTPKTAIEGSYIDKKCPF
TGLVSIRGKILTGTVVSTKMHRTIVIRRAYLHYIPKYNRYEKRHKNVPVHVSPAFRVQVG
DIVTVGQCRPISKTVRFNVVKVSAAAGKANKQFAKF

Sequence of entity 9 (Y), FASTA

>8CAS_9 40S ribosomal protein S13 (chains Y)
MGRMHSAGKGISSSAIPYSRNAPAWFKLSSESVIEQIVKYARKGLTPSQIGVLLRDAHGV
TQARVITGNKIMRILKSNGLAPEIPEDLYYLIKKAVSVRKHLERNRKDKDAKFRLILIES
RIHRLARYYRTVAVLPPNWKYESATASALVN

Sequence of entity 10 (Z), FASTA

>8CAS_10 40S ribosomal protein S14-A (chains Z)
MSNVVQARDNSQVFGVARIYASFNDTFVHVTDLSGKETIARVTGGMKVKADRDESSPYAA
MLAAQDVAAKCKEVGITAVHVKIRATGGTRTKTPGPGGQAALRALARSGLRIGRIEDVTP
VPSDSTRKKGGRRGRRL

Sequence of entity 11 (a), FASTA

>8CAS_11 40S ribosomal protein S21-A (chains a)
MENDKGQLVELYVPRKCSATNRIIKADDHASVQINVAKVDEEGRAIPGEYVTYALSGYVR
SRGESDDSLNRLAQNDGLLKNVWSYSR

Sequence of entity 12 (b), FASTA

>8CAS_12 40S ribosomal protein S22-A (chains b)
MTRSSVLADALNAINNAEKTGKRQVLIRPSSKVIIKFLQVMQKHGYIGEFEYIDDHRSGK
IVVQLNGRLNKCGVISPRFNVKIGDIEKWTANLLPARQFGYVILTTSAGIMDHEEARRKH
VSGKILGFVY

Ligands and cofactors

ID	Name	Formula	Copies
GCP	Phosphomethylphosphonic acid guanylate ester	C11 H18 N5 O13 P3	1
MET	Methionine	C5 H11 N O2 S	1
SF4	Iron/sulfur cluster	Fe4 S4	2
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	1
MG	Magnesium ion	Mg	5
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	1
ZN	Zinc ion	Zn	4

Primary citation

Molecular basis for recognition and deubiquitination of 40S ribosomes by Otu2. Ikeuchi, K., Ivic, N., Buschauer, R. et al. Nat Commun (2023) 14:2730-2730. DOI 10.1038/s41467-023-38161-w · PubMed

Other PDB entries of the same protein (UniProt P32905 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9PN5 1.75 Å, Composite map of hypomethylated 80S ribosome treated with hygromycin B
8CCS 1.97 Å, 80S S. cerevisiae ribosome with ligands in hybrid-1 pre-translocation (PRE-H1) complex
8CDR 2.04 Å, Translocation intermediate 2 (TI-2) of 80S S. cerevisiae ribosome with ligands and eEF2…
8CEH 2.05 Å, Translocation intermediate 4 (TI-4) of 80S S. cerevisiae ribosome with ligands and eEF2…
8EVT 2.2 Å, Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome…
8T2Y 2.2 Å, Hypomethylated yeast 80S bound with cycloheximide, P-site tRNA, and A-site tRNA,…
8CGN 2.28 Å, Non-rotated 80S S. cerevisiae ribosome with ligands
8ZHC 2.3 Å, pre-frameshift complex of yeast 80S ribosome with eRF1 and mRNA of WNV
8EVP 2.38 Å, Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome…
9DP7 2.38 Å, Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome…
7ZW0 2.4 Å, FAP-80S Complex - Rotated state
8BN3 2.4 Å, Yeast 80S, ES7s delta, eIF5A, Stm1 containing

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