7A1G: 40S ribosomal protein S0-A

Structure of a crosslinked yeast ABCE1-bound 43S pre-initiation complex. Determined by electron microscopy at 3.0 Å resolution. Released 14 Oct 2020.

Method: Electron microscopy
Resolution: 3.0 Å
Organisms: Saccharomyces cerevisiae S288C, Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains: 37
Atoms: 81,866
Mol. weight: 1246.02 kDa
Ligands: ADP, SF4, ZN, MG
Released: 14 Oct 2020

Explore 7A1G in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7A1G contains 226 α-helices and 268 β-strands across 36 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: 2 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	61
β-strand	6-8	3	61
β-strand	16	1	62
β-strand	23	1	62
β-strand	32-39	8	63
β-strand	45-55	11	63
α-helix	57-61	5
α-helix	65-75	11

Chain A: 12 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	7-28	22
α-helix	30-32	3
β-strand	37-42	6	75
β-strand	45-52	8	75
α-helix	55-59	5
α-helix	61-63	3
α-helix	64-77	14
α-helix	79-80	2
β-strand	84-90	7	75
α-helix	94-96	3
α-helix	98-111	14
β-strand	114	1	76
α-helix	115-128	14
β-strand	131-140	10	77
β-strand	148-155	8	77
α-helix	163-167	5
β-strand	168-176	9	77
β-strand	177	1	78
β-strand	181-190	10	77
α-helix	192-194	3
β-strand	207-208	2	79
α-helix	209-213	5
β-strand	221-223	3	37

Chain b: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	6-20	15
β-strand	24-27	4	32
α-helix	32-43	12
β-strand	50-53	4	32
β-strand	60-64	5	32
β-strand	72-74	3	64
β-strand	80-81	2	64
α-helix	83-93	11
β-strand	101-106	6	64
β-strand	109-112	4	64
α-helix	113-119	7
β-strand	123-129	7	64

Chain B: 8 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	31-35	5
α-helix	83-86	4
α-helix	89-95	7
α-helix	107-124	18
α-helix	129-139	11
β-strand	144-149	6	44
β-strand	156-161	6	44
α-helix	164-182	19
α-helix	190-203	14
α-helix	209-223	15

Chain c: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	12-23	12
α-helix	28-34	7
α-helix	36-39	4
β-strand	48-57	10	65
α-helix	59	1
β-strand	60	1	66
α-helix	61	1
β-strand	68	1	66
β-strand	71-76	6	65
β-strand	82-86	5	65
α-helix	92-95	4
β-strand	101-106	6	65
β-strand	122-127	6	65
β-strand	130-131	2	65
α-helix	132-136	5

Chain C: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	5-18	14
β-strand	20-22	3	80
α-helix	39-50	12
β-strand	55-56	2	80
β-strand	65-68	4	80
α-helix	70-80	11
α-helix	82-83	2

Chain d: 6 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	7-15	9	67
β-strand	20-27	8	67
α-helix	37-48	12
β-strand	55-62	8	67
α-helix	63	1
β-strand	69-76	8	67
α-helix	79-85	7
α-helix	88-94	7
α-helix	105-116	12
α-helix	123-132	10

Chain D: 5 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	28-36	9
β-strand	41	1	81
α-helix	45-52	8
β-strand	59-63	5	81
α-helix	70-78	9
β-strand	89-91	3	81
α-helix	94-100	7
β-strand	121-123	3	81
α-helix	131-141	11

28 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
18S ribosomal RNA	2	RNA	1771	Saccharomyces cerevisiae S288C
40S ribosomal protein S0-A	P	protein	206	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P32905 (AlphaFold model)
40S ribosomal protein S1-A	Q	protein	232	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P33442 (AlphaFold model)
40S ribosomal protein S2	R	protein	216	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P25443 (AlphaFold model)
40S ribosomal protein S4-A	S	protein	258	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P0CX35 (AlphaFold model)
40S ribosomal protein S6-A	T	protein	228	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P0CX37
40S ribosomal protein S7-A	U	protein	184	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P26786
40S ribosomal protein S8-A	V	protein	200	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P0CX39
40S ribosomal protein S9-A	W	protein	184	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	O13516
40S ribosomal protein S11-A	X	protein	142	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P0CX47
40S ribosomal protein S13	Y	protein	150	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P05756
40S ribosomal protein S14-B	Z	protein	127	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P39516

24 more molecules are not listed.

Sequence of entity 1 (2), FASTA

>7A1G_1 18S ribosomal RNA (chains 2)
UAUCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCU
AAGUAUAAGCAAUUUAUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUCGUUUAU
UUGAUAGUUCCUUUACUACAUGGUAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCUUAA
AAUCUCGACCCUUUGGAAGAGAUGUAUUUAUUAGAUAAAAAAUCAAUGUCUUCGGACUCU
UUGAUGAUUCAUAAUAACUUUUCGAAUCGCAUGGCCUUGUGCUGGCGAUGGUUCAUUCAA
AUUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGUGGCCUACCAUGGUUUCAACGGGUAA
CGGGGAAUAAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGA
AGGCAGCAGGCGCGCAAAUUACCCAAUCCUAAUUCAGGGAGGUAGUGACAAUAAAUAACG
AUACAGGGCCCAUUCGGGUCUUGUAAUUGGAAUGAGUACAAUGUAAAUACCUUAACGAGG
AACAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAU
AUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGAACUUUGGGCCCGGUUGGCCGGUCGG
AUUUCCAACGGGGCCUUUCCUUCUGGCUAACCUUGAGCUUGGCGAACCAGGACUUUUACU
UUGAAAAAAUUAGAGUGUUCAAAGCAGGCGUAUUGCUCGAAUAUAUUAGCAUGGAAUAAU
AGAAUAGGACGUUUGGUUCUAUUUUGUUGGUUUCUAGGACCAUCGUAAUGAUUAAUAGGG
ACGGUCGGGGGCAUCAGUAUUCAAUUGUCAGAGGUGAAAUUCUUGGAUUUAUUGAAGACU
AACUACUGCGAAAGCAUUUGCCAAGGACGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGA
UCGAAGAUGAUCAGAUACCGUCGUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCGGG
UGGUGUUUUUUUAAUGACCCACUCGGCACCUUACGAGAAAUCAAAGUCUUUGGGUUCUGG
GGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGU
GGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUCACCAGGUCCAGACACAAUAAG
GAUUGACAGAUUGAGAGCUCUUUCUUGAUUUUGUGGGUGGUGGUGCAUGGCCGUUCUUAG
UUGGUGGAGUGAUUUGUCUGCUUAAUUGCGAUAACGAACGAGACCUUAACCUACUAAAUA
GUGGUGCUAGCAUUUGCUGGUUAUCCACUUCUUAGAGGGACUAUCGGUUUCAAGCCGAUG
GAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGACGUUCUGGGCCGCACGCGCGCU
ACACUGACGGAGCCAGCGAGUCUAACCUUGGCCGAGAGGUCUUGGUAAUCUUGUGAAACU
CCGUCGUGCUGGGGAUAGAGCAUUGUAAUUAUUGCUCUUCAACGAGGAAUUCCUAGUAAG
CGCAAGUCAUCAGCUUGCGUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUA
GUACCGAUUGAAUGGCUUAGUGAGGCCUCAGGAUCUGCUUAGAGAAGGGGGCAACUCCAU
CUCAGAGCGGAGAAUUUGGACAAACUUGGUCAUUUAGAGGAACUAAAAGUCGUAACAAGG
UUUCCGUAGGUGAACCUGCGGAAGGAUCAUU

Sequence of entity 2 (P), FASTA

>7A1G_2 40S ribosomal protein S0-A (chains P)
SLPATFDLTPEDAQLLLAANTHLGARNVQVHQEPYVFNARPDGVHVINVGKTWEKLVLAA
RIIAAIPNPEDVVAISSRTFGQRAVLKFAAHTGATPIAGRFTPGSFTNYITRSFKEPRLV
IVTDPRSDAQAIKEASYVNIPVIALTDLDSPSEFVDVAIPCNNRGKHSIGLIWYLLAREV
LRLRGALVDRTQPWSIMPDLYFYRDP

Sequence of entity 3 (Q), FASTA

>7A1G_3 40S ribosomal protein S1-A (chains Q)
AVGKNKRLSKGKKGQKKRVVDPFTRKEWFDIKAPSTFENRNVGKTLVNKSTGLKSASDAL
KGRVVEVCLADLQGSEDHSFRKIKLRVDEVQGKNLLTNFHGMDFTTDKLRSMVRKWQTLI
EANVTVKTSDDYVLRIFAIAFTRKQANQVKRHSYAQSSHIRAIRKVISEILTKEVQGSTL
AQLTSKLIPEVINKEIENATKDIFPLQNIHVRKVKLLKQPKFDVGALMALHG

Sequence of entity 4 (R), FASTA

>7A1G_4 40S ribosomal protein S2 (chains R)
GWVPVTKLGRLVKAGKITTIEEIFLHSLPVKEFQIIDTLLPGLQDEVMNIKPVQKQTRAG
QRTRFKAVVVVGDSNGHVGLGIKTAKEVAGAIRAGIIIAKLSVIPIRRGYWGTNLGQPHS
LATKTTGKCGSVTVRLIPAPRGSGIVASPAVKKLLQLAGVEDVYTQSNGKTRTLENTLKA
AFVAIGNTYGFLTPNLWAEQPLPVSPLDIYSDEASA

Sequence of entity 5 (S), FASTA

>7A1G_5 40S ribosomal protein S4-A (chains S)
ARGPKKHLKRLAAPHHWLLDKLSGCYAPRPSAGPHKLRESLPLIVFLRNRLKYALNGREV
KAILMQRHVKVDGKVRTDTTYPAGFMDVITLDATNENFRLVYDVKGRFAVHRITDEEASY
KLGKVKKVQLGKKGVPYVVTHDGRTIRYPDPNIKVNDTVKIDLASGKITDFIKFDAGKLV
YVTGGRNLGRIGTIVHKERHDGGFDLVHIKDSLDNTFVTRLNNVFVIGEQGKPYISLPKG
KGIKLSIAEERDRRRAQQ

Sequence of entity 6 (T), FASTA

>7A1G_6 40S ribosomal protein S6-A (chains T)
MKLNISYPVNGSQKTFEIDDEHRIRVFFDKRIGQEVDGEAVGDEFKGYVFKISGGNDKQG
FPMKQGVLLPTRIKLLLTKNVSCYRPRRDGERKRKSVRGAIVGPDLAVLALVIVKKGEQE
LEGLTDTTVPKRLGPKRANNIRKFFGLSKEDDVRDFVIRREVTKGEKTYTKAPKIQRLVT
PQRLQRKRHQRALKVRNAQAQREAAAEYAQLLAKRLSERKAEKAEIRK

Sequence of entity 7 (U), FASTA

>7A1G_7 40S ribosomal protein S7-A (chains U)
PQAKILSQAPTELELQVAQAFVELENSSPELKAELRPLQFKSIREIDVAGGKKALAIFVP
VPSLAGFHKVQTKLTRELEKKFQDRHVIFLAERRILPKPSRTSRQVQKRPRSRTLTAVHD
KILEDLVFPTEIVGKRVRYLVGGNKIQKVLLDSKDVQQIDYKLESFQAVYNKLTGKQIVF
EIPS

Sequence of entity 8 (V), FASTA

>7A1G_8 40S ribosomal protein S8-A (chains V)
MGISRDSRHKRSATGAKRAQFRKKRKFELGRQPANTKIGAKRIHSVRTRGGNKKYRALRI
ETGNFSWASEGISKKTRIAGVVYHPSNNELVRTNTLTKAAIVQIDATPFRQWFEAHYGQT
LGKKKNVKEEETVAKSKNAERKWAARAASAKIESSVESQFSAGRLYACISSRPGQSGRCD
GYILEGEELAFYLRRLTAKK

Sequence of entity 9 (W), FASTA

>7A1G_9 40S ribosomal protein S9-A (chains W)
PRAPRTYSKTYSTPKRPYESSRLDAELKLAGEFGLKNKKEIYRISFQLSKIRRAARDLLT
RDEKDPKRLFEGNALIRRLVRVGVLSEDKKKLDYVLALKVEDFLERRLQTQVYKLGLAKS
VHHARVLITQRHIAVGKQIVNIPSFMVRLDSEKHIDFAPTSPFGGARPGRVARRNAARKA
EASG

Sequence of entity 10 (X), FASTA

>7A1G_10 40S ribosomal protein S11-A (chains X)
ELTVQSERAFQKQPHIFNNPKVKTSKRTKRWYKNAGLGFKTPKTAIEGSYIDKKCPFTGL
VSIRGKILTGTVVSTKMHRTIVIRRAYLHYIPKYNRYEKRHKNVPVHVSPAFRVQVGDIV
TVGQCRPISKTVRFNVVKVSAA

Sequence of entity 11 (Y), FASTA

>7A1G_11 40S ribosomal protein S13 (chains Y)
GRMHSAGKGISSSAIPYSRNAPAWFKLSSESVIEQIVKYARKGLTPSQIGVLLRDAHGVT
QARVITGNKIMRILKSNGLAPEIPEDLYYLIKKAVSVRKHLERNRKDKDAKFRLILIESR
IHRLARYYRTVAVLPPNWKYESATASALVN

Sequence of entity 12 (Z), FASTA

>7A1G_12 40S ribosomal protein S14-B (chains Z)
SQVFGVARIYASFNDTFVHVTDLSGKETIARVTGGMKVKADRDESSPYAAMLAAQDVAAK
CKEVGITAVHVKIRATGGTRTKTPGPGGQAALRALARSGLRIGRIEDVTPVPSDSTRKKG
GRRGRRL

Ligands and cofactors

ID	Name	Formula	Copies
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	1
SF4	Iron/sulfur cluster	Fe4 S4	2
ZN	Zinc ion	Zn	2
MG	Magnesium ion	Mg	80

Primary citation

A structural inventory of native ribosomal ABCE1-43S pre-initiation complexes. Kratzat, H., Mackens-Kiani, T., Ameismeier, M. et al. EMBO J (2021) 40:e105179-e105179. DOI 10.15252/embj.2020105179 · 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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