5DGF: 40S ribosomal protein S0-A

Name: PDB 5DGF: Complex of yeast 80S ribosome with hypusine-containing/non-modified eIF5A and/or a peptidyl-tRNA analog
Published: 2016-12-14
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Complex of yeast 80S ribosome with hypusine-containing/non-modified eIF5A and/or a peptidyl-tRNA analog. Determined by X-ray diffraction at 3.3 Å resolution. Released 14 Dec 2016.

Method: X-ray diffraction
Resolution: 3.3 Å
Organism: Saccharomyces cerevisiae S288c
Chains: 165
Atoms: 404,292
Mol. weight: 6286.47 kDa
Ligands: ZN, SPS, MG, OHX
Released: 14 Dec 2016

Explore 5DGF in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5DGF contains 953 α-helices and 1,092 β-strands across 155 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 c0: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	5-12	8
α-helix	14-17	4
β-strand	20-21	2	190
α-helix	39-50	12
β-strand	51	1	191
β-strand	53	1	191
β-strand	55-59	5	190
β-strand	64-68	5	190
α-helix	70-76	7

Chain C0: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	5-18	14
β-strand	21-24	4	179
α-helix	39-51	13
β-strand	55-58	4	179
β-strand	63-68	6	179
α-helix	70-79	10
α-helix	82-83	2

Chain c1: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	43-45	3
α-helix	46-49	4
β-strand	72-77	6	199
β-strand	84-94	11	199
α-helix	95-97	3
β-strand	99-110	12	199
β-strand	119	1	200
β-strand	121	1	200
β-strand	122-127	6	199
β-strand	137-143	7	199

Chain C1: 1 helix, 5 β-strands

Element	Residues	Length	Sheet
α-helix	46-50	5
β-strand	70-77	8	185
β-strand	83-94	12	185
β-strand	99-110	12	185
β-strand	123-127	5	185
β-strand	137-142	6	185

Chain c2: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	31-33	3
β-strand	41-43	3	217
α-helix	46-52	7
β-strand	60-62	3	217
α-helix	70-79	10
α-helix	94-99	6
β-strand	120-123	4	217
α-helix	131-133	3
α-helix	135-139	5

Chain C2: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	27-36	10
β-strand	41-43	3	193
α-helix	45-53	9
β-strand	59-61	3	193
α-helix	70-79	10
α-helix	94-99	6
β-strand	121-123	3	193
α-helix	131-140	10

Chain c3: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	30-42	13
α-helix	47-56	10
α-helix	64-67	4
α-helix	71-78	8
α-helix	86-102	17
α-helix	109-131	23
α-helix	148-150	3

Chain C3: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	30-43	14
α-helix	47-56	10
α-helix	71-77	7
α-helix	86-104	19
α-helix	109-131	23
α-helix	143-149	7

146 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, 6	RNA	1800	Saccharomyces cerevisiae S288c
40S ribosomal protein S0-A	S0, s0	protein	251	Saccharomyces cerevisiae S288c	P32905 (AlphaFold model)
40S ribosomal protein S1-A	S1, s1	protein	254	Saccharomyces cerevisiae S288c	P33442 (AlphaFold model)
40S ribosomal protein S2	S2, s2	protein	253	Saccharomyces cerevisiae S288c	P25443 (AlphaFold model)
40S ribosomal protein S3	S3, s3	protein	239	Saccharomyces cerevisiae S288c	P05750 (AlphaFold model)
40S ribosomal protein S4-A	S4, s4	protein	260	Saccharomyces cerevisiae S288c	P0CX35
40S ribosomal protein S5	S5, s5	protein	224	Saccharomyces cerevisiae S288c	P26783
40S ribosomal protein S6-A	S6, s6	protein	236	Saccharomyces cerevisiae S288c	P0CX37
40S ribosomal protein S7-A	S7, s7	protein	189	Saccharomyces cerevisiae S288c	P26786
40S ribosomal protein S8-A	S8, s8	protein	200	Saccharomyces cerevisiae S288c	P0CX39
40S ribosomal protein S9-A	S9, s9	protein	196	Saccharomyces cerevisiae S288c	O13516
40S ribosomal protein S10-A	C0, c0	protein	96	Saccharomyces cerevisiae S288c	Q08745

72 more molecules are not listed.

Sequence of entity 1 (2, 6), FASTA

>5DGF_1 18S ribosomal RNA (chains 2, 6)
UAUCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCU
AAGUAUAAGCAAUUUAUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUCGUUUAU
UUGAUAGUUCCUUUACUACAUGGUAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCUUAA
AAUCUCGACCCUUUGGAAGAGAUGUAUUUAUUAGAUAAAAAAUCAAUGUCUUCGGACUCU
UUGAUGAUUCAUAAUAACUUUUCGAAUCGCAUGGCCUUGUGCUGGCGAUGGUUCAUUCAA
AUUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGUGGCCUACCAUGGUUUCAACGGGUAA
CGGGGAAUAAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGA
AGGCAGCAGGCGCGCAAAUUACCCAAUCCUAAUUCAGGGAGGUAGUGACAAUAAAUAACG
AUACAGGGCCCAUUCGGGUCUUGUAAUUGGAAUGAGUACAAUGUAAAUACCUUAACGAGG
AACAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAU
AUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGAACUUUGGGCCCGGUUGGCCGGUCCG
AUUUUUUCGUGUACUGGAUUUCCAACGGGGCCUUUCCUUCUGGCUAACCUUGAGUCCUUG
UGGCUCUUGGCGAACCAGGACUUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCGUA
UUGCUCGAAUAUAUUAGCAUGGAAUAAUAGAAUAGGACGUUUGGUUCUAUUUUGUUGGUU
UCUAGGACCAUCGUAAUGAUUAAUAGGGACGGUCGGGGGCAUCAGUAUUCAAUUGUCAGA
GGUGAAAUUCUUGGAUUUAUUGAAGACUAACUACUGCGAAAGCAUUUGCCAAGGACGUUU
UCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGAUGAUCAGAUACCGUCGUAGUCUUAA
CCAUAAACUAUGCCGACUAGGGAUCGGGUGGUGUUUUUUUAAUGACCCACUCGGCACCUU
ACGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAG
GAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGG
GAAACUCACCAGGUCCAGACACAAUAAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUUU
GUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGCUUAAUUGCGAU
AACGAACGAGACCUUAACCUACUAAAUAGUGGUGCUAGCAUUUGCUGGUUAUCCACUUCU
UAGAGGGACUAUCGGUUUCAAGCCGAUGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCC
CUUAGACGUUCUGGGCCGCACGCGCGCUACACUGACGGAGCCAGCGAGUCUAACCUUGGC
CGAGAGGUCUUGGUAAUCUUGUGAAACUCCGUCGUGCUGGGGAUAGAGCAUUGUAAUUAU
UGCUCUUCAACGAGGAAUUCCUAGUAAGCGCAAGUCAUCAGCUUGCGUUGAUUACGUCCC
UGCCCUUUGUACACACCGCCCGUCGCUAGUACCGAUUGAAUGGCUUAGUGAGGCCUCAGG
AUCUGCUUAGAGAAGGGGGCAACUCCAUCUCAGAGCGGAGAAUUUGGACAAACUUGGUCA
UUUAGAGGAACUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA

Sequence of entity 2 (S0, s0), FASTA

>5DGF_2 40S ribosomal protein S0-A (chains S0, s0)
SLPATFDLTPEDAQLLLAANTHLGARNVQVHQEPYVFNARPDGVHVINVGKTWEKLVLAA
RIIAAIPNPEDVVAISSRTFGQRAVLKFAAHTGATPIAGRFTPGSFTNYITRSFKEPRLV
IVTDPRSDAQAIKEASYVNIPVIALTDLDSPSEFVDVAIPCNNRGKHSIGLIWYLLAREV
LRLRGALVDRTQPWSIMPDLYFYRDPEEVEQQVAEEATTEEAGEEEAKEEVTEEQAEATE
WAEENADNVEW

Sequence of entity 3 (S1, s1), FASTA

>5DGF_3 40S ribosomal protein S1-A (chains S1, s1)
AVGKNKRLSKGKKGQKKRVVDPFTRKEWFDIKAPSTFENRNVGKTLVNKSTGLKSASDAL
KGRVVEVCLADLQGSEDHSFRKIKLRVDEVQGKNLLTNFHGMDFTTDKLRSMVRKWQTLI
EANVTVKTSDDYVLRIFAIAFTRKQANQVKRHSYAQSSHIRAIRKVISEILTKEVQGSTL
AQLTSKLIPEVINKEIENATKDIFPLQNIHVRKVKLLKQPKFDVGALMALHGEGSGEEKG
KKVTGFKDEVLETV

Sequence of entity 4 (S2, s2), FASTA

>5DGF_4 40S ribosomal protein S2 (chains S2, s2)
SAPEAQQQKRGGFGGRNRGRPNRRGPRNTEEKGWVPVTKLGRLVKAGKITTIEEIFLHSL
PVKEFQIIDTLLPGLQDEVMNIKPVQKQTRAGQRTRFKAVVVVGDSNGHVGLGIKTAKEV
AGAIRAGIIIAKLSVIPIRRGYWGTNLGQPHSLATKTTGKCGSVTVRLIPAPRGSGIVAS
PAVKKLLQLAGVEDVYTQSNGKTRTLENTLKAAFVAIGNTYGFLTPNLWAEQPLPVSPLD
IYSDEASAQKKRF

Sequence of entity 5 (S3, s3), FASTA

>5DGF_5 40S ribosomal protein S3 (chains S3, s3)
VALISKKRKLVADGVFYAELNEFFTRELAEEGYSGVEVRVTPTKTEVIIRATRTQDVLGE
NGRRINELTLLVQKRFKYAPGTIVLYAERVQDRGLSAVAQAESMKFKLLNGLAIRRAAYG
VVRYVMESGAKGCEVVVSGKLRAARAKAMKFADGFLIHSGQPVNDFIDTATRHVLMRQGV
LGIKVKIMRDPAKSRTGPKALPDAVTIIEPKEEEPILAPSVKDYRPAEETEAQAEPVEA

Sequence of entity 6 (S4, s4), FASTA

>5DGF_6 40S ribosomal protein S4-A (chains S4, s4)
ARGPKKHLKRLAAPHHWLLDKLSGCYAPRPSAGPHKLRESLPLIVFLRNRLKYALNGREV
KAILMQRHVKVDGKVRTDTTYPAGFMDVITLDATNENFRLVYDVKGRFAVHRITDEEASY
KLGKVKKVQLGKKGVPYVVTHDGRTIRYPDPNIKVNDTVKIDLASGKITDFIKFDAGKLV
YVTGGRNLGRIGTIVHKERHDGGFDLVHIKDSLDNTFVTRLNNVFVIGEQGKPYISLPKG
KGIKLSIAEERDRRRAQQGL

Sequence of entity 7 (S5, s5), FASTA

>5DGF_7 40S ribosomal protein S5 (chains S5, s5)
SDTEAPVEVQEDFEVVEEFTPVVLATPIPEEVQQAQTEIKLFNKWSFEEVEVKDASLVDY
VQVRQPIFVAHTAGRYANKRFRKAQCPIIERLTNSLMMNGRNNGKKLKAVRIIKHTLDII
NVLTDQNPIQVVVDAITNTGPREDTTRVGGGGAARRQAVDVSPLRRVNQAIALLTIGARE
AAFRNIKTIAETLAEELINAAKGSSTSYAIKKKDELERVAKSNR

Sequence of entity 8 (S6, s6), FASTA

>5DGF_8 40S ribosomal protein S6-A (chains S6, s6)
MKLNISYPVNGSQKTFEIDDEHRIRVFFDKRIGQEVDGEAVGDEFKGYVFKISGGNDKQG
FPMKQGVLLPTRIKLLLTKNVSCYRPRRDGERKRKSVRGAIVGPDLAVLALVIVKKGEQE
LEGLTDTTVPKRLGPKRANNIRKFFGLSKEDDVRDFVIRREVTKGEKTYTKAPKIQRLVT
PQRLQRKRHQRALKVRNAQAQREAAAEYAQLLAKRLSERKAEKAEIRKRRASSLKA

Sequence of entity 9 (S7, s7), FASTA

>5DGF_9 40S ribosomal protein S7-A (chains S7, s7)
SAPQAKILSQAPTELELQVAQAFVELENSSPELKAELRPLQFKSIREIDVAGGKKALAIF
VPVPSLAGFHKVQTKLTRELEKKFQDRHVIFLAERRILPKPSRTSRQVQKRPRSRTLTAV
HDKILEDLVFPTEIVGKRVRYLVGGNKIQKVLLDSKDVQQIDYKLESFQAVYNKLTGKQI
VFEIPSETH

Sequence of entity 10 (S8, s8), FASTA

>5DGF_10 40S ribosomal protein S8-A (chains S8, s8)
MGISRDSRHKRSATGAKRAQFRKKRKFELGRQPANTKIGAKRIHSVRTRGGNKKYRALRI
ETGNFSWASEGISKKTRIAGVVYHPSNNELVRTNTLTKAAIVQIDATPFRQWFEAHYGQT
LGKKKNVKEEETVAKSKNAERKWAARAASAKIESSVESQFSAGRLYACISSRPGQSGRCD
GYILEGEELAFYLRRLTAKK

Sequence of entity 11 (S9, s9), FASTA

>5DGF_11 40S ribosomal protein S9-A (chains S9, s9)
PRAPRTYSKTYSTPKRPYESSRLDAELKLAGEFGLKNKKEIYRISFQLSKIRRAARDLLT
RDEKDPKRLFEGNALIRRLVRVGVLSEDKKKLDYVLALKVEDFLERRLQTQVYKLGLAKS
VHHARVLITQRHIAVGKQIVNIPSFMVRLDSEKHIDFAPTSPFGGARPGRVARRNAARKA
EASGEAADEADEADEE

Sequence of entity 12 (C0, c0), FASTA

>5DGF_12 40S ribosomal protein S10-A (chains C0, c0)
MLMPKEDRNKIHQYLFQEGVVVAKKDFNQAKHEEIDTKNLYVIKALQSLTSKGYVKTQFS
WQYYYYTLTEEGVEYLREYLNLPXXXXXXXXXXXXX

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	16
SPS	Sparsomycin	C13 H19 N3 O5 S2	2
MG	Magnesium ion	Mg	12
OHX	osmium (III) hexammine	H12 N6 Os	3

Primary citation

Coping with proline stalling: structural basis of hypusine-induced protein synthesis by the eukaryotic ribosome. Melnikov, S., Mailliot, J., Shin, B.-S. et al. To be published.

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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