6GSM: 40S ribosomal protein S0

Structure of a partial yeast 48S preinitiation complex in open conformation. Determined by electron microscopy at 5.15 Å resolution. Released 31 Jul 2019.

Method: Electron microscopy
Resolution: 5.15 Å
Organisms: Saccharomyces cerevisiae S288C, Kluyveromyces lactis NRRL Y-1140, Kluyveromyces lactis
Chains: 47
Atoms: 103,158
Mol. weight: 1532.96 kDa
Ligands: GCP, ZN, MG, 7NO
Released: 31 Jul 2019

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

Secondary structure: helices and β-sheets

6GSM contains 295 α-helices and 368 β-strands across 44 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: 3 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	23	1	6
β-strand	27	1	6
β-strand	36-37	2	7
α-helix	50-56	7
β-strand	72-73	2	7
α-helix	75-78	4
α-helix	89-91	3

Chain A: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	11-20	10
β-strand	37-38	2	3
β-strand	47-48	2	3
α-helix	50-66	17
β-strand	73-77	5	4
α-helix	84-92	9
β-strand	97-99	3	4
β-strand	120-123	4	4
α-helix	130-138	9
β-strand	143-145	3	4
β-strand	156-159	4	4
α-helix	167-185	19
α-helix	199-201	3

Chain b: 2 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	12-17	6
α-helix	19	1
β-strand	32-33	2	9
β-strand	46-47	2	9
β-strand	54-55	2	10
β-strand	62-65	4	10
β-strand	72-73	2	10
β-strand	81	1	9

Chain B: 9 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	27-33	7	8
β-strand	42-49	8	8
β-strand	64-69	6	8
α-helix	70-74	5
α-helix	77-79	3
β-strand	82-91	10	8
β-strand	95-105	11	8
α-helix	107-112	6
α-helix	119	1
β-strand	120-128	9	8
β-strand	134-142	9	8
α-helix	144-146	3
α-helix	158-177	20
α-helix	181-188	8
α-helix	192-200	9
β-strand	208-217	10	8
α-helix	226-231	6

Chain c: 0 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	8-19	12	15
β-strand	25-31	7	15
β-strand	39-42	4	15
β-strand	44-45	2	15
β-strand	53-56	4	15

Chain C: 7 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	45-52	8
α-helix	58-63	6
α-helix	72-77	6
β-strand	82-93	12	11
β-strand	100-110	11	11
β-strand	115-119	5	11
β-strand	123	1	11
α-helix	126-139	14
β-strand	141-143	3	11
β-strand	146-147	2	12
β-strand	158-159	2	12
β-strand	163-167	5	13
β-strand	170-175	6	13
β-strand	183	1	14
α-helix	187-196	10
β-strand	201	1	14
β-strand	202-206	5	13
α-helix	212-225	14
α-helix	244-247	4

Chain d: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	40-45	6
α-helix	47-50	4
β-strand	53	1	120

Chain D: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	7-29	23
β-strand	37-41	5	16
β-strand	46-51	6	16
α-helix	55-59	5
α-helix	66-76	11
β-strand	84-89	6	16
α-helix	98-109	12
α-helix	115-130	16
β-strand	134-141	8	17
β-strand	147-154	8	17
α-helix	162-164	3
β-strand	168-176	9	17
β-strand	181-189	9	17
α-helix	190-191	2
β-strand	208	1	18

36 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
Met-tRNAi	1	RNA	76	Saccharomyces cerevisiae S288C
18S ribosomal RNA	2	RNA	1798	Kluyveromyces lactis NRRL Y-1140
40S ribosomal protein S0	A	protein	208	Kluyveromyces lactis NRRL Y-1140	Q6CN12 (AlphaFold model)
mRNA (5'-r(papap*u)-3')	3	RNA	3	Kluyveromyces lactis
40S ribosomal protein S1	B	protein	231	Kluyveromyces lactis NRRL Y-1140	Q6CWD0 (AlphaFold model)
KLLA0F09812p	C	protein	217	Kluyveromyces lactis NRRL Y-1140	Q6CKL3 (AlphaFold model)
KLLA0D08305p	D	protein	223	Kluyveromyces lactis NRRL Y-1140	Q6CRK7 (AlphaFold model)
40S ribosomal protein S4	E	protein	260	Kluyveromyces lactis NRRL Y-1140	Q6CWJ2
KLLA0D10659p	F	protein	206	Kluyveromyces lactis NRRL Y-1140	Q6CRA3
40S ribosomal protein S6	G	protein	226	Kluyveromyces lactis NRRL Y-1140	Q6CM04
40S ribosomal protein S7	H	protein	184	Kluyveromyces lactis NRRL Y-1140	Q6CTD6
40S ribosomal protein S8	I	protein	200	Kluyveromyces lactis NRRL Y-1140	Q6CMG3

35 more molecules are not listed.

Sequence of entity 1 (1), FASTA

>6GSM_1 Met-tRNAi (chains 1)
AGCGCCGUGGCGCAGUGGAAGCGCGCAGGGCUCAUAACCCUGAUGUCCUCGGAUCGAAAC
CGAGCGGCGCUACCAX

Sequence of entity 2 (2), FASTA

>6GSM_2 18S ribosomal RNA (chains 2)
UAUCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCU
AAGUAUAAGCAAUUUAUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUCGUUUAU
UUGAUAGUUCCUUUACUACAUGGAUAUCUGUGGUAAUUCUAGAGCUAAUACAUGCUUAAA
AUCUCGACCCUUUGGAAGAGAUGUAUUUAUUAGAUAAAAAAUCAAUGUCUUCGGACUCCU
UGAUGAUUCAUAAUAACUUUUCGAAUCGCAUGGCCUUGUGCUGGCGAUGGUUCAUUCAAA
UUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGUGGCCUACCAUGGUUUCAACGGGUAAC
GGGGAAUAAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAA
GGCAGCAGGCGCGCAAAUUACCCAAUCCUAAUUCAGGGAGGUAGUGACAAUAAAUAACGA
UACAGGGCCCAUUCGGGUCUUGUAAUUGGAAUGAGUACAAUGUAAAUACCUUAACGAGGA
ACAACUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAGUAGCGUAUA
UUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGAACUUUGGGUCUGGUUGUCCGGUCCGA
CUUUAUGUCGCGCACUGGUUUUCAACCGGAUCUUUCCUUCUGGCUAACCUGUACUCCUUG
UGGGUGCAGGCGAACCAGGACUUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCGAA
AGCUCGAAUAUAUUAGCAUGGAAUAAUGGAAUAGGACGUUUGGUUCUAUUUUGUUGGUUU
CUAGGACCAUCGUAAUGAUUAAUAGGGACGGUCGGGGGCAUCAGUAUUCAAUUGUCAGAG
GUGAAAUUCUUGGAUUUAUUGAAGACUAACUACUGCGAAAGCAUUUGCCAAGGACGUUUU
CAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGAUGAUCAGAUACCGUCGUAGUCUUAAC
CAUAAACUAUGCCGACUAGGGAUCGGGUGGUGUUUUUCUUAUGACCCACUCGGCACCUUA
CGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGG
AAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGG
AAACUCACCAGGUCCAGACACAAUAAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUUUG
UGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGCUUAAUUGCGAUA
ACGAACGAGACCUUAACCUACUAAAUAGGGUUGCUGGCACUUGCCGGUUGACUCUUCUUA
GAGGGACUAUCGGUUUCAAGCCGAUGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCU
UAGACGUUCUGGGCCGCACGCGCGCUACACUGACGGAGCCAGCGAGUACAACCUUGGCCG
AGAGGUCUGGGUAAUCUUGUGAAACUCCGUCGUGCUGGGGAUAGAGCAUUGUAAUUAUUG
CUCUUCAACGAGGAAUUCCUAGUAAGCGCAAGUCAUCAGCUUGCGUUGAUUACGUCCCUG
CCCUUUGUACACACCGCCCGUCGCUAGUACCGAUUGAAUGGCUUAGUGAGGCCUCAGGAU
UUGCUUAGAGAAGGGGGCAACUCCAUCUCAGAGCGAAGAAUCUGGUCAAACUUGGUCAUU
UAGAGGAACUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA

Sequence of entity 3 (A), FASTA

>6GSM_3 40S ribosomal protein S0 (chains A)
SLPSTFDLTSEDAQLLLAARVHLGAKNVQVHQEPYVYKARPDGVNVINVGKTWEKIVLAA
RIIAAIPNPEDVVAISSRTYGQRAVLKYAAHTGATPIAGRFTPGSFTNYITRSFKEPRLV
IVTDPRSDAQAIKESSYVNIPVIALTDLDSPSEYVDVAIPCNNRGKHSIGLIWYLLAREV
LRLRGALPDRTQPWAIMPDLYFYRNPEE

Sequence of entity 4 (3), FASTA

>6GSM_4 mRNA (5'-R(P*AP*AP*U)-3') (chains 3)
AAU

Sequence of entity 5 (B), FASTA

>6GSM_5 40S ribosomal protein S1 (chains B)
VGKNKRLSKGKKGLKKRVVDPFTRKEWYDIKAPSTFENRNVGKTLVNKSVGLKNASDSLK
GRVVEVCLADLQGSEDHSFRKVKLRVDEVQGKNLLTNFHGMDFTTDKLRSMVRKWQTLIE
ANVTVKTSDDYVLRIFAIAFTRKQANQVKRTSYAQSSHIRQIRKVISEILTREVQNSTLA
QLTSKLIPEVINKEIENATKDIFPLQNVHIRKVKLLKQPKFDLGSLLSLHG

Sequence of entity 6 (C), FASTA

>6GSM_6 KLLA0F09812p (chains C)
GWVPVTKLGRLVKAGKISSIEEIFLHSLPVKEFQIIDQLLPNLKDEVMNIKPVQKQTRAG
QRTRFKAVVVVGDSNGHVGLGIKTAKEVAGAIRAGIIIAKLSVIPIRRGYWGTNLGQPHS
LATKTSGKCGSVSVRLIPAPRGSGIVASPAVKKLMQLAGVEDVYTSSTGSTRTLENTLKA
AFVAIGNTYGFLTPNLWEVQALTPSPMDVYADYATAS

Sequence of entity 7 (D), FASTA

>6GSM_7 KLLA0D08305p (chains D)
AIISKKRKLVADGVFYAELNEFFTRELAEEGYSGVEVRVTPTKTEIIIRATKVQDVVGEN
GRRINELTLLIEKRFKYKRGTIALYAERVHDRGLSAVAQAESMKFKLLNGLAIRRAAYGV
VRYVMESGAKGCEVVISGKLRAARAKSMKFADGFLIHSGQPVNDFIETATRHVLLRQGVL
GIKVKIMKDPSRNTSGPKALPDAVTIIEPKEEEPVLEPSVKDY

Sequence of entity 8 (E), FASTA

>6GSM_8 40S ribosomal protein S4 (chains E)
ARGPKKHLKRLAAPHHWMLDKLSGCYAPRPSAGPHKLRESLPLIVFLRNRLKYALNGREV
KAILMQRHVKVDGKVRTDTTFPAGFMDVITLEATNENFRLVYDVKGRFAVHRITDEEASY
KLAKVKKVQLGKKGIPYVVTHDGRTIRYPDPNIKVNDTVKVDLATGTITDFIKFDTGKLV
YVTGGRNLGRVGTIVHRERHEGGFDLVHIKDSLENTFVTRLNNVFVIGEPGRPWISLPKG
KGIKLTISEERDRRRAQHGL

Sequence of entity 9 (F), FASTA

>6GSM_9 KLLA0D10659p (chains F)
FVPVELATTIPVEIQQAQQEIKLFNKWSFEDVEVKDASLVDYIQISKPIYVAHTAGRYAN
KRFRKAQCPIVERLTNSLMMNGRNNGKKLKAVRIVKHTLEIINVLTDQNPLQVVVDAIIN
SGPREDTTRVGGGGAARRQAVDVSPLRRVNQSIALLTIGAREAAFRNIKTIAETLAEELI
NAAKGSSTSYAIKKKDELERVAKSNR

Sequence of entity 10 (G), FASTA

>6GSM_10 40S ribosomal protein S6 (chains G)
MKLNISYPINGTQKCIEIDDEHRVRVFYDKRIGQEVDGESVGDEFKGYVFKIAGGNDKQG
FPMKQGVLLPTRVKLLLAKGHSCYRPRRNGERKRKSVRGAIVGPDLAVLALIITKKGEQE
IEGITNDTVPKRLGPKRANNIRKFFGLTKEDDVRDYVIRREVTKGDKSYTKAPKIQRLVT
PQRLQRKRQQKSLKIKNAQAQREAAAEYAQLLAKRLSERKAEKAEV

Sequence of entity 11 (H), FASTA

>6GSM_11 40S ribosomal protein S7 (chains H)
PQAKILSQAPTELELQVAQAFIDLENNSPELKADLRALQFKSIREIEVAGGKKALAVFVP
VPSLAAYHKVQIKLTRELEKKFQDRHVIFLAERRILPKPSRKSRQTQKRPRSRTLTAVHD
KILEDLVFPTEIVGKRVRYLVGGNKIQKILLNSKDVQHIDNKLESFQAVYNKLTGKQIVF
EIPS

Sequence of entity 12 (I), FASTA

>6GSM_12 40S ribosomal protein S8 (chains I)
GISRDSRHKRAATGAKRAQFRKKRKFELGRQAANTKIGTKRIHPVRTRGGNQKFRALRIE
TGNFSWASEGVARKTRITGVVYHPSNNELVRTNTLTKAAIVQIDATPFRQWYESHYGQSL
GKKKNTKAEEETATTSKNTERKWAARAAEAKIEHAVDSQFGAGRLYAAISSRPGQSGRCD
GYILEGEELAFYLRRLTAKK

Ligands and cofactors

ID	Name	Formula	Copies
GCP	Phosphomethylphosphonic acid guanylate ester	C11 H18 N5 O13 P3	1
ZN	Zinc ion	Zn	4
MG	Magnesium ion	Mg	82
7NO	[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-2-(phosphonooxymeth…	C15 H23 N6 O8 P S	1

Primary citation

Large-scale movement of eIF3 domains during translation initiation modulate start codon selection. Llacer, J.L., Hussain, T., Dong, J. et al. Nucleic Acids Res (2021). DOI 10.1093/nar/gkab908 · PubMed

Other PDB entries of the same protein (UniProt Q6CN12 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6FYY 3.02 Å, Structure of a partial yeast 48S preinitiation complex with eIF5 N-terminal domain…
8RW1 3.35 Å, Structure of a yeast 48S-AUC preinitiation complex in closed conformation
8S8D 3.45 Å, Structure of a yeast 48S-AUC preinitiation complex in closed conformation (model…
3JAM 3.46 Å, CryoEM structure of 40S-eIF1A-eIF1 complex from yeast
6FYX 3.5 Å, Structure of a partial yeast 48S preinitiation complex with eIF5 N-terminal domain…
5IT7 3.6 Å, Structure of the Kluyveromyces lactis 80S ribosome in complex with the cricket paralysis…
6UZ7 3.6 Å, K.lactis 80S ribosome with p/PE tRNA and eIF5B
3J80 3.75 Å, CryoEM structure of 40S-eIF1-eIF1A preinitiation complex
5IT9 3.8 Å, Structure of the yeast Kluyveromyces lactis small ribosomal subunit in complex with the…
8S8E 3.85 Å, Structure of a yeast 48S-AUC preinitiation complex in closed conformation (model…
8S8F 3.95 Å, Structure of a yeast 48S-AUC preinitiation complex in closed conformation (model…
3J81 4.0 Å, CryoEM structure of a partial yeast 48S preinitiation complex

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