8S8F: Small ribosomal subunit protein uS2

Structure of a yeast 48S-AUC preinitiation complex in closed conformation (model py48S-AUC-3.2). Determined by electron microscopy at 3.95 Å resolution. Released 11 Sept 2024.

Method: Electron microscopy
Resolution: 3.95 Å
Organisms: Kluyveromyces lactis NRRL Y-1140, Saccharomyces cerevisiae S288C, Kluyveromyces lactis
Chains: 42
Atoms: 85,732
Mol. weight: 1373.76 kDa
Ligands: MG, ZN, GCP, MET
Released: 11 Sept 2024

Explore 8S8F in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8S8F contains 212 α-helices and 287 β-strands across 39 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, 5 β-strands

Element	Residues	Length	Sheet
β-strand	20-22	3	73
β-strand	29-31	3	73
β-strand	37-43	7	74
α-helix	47-55	9
β-strand	57	1	54
β-strand	66-72	7	74
α-helix	76-80	5

Chain A: 8 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	5-7	3
α-helix	11-19	9
β-strand	37	1	1
β-strand	41	1	2
β-strand	45	1	2
β-strand	48	1	1
α-helix	50-66	17
α-helix	70-72	3
β-strand	73-77	5	3
α-helix	80-92	13
β-strand	96-99	4	3
β-strand	120-123	4	3
α-helix	130-138	9
β-strand	143-145	3	3
β-strand	159	1	3
α-helix	169-185	17
α-helix	207-217	11

Chain b: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	12-17	6
α-helix	19	1
β-strand	32-36	5	75
β-strand	43-47	5	75
β-strand	65	1	76
α-helix	71	1
β-strand	72	1	76
β-strand	78-81	4	75

Chain B: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	27-33	7	7
β-strand	42-49	8	7
α-helix	57-61	5
β-strand	65-69	5	7
α-helix	70-74	5
α-helix	77-79	3
β-strand	82-91	10	7
β-strand	96-105	10	7
α-helix	107-113	7
β-strand	120-128	9	7
β-strand	134-142	9	7
α-helix	158-178	21
α-helix	181-188	8
α-helix	192-200	9
β-strand	208-219	12	7
α-helix	225-231	7

Chain c: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	8-19	12	29
β-strand	25-32	8	29
β-strand	39-45	7	29
β-strand	53-56	4	29
α-helix	61-63	3

Chain C: 8 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	46-52	7
α-helix	59-62	4
α-helix	71-77	7
β-strand	82-94	13	11
β-strand	99-110	12	11
β-strand	115-123	9	11
α-helix	126-139	14
β-strand	142-143	2	11
β-strand	146-147	2	12
β-strand	158-159	2	12
β-strand	163-167	5	13
β-strand	170-176	7	13
β-strand	183-184	2	13
α-helix	187-196	10
β-strand	201-206	6	13
α-helix	212-224	13
α-helix	236-238	3
α-helix	244-247	4

Chain d: 2 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	30-31	2	32
α-helix	33-35	3
β-strand	38-39	2	32
α-helix	40-50	11
β-strand	53	1	16

Chain D: 7 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	7-28	22
β-strand	34-40	7	77
β-strand	47-52	6	77
α-helix	55-59	5
α-helix	65-76	12
β-strand	86-90	5	77
α-helix	98-111	14
α-helix	115-128	14
β-strand	133-140	8	78
β-strand	148-155	8	78
α-helix	163-166	4
β-strand	168-177	10	78
β-strand	180-189	10	78
β-strand	207-208	2	79
α-helix	209-212	4
β-strand	222-223	2	44

31 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	1798	Kluyveromyces lactis NRRL Y-1140
Small ribosomal subunit protein uS2	A	protein	254	Kluyveromyces lactis NRRL Y-1140	Q6CN12 (AlphaFold model)
Small ribosomal subunit protein eS1	B	protein	255	Kluyveromyces lactis NRRL Y-1140	Q6CWD0 (AlphaFold model)
Small ribosomal subunit protein uS5	C	protein	259	Kluyveromyces lactis NRRL Y-1140	Q6CKL3 (AlphaFold model)
40S ribosomal protein S4	E	protein	261	Kluyveromyces lactis NRRL Y-1140	Q6CWJ2 (AlphaFold model)
Small ribosomal subunit protein eS6	G	protein	236	Kluyveromyces lactis NRRL Y-1140	Q6CM04
40S ribosomal protein S7	H	protein	190	Kluyveromyces lactis NRRL Y-1140	Q6CTD6
40S ribosomal protein S8	I	protein	201	Kluyveromyces lactis NRRL Y-1140	Q6CMG3
KLLA0E23673p	J	protein	188	Kluyveromyces lactis NRRL Y-1140	Q6CM18
KLLA0A10483p	L	protein	156	Kluyveromyces lactis NRRL Y-1140	Q6CX80
KLLA0F18040p	N	protein	151	Kluyveromyces lactis NRRL Y-1140	Q6CJK0
Small ribosomal subunit protein uS11	O	protein	137	Kluyveromyces lactis NRRL Y-1140	P27069

30 more molecules are not listed.

Sequence of entity 1 (2), FASTA

>8S8F_1 18S ribosomal RNA (chains 2)
UAUCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCU
AAGUAUAAGCAAUUUAUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUCGUUUAU
UUGAUAGUUCCUUUACUACAUGGAUAUCUGUGGUAAUUCUAGAGCUAAUACAUGCUUAAA
AUCUCGACCCUUUGGAAGAGAUGUAUUUAUUAGAUAAAAAAUCAAUGUCUUCGGACUCCU
UGAUGAUUCAUAAUAACUUUUCGAAUCGCAUGGCCUUGUGCUGGCGAUGGUUCAUUCAAA
UUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGUGGCCUACCAUGGUUUCAACGGGUAAC
GGGGAAUAAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAA
GGCAGCAGGCGCGCAAAUUACCCAAUCCUAAUUCAGGGAGGUAGUGACAAUAAAUAACGA
UACAGGGCCCAUUCGGGUCUUGUAAUUGGAAUGAGUACAAUGUAAAUACCUUAACGAGGA
ACAACUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAGUAGCGUAUA
UUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGAACUUUGGGUCUGGUUGUCCGGUCCGA
CUUUAUGUCGCGCACUGGUUUUCAACCGGAUCUUUCCUUCUGGCUAACCUGUACUCCUUG
UGGGUGCAGGCGAACCAGGACUUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCGAA
AGCUCGAAUAUAUUAGCAUGGAAUAAUGGAAUAGGACGUUUGGUUCUAUUUUGUUGGUUU
CUAGGACCAUCGUAAUGAUUAAUAGGGACGGUCGGGGGCAUCAGUAUUCAAUUGUCAGAG
GUGAAAUUCUUGGAUUUAUUGAAGACUAACUACUGCGAAAGCAUUUGCCAAGGACGUUUU
CAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGAUGAUCAGAUACCGUCGUAGUCUUAAC
CAUAAACUAUGCCGACUAGGGAUCGGGUGGUGUUUUUCUUAUGACCCACUCGGCACCUUA
CGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGG
AAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACXCAACACGGGG
AAACUCACCAGGUCCAGACACAAUAAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUUUG
UGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGCUUAAUUGCGAUA
ACGAACGAGACCUUAACCUACUAAAUAGGGUUGCUGGCACUUGCCGGUUGACUCUUCUUA
GAGGGACUAUCGGUUUCAAGCCGAUGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCU
UAGACGUUCUGGGCCGCACGCGCGCUACACUGACGGAGCCAGCGAGUACAACCUUGGCCG
AGAGGUCUGGGUAAUCUUGUGAAACUCCGUCGUGCUGGGGAUAGAGCAUUGUAAUUAUUG
CUCUUCAACGAGGAAUUCCUAGUAAGCGCAAGUCAUCAGCUUGCGUUGAUUACGUCCCUG
CCCUUUGUACACACCGCCCGUCGCUAGUACCGAUUGAAUGGCUUAGUGAGGCCUCAGGAU
UUGCUUAGAGAAGGGGGCAACUCCAUCUCAGAGCGAAGAAUCUGGUCAAACUUGGUCAUU
UAGAGGAACUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA

Sequence of entity 2 (A), FASTA

>8S8F_2 Small ribosomal subunit protein uS2 (chains A)
MSLPSTFDLTSEDAQLLLAARVHLGAKNVQVHQEPYVYKARPDGVNVINVGKTWEKIVLA
ARIIAAIPNPEDVVAISSRTYGQRAVLKYAAHTGATPIAGRFTPGSFTNYITRSFKEPRL
VIVTDPRSDAQAIKESSYVNIPVIALTDLDSPSEYVDVAIPCNNRGKHSIGLIWYLLARE
VLRLRGALPDRTQPWAIMPDLYFYRNPEEIEQQTAEEEAVASGEQTEEAVDATEEQTEAA
EWAEEGQAQEEEWN

Sequence of entity 3 (B), FASTA

>8S8F_3 Small ribosomal subunit protein eS1 (chains B)
MAVGKNKRLSKGKKGLKKRVVDPFTRKEWYDIKAPSTFENRNVGKTLVNKSVGLKNASDS
LKGRVVEVCLADLQGSEDHSFRKVKLRVDEVQGKNLLTNFHGMDFTTDKLRSMVRKWQTL
IEANVTVKTSDDYVLRIFAIAFTRKQANQVKRTSYAQSSHIRQIRKVISEILTREVQNST
LAQLTSKLIPEVINKEIENATKDIFPLQNVHIRKVKLLKQPKFDLGSLLSLHGEASAEEK
GKKVAGFKDEILETV

Sequence of entity 4 (C), FASTA

>8S8F_4 Small ribosomal subunit protein uS5 (chains C)
MSAPQAQGQQAPRRGGFGGANRGGRGGRRGGRRDQEEKGWVPVTKLGRLVKAGKISSIEE
IFLHSLPVKEFQIIDQLLPNLKDEVMNIKPVQKQTRAGQRTRFKAVVVVGDSNGHVGLGI
KTAKEVAGAIRAGIIIAKLSVIPIRRGYWGTNLGQPHSLATKTSGKCGSVSVRLIPAPRG
SGIVASPAVKKLMQLAGVEDVYTSSTGSTRTLENTLKAAFVAIGNTYGFLTPNLWEVQAL
TPSPMDVYADYATASKKKL

Sequence of entity 5 (E), FASTA

>8S8F_5 40S ribosomal protein S4 (chains E)
MARGPKKHLKRLAAPHHWMLDKLSGCYAPRPSAGPHKLRESLPLIVFLRNRLKYALNGRE
VKAILMQRHVKVDGKVRTDTTFPAGFMDVITLEATNENFRLVYDVKGRFAVHRITDEEAS
YKLAKVKKVQLGKKGIPYVVTHDGRTIRYPDPNIKVNDTVKVDLATGTITDFIKFDTGKL
VYVTGGRNLGRVGTIVHRERHEGGFDLVHIKDSLENTFVTRLNNVFVIGEPGRPWISLPK
GKGIKLTISEERDRRRAQHGL

Sequence of entity 6 (G), FASTA

>8S8F_6 Small ribosomal subunit protein eS6 (chains G)
MKLNISYPINGTQKCIEIDDEHRVRVFYDKRIGQEVDGESVGDEFKGYVFKIAGGNDKQG
FPMKQGVLLPTRVKLLLAKGHSCYRPRRNGERKRKSVRGAIVGPDLAVLALIITKKGEQE
IEGITNDTVPKRLGPKRANNIRKFFGLTKEDDVRDYVIRREVTKGDKSYTKAPKIQRLVT
PQRLQRKRQQKSLKIKNAQAQREAAAEYAQLLAKRLSERKAEKAEVRKRRASSLKA

Sequence of entity 7 (H), FASTA

>8S8F_7 40S ribosomal protein S7 (chains H)
MSDPQAKILSQAPTELELQVAQAFIDLENNSPELKADLRALQFKSIREIEVAGGKKALAV
FVPVPSLAAYHKVQIKLTRELEKKFQDRHVIFLAERRILPKPSRKSRQTQKRPRSRTLTA
VHDKILEDLVFPTEIVGKRVRYLVGGNKIQKILLNSKDVQHIDNKLESFQAVYNKLTGKQ
IVFEIPSETH

Sequence of entity 8 (I), FASTA

>8S8F_8 40S ribosomal protein S8 (chains I)
MGISRDSRHKRAATGAKRAQFRKKRKFELGRQAANTKIGTKRIHPVRTRGGNQKFRALRI
ETGNFSWASEGVARKTRITGVVYHPSNNELVRTNTLTKAAIVQIDATPFRQWYESHYGQS
LGKKKNTKAEEETATTSKNTERKWAARAAEAKIEHAVDSQFGAGRLYAAISSRPGQSGRC
DGYILEGEELAFYLRRLTAKK

Sequence of entity 9 (J), FASTA

>8S8F_9 KLLA0E23673p (chains J)
MPRAPRTYSKTYSTPKRPYESARLDAELKLAGEYGLKNKREIYRISFQLSKIRRAARDLL
TRDEKDPKRLFEGNALIRRLVRIGVLSEDKKKLDYVLALKVEDFLERRLQTQVYKLGLAK
SVHHARVLISQRHIAVGKQIVNIPSFMVRLESEKHIDFARTSPFGGARPGRVARKRAAAA
GGEEADEE

Sequence of entity 10 (L), FASTA

>8S8F_10 KLLA0A10483p (chains L)
MSTELTVQSERAFQKQPHIFTNPKAKANRKTKRWYKNVGLGFKTPKTAIEGSYIDKKCPF
TGLVSIRGKILTGTVVSTRMHRTIVIRRDYLHYVPKYNRYEKRHKNVPAHVSPAFRVQVG
DIVTVGQCRPISKTVRFNVLKVASATGKANKQFAKF

Sequence of entity 11 (N), FASTA

>8S8F_11 KLLA0F18040p (chains N)
MGRMHSKGKGMSSSAIPYSRNAPAWFKGSSDGVVEQIIKYARKGLTPSQIGVLLRDAHGV
TQAKVITGNKILRILKSNGLAPEIPEDLYFLIKKAVSVRKHLERNRKDKDAKFRLILIES
RIHRLARYYRTVSVLPPNWKYESATASALVN

Sequence of entity 12 (O), FASTA

>8S8F_12 Small ribosomal subunit protein uS11 (chains O)
MANVVQAKDNSQVFGVARIFASFNDTFVHVTDLSGRETIARVTGGMKVKADRDESSPYAA
MLAAQDVAAKCKEVGITAVHIKIRATGGTRSKTPGPGGQAALRALARSGLRIGRIEDVTP
VPSDSTRKKGGRRGRRL

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	116
ZN	Zinc ion	Zn	4
GCP	Phosphomethylphosphonic acid guanylate ester	C11 H18 N5 O13 P3	1
MET	Methionine	C5 H11 N O2 S	1

Primary citation

Structural basis of AUC codon discrimination during translation initiation in yeast. Villamayor-Belinchon, L., Sharma, P., Gordiyenko, Y. et al. Nucleic Acids Res (2024) 52:11317-11335. DOI 10.1093/nar/gkae737 · 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…
3J81 4.0 Å, CryoEM structure of a partial yeast 48S preinitiation complex
8S8G 4.0 Å, Structure of a yeast 48S-AUC preinitiation complex in closed conformation (model…

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