9PN5: Small ribosomal subunit protein uS2A

Name: PDB 9PN5: Composite map of hypomethylated 80S ribosome treated with hygromycin B
Published: 2026-05-20
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Composite map of hypomethylated 80S ribosome treated with hygromycin B. Determined by electron microscopy at 1.75 Å resolution. Released 20 May 2026.

Method: Electron microscopy
Resolution: 1.75 Å
Organism: Saccharomyces cerevisiae BY4741
Chains: 78
Atoms: 200,291
Mol. weight: 3043.23 kDa
Ligands: ZN, MG
Released: 20 May 2026

Explore 9PN5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9PN5 contains 555 α-helices and 520 β-strands across 74 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 Aa: 7 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
α-helix	7-10	4
α-helix	42-48	7
α-helix	65-68	4
β-strand	72-74	3	81
α-helix	75-81	7
α-helix	84-91	8
β-strand	99-100	2	140
β-strand	101-103	3	82
β-strand	111-113	3	81
β-strand	124-127	4	82
β-strand	129-130	2	81
α-helix	132-140	9
β-strand	144-147	4	82

Chain AA: 12 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	6-9	4
α-helix	10-12	3
α-helix	14-16	3
α-helix	29-32	4
α-helix	34-38	5
β-strand	41-49	9	63
β-strand	58-64	7	63
β-strand	71-77	7	63
α-helix	78	1
β-strand	79	1	64
β-strand	83	1	65
β-strand	87-90	4	63
β-strand	101-103	3	63
α-helix	104-106	3
β-strand	112-114	3	63
β-strand	116	1	66
β-strand	126	1	66
β-strand	134-140	7	63
β-strand	145-149	5	63
β-strand	155-159	5	63
β-strand	163-166	4	63
β-strand	169	1	64
α-helix	174-176	3
α-helix	182-190	9
α-helix	201-203	3
α-helix	206-208	3
β-strand	224-225	2	67
α-helix	229-230	2
β-strand	237-238	2	67

Chain Ab: 3 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	12-18	7
β-strand	22	1	26
α-helix	23-26	4
α-helix	37-58	22

Chain AB: 19 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	9-10	2
α-helix	14-16	3
α-helix	33-35	3
α-helix	40-41	2
β-strand	42-43	2	71
β-strand	45-59	15	72
β-strand	71-80	10	72
α-helix	82-83	2
β-strand	84-95	12	73
β-strand	98-106	9	73
α-helix	112-115	4
α-helix	116-118	3
α-helix	122-124	3
α-helix	133-137	5
α-helix	142-154	13
β-strand	157-163	7	73
α-helix	166-168	3
α-helix	176-177	2
β-strand	178-182	5	73
β-strand	183-184	2	71
α-helix	188-197	10
β-strand	202-203	2	73
α-helix	205-207	3
β-strand	214-220	7	72
α-helix	221-222	2
β-strand	223-227	5	74
α-helix	229-233	5
α-helix	235-239	5
β-strand	268-271	4	74
β-strand	274-286	13	72
α-helix	307	1
β-strand	311	1	75
β-strand	315	1	75
β-strand	321-325	5	72
β-strand	335-340	6	72
β-strand	356-359	4	72
α-helix	373-380	8

Chain Ac: 4 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	10-20	11
β-strand	22-25	4	87
α-helix	27-35	9
β-strand	41-44	4	87
α-helix	50-63	14
β-strand	66-69	4	87
α-helix	74-80	7
β-strand	89-94	6	87

Chain AC: 27 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	6-9	4	78
α-helix	10	1
β-strand	15-20	6	78
α-helix	25-27	3
α-helix	32-42	11
α-helix	47-49	3
β-strand	63-64	2	79
β-strand	75-76	2	79
β-strand	88	1	79
α-helix	98-99	2
α-helix	115-128	14
α-helix	132-137	6
β-strand	150-152	3	78
α-helix	154-158	5
α-helix	162-171	10
α-helix	175-183	9
β-strand	186-187	2	80
α-helix	188	1
α-helix	191-194	4
β-strand	199-200	2	80
β-strand	206-209	4	78
α-helix	215-220	6
β-strand	226-229	4	78
α-helix	230-232	3
α-helix	235-238	4
α-helix	240-242	3
β-strand	248-251	4	78
α-helix	252-262	11
α-helix	276-279	4
α-helix	286-290	5
α-helix	293-296	4
α-helix	300-302	3
α-helix	307-309	3
α-helix	321-326	6
α-helix	331-337	7
α-helix	339-341	3
α-helix	342-346	5
α-helix	353-360	8

Chain Ad: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	8-15	8	90
α-helix	16-20	5
α-helix	25-27	3
α-helix	28-44	17
β-strand	49-51	3	90
α-helix	53-59	7
β-strand	70-79	10	90
β-strand	89-95	7	90
β-strand	107-108	2	90

Chain AD: 19 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	10-15	6
α-helix	16-20	5
α-helix	21-24	4
α-helix	30-37	8
α-helix	41-43	3
β-strand	50-56	7	92
β-strand	59-68	10	92
β-strand	71-79	9	92
α-helix	80-86	7
α-helix	95-112	18
α-helix	134-135	2
α-helix	139-142	4
β-strand	143	1	93
β-strand	145-147	3	92
α-helix	158-169	12
β-strand	172	1	93
β-strand	183	1	94
β-strand	190	1	94
α-helix	192-199	8
α-helix	202-214	13
α-helix	217-221	5
α-helix	224-228	5
α-helix	233-235	3
α-helix	236-249	14
α-helix	262-270	9
α-helix	276-278	3
α-helix	279-293	15

66 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
Small ribosomal subunit protein uS2A	BA	protein	252	Saccharomyces cerevisiae BY4741	P32905 (AlphaFold model)
Small ribosomal subunit protein eS1A	BB	protein	255	Saccharomyces cerevisiae BY4741	P33442 (AlphaFold model)
Small ribosomal subunit protein uS5	BC	protein	254	Saccharomyces cerevisiae BY4741	P25443 (AlphaFold model)
Small ribosomal subunit protein eS4A	BE	protein	261	Saccharomyces cerevisiae BY4741	P0CX35 (AlphaFold model)
Small ribosomal subunit protein eS6A	BG	protein	236	Saccharomyces cerevisiae BY4741	P0CX37
Small ribosomal subunit protein eS7A	BH	protein	190	Saccharomyces cerevisiae BY4741	P26786
Small ribosomal subunit protein eS8A	BI	protein	200	Saccharomyces cerevisiae BY4741	P0CX39
Small ribosomal subunit protein uS4A	BJ	protein	197	Saccharomyces cerevisiae BY4741	O13516
Small ribosomal subunit protein uS17A	BL	protein	156	Saccharomyces cerevisiae BY4741	P0CX47
Small ribosomal subunit protein uS15	BN	protein	151	Saccharomyces cerevisiae BY4741	P05756
Small ribosomal subunit protein uS11A	BO	protein	137	Saccharomyces cerevisiae BY4741	P06367
Small ribosomal subunit protein eS21A	BV	protein	87	Saccharomyces cerevisiae BY4741	P0C0V8

66 more molecules are not listed.

Sequence of entity 1 (BA), FASTA

>9PN5_1 Small ribosomal subunit protein uS2A (chains BA)
MSLPATFDLTPEDAQLLLAANTHLGARNVQVHQEPYVFNARPDGVHVINVGKTWEKLVLA
ARIIAAIPNPEDVVAISSRTFGQRAVLKFAAHTGATPIAGRFTPGSFTNYITRSFKEPRL
VIVTDPRSDAQAIKEASYVNIPVIALTDLDSPSEFVDVAIPCNNRGKHSIGLIWYLLARE
VLRLRGALVDRTQPWSIMPDLYFYRDPEEVEQQVAEEATTEEAGEEEAKEEVTEEQAEAT
EWAEENADNVEW

Sequence of entity 2 (BB), FASTA

>9PN5_2 Small ribosomal subunit protein eS1A (chains BB)
MAVGKNKRLSKGKKGQKKRVVDPFTRKEWFDIKAPSTFENRNVGKTLVNKSTGLKSASDA
LKGRVVEVCLADLQGSEDHSFRKIKLRVDEVQGKNLLTNFHGMDFTTDKLRSMVRKWQTL
IEANVTVKTSDDYVLRIFAIAFTRKQANQVKRHSYAQSSHIRAIRKVISEILTKEVQGST
LAQLTSKLIPEVINKEIENATKDIFPLQNIHVRKVKLLKQPKFDVGALMALHGEGSGEEK
GKKVTGFKDEVLETV

Sequence of entity 3 (BC), FASTA

>9PN5_3 Small ribosomal subunit protein uS5 (chains BC)
MSAPEAQQQKRGGFGGRNRGRPNRRGPRNTEEKGWVPVTKLGRLVKAGKITTIEEIFLHS
LPVKEFQIIDTLLPGLQDEVMNIKPVQKQTRAGQRTRFKAVVVVGDSNGHVGLGIKTAKE
VAGAIRAGIIIAKLSVIPIRRGYWGTNLGQPHSLATKTTGKCGSVTVRLIPAPRGSGIVA
SPAVKKLLQLAGVEDVYTQSNGKTRTLENTLKAAFVAIGNTYGFLTPNLWAEQPLPVSPL
DIYSDEASAQKKRF

Sequence of entity 4 (BE), FASTA

>9PN5_4 Small ribosomal subunit protein eS4A (chains BE)
MARGPKKHLKRLAAPHHWLLDKLSGCYAPRPSAGPHKLRESLPLIVFLRNRLKYALNGRE
VKAILMQRHVKVDGKVRTDTTYPAGFMDVITLDATNENFRLVYDVKGRFAVHRITDEEAS
YKLGKVKKVQLGKKGVPYVVTHDGRTIRYPDPNIKVNDTVKIDLASGKITDFIKFDAGKL
VYVTGGRNLGRIGTIVHKERHDGGFDLVHIKDSLDNTFVTRLNNVFVIGEQGKPYISLPK
GKGIKLSIAEERDRRRAQQGL

Sequence of entity 5 (BG), FASTA

>9PN5_5 Small ribosomal subunit protein eS6A (chains BG)
MKLNISYPVNGSQKTFEIDDEHRIRVFFDKRIGQEVDGEAVGDEFKGYVFKISGGNDKQG
FPMKQGVLLPTRIKLLLTKNVSCYRPRRDGERKRKSVRGAIVGPDLAVLALVIVKKGEQE
LEGLTDTTVPKRLGPKRANNIRKFFGLSKEDDVRDFVIRREVTKGEKTYTKAPKIQRLVT
PQRLQRKRHQRALKVRNAQAQREAAAEYAQLLAKRLSERKAEKAEIRKRRASSLKA

Sequence of entity 6 (BH), FASTA

>9PN5_6 Small ribosomal subunit protein eS7A (chains BH)
MSAPQAKILSQAPTELELQVAQAFVELENSSPELKAELRPLQFKSIREIDVAGGKKALAI
FVPVPSLAGFHKVQTKLTRELEKKFQDRHVIFLAERRILPKPSRTSRQVQKRPRSRTLTA
VHDKILEDLVFPTEIVGKRVRYLVGGNKIQKVLLDSKDVQQIDYKLESFQAVYNKLTGKQ
IVFEIPSETH

Sequence of entity 7 (BI), FASTA

>9PN5_7 Small ribosomal subunit protein eS8A (chains BI)
MGISRDSRHKRSATGAKRAQFRKKRKFELGRQPANTKIGAKRIHSVRTRGGNKKYRALRI
ETGNFSWASEGISKKTRIAGVVYHPSNNELVRTNTLTKAAIVQIDATPFRQWFEAHYGQT
LGKKKNVKEEETVAKSKNAERKWAARAASAKIESSVESQFSAGRLYACISSRPGQSGRCD
GYILEGEELAFYLRRLTAKK

Sequence of entity 8 (BJ), FASTA

>9PN5_8 Small ribosomal subunit protein uS4A (chains BJ)
MPRAPRTYSKTYSTPKRPYESSRLDAELKLAGEFGLKNKKEIYRISFQLSKIRRAARDLL
TRDEKDPKRLFEGNALIRRLVRVGVLSEDKKKLDYVLALKVEDFLERRLQTQVYKLGLAK
SVHHARVLITQRHIAVGKQIVNIPSFMVRLDSEKHIDFAPTSPFGGARPGRVARRNAARK
AEASGEAADEADEADEE

Sequence of entity 9 (BL), FASTA

>9PN5_9 Small ribosomal subunit protein uS17A (chains BL)
MSTELTVQSERAFQKQPHIFNNPKVKTSKRTKRWYKNAGLGFKTPKTAIEGSYIDKKCPF
TGLVSIRGKILTGTVVSTKMHRTIVIRRAYLHYIPKYNRYEKRHKNVPVHVSPAFRVQVG
DIVTVGQCRPISKTVRFNVVKVSAAAGKANKQFAKF

Sequence of entity 10 (BN), FASTA

>9PN5_10 Small ribosomal subunit protein uS15 (chains BN)
MGRMHSAGKGISSSAIPYSRNAPAWFKLSSESVIEQIVKYARKGLTPSQIGVLLRDAHGV
TQARVITGNKIMRILKSNGLAPEIPEDLYYLIKKAVSVRKHLERNRKDKDAKFRLILIES
RIHRLARYYRTVAVLPPNWKYESATASALVN

Sequence of entity 11 (BO), FASTA

>9PN5_11 Small ribosomal subunit protein uS11A (chains BO)
MSNVVQARDNSQVFGVARIYASFNDTFVHVTDLSGKETIARVTGGMKVKADRDESSPYAA
MLAAQDVAAKCKEVGITAVHVKIRATGGTRTKTPGPGGQAALRALARSGLRIGRIEDVTP
VPSDSTRKKGGRRGRRL

Sequence of entity 12 (BV), FASTA

>9PN5_12 Small ribosomal subunit protein eS21A (chains BV)
MENDKGQLVELYVPRKCSATNRIIKADDHASVQINVAKVDEEGRAIPGEYVTYALSGYVR
SRGESDDSLNRLAQNDGLLKNVWSYSR

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1
MG	Magnesium ion	Mg	174

Water and common crystallization additives (K) are not listed.

Primary citation

2'-O-Methylation maintains ribosome structural and translation integrity. Zhao, Y., Rai, J., Cohen, L.N. et al. Mol Cell (2026) 86:1495-1510.e7. DOI 10.1016/j.molcel.2026.03.008 · PubMed

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

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
8T2Z 2.4 Å, Hypomethylated yeast 80S bound with cycloheximide, P-site tRNA, and A-site tRNA,…

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