7MPJ: 40S ribosomal protein S0-A

Name: PDB 7MPJ: Stm1 bound vacant 80S structure isolated from wild-type
Published: 2022-05-11
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Stm1 bound vacant 80S structure isolated from wild-type. Determined by electron microscopy at 2.7 Å resolution. Released 11 May 2022.

Method: Electron microscopy
Resolution: 2.7 Å
Organisms: Saccharomyces cerevisiae, Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains: 79
Atoms: 199,813
Mol. weight: 2949.98 kDa
Ligands: ZN, MG
Released: 11 May 2022

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

Secondary structure: helices and β-sheets

7MPJ contains 501 α-helices and 514 β-strands across 75 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: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
α-helix	42-45	4
β-strand	53	1	15
β-strand	72-74	3	75
α-helix	84-91	8
β-strand	99-100	2	144
β-strand	101-103	3	76
α-helix	105-107	3
β-strand	111-113	3	75
β-strand	124-127	4	76
β-strand	129-130	2	75
α-helix	132-140	9
β-strand	144-147	4	76

Chain AA: 10 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	6-9	4
α-helix	10-12	3
β-strand	18	1	78
α-helix	29-31	3
α-helix	34-38	5
β-strand	40-50	11	79
β-strand	57-64	8	79
β-strand	71-77	7	79
α-helix	78	1
β-strand	79	1	80
β-strand	83	1	9
β-strand	87-91	5	79
β-strand	101-103	3	79
α-helix	104-106	3
β-strand	112-114	3	79
β-strand	116	1	81
β-strand	126	1	81
β-strand	134-140	7	79
β-strand	145-149	5	79
β-strand	155-159	5	79
β-strand	163-166	4	79
α-helix	168	1
β-strand	169	1	80
α-helix	174-176	3
α-helix	182-190	9
β-strand	193	1	78
α-helix	201-203	3
β-strand	224-225	2	82
β-strand	237-238	2	82

Chain Ab: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	12-16	5
β-strand	22	1	37
α-helix	37-58	22

Chain AB: 14 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	83
β-strand	45-59	15	84
β-strand	71-80	10	84
α-helix	82-83	2
β-strand	84-95	12	85
β-strand	98-106	9	85
α-helix	112-115	4
α-helix	116-118	3
α-helix	134-136	3
α-helix	142-153	12
β-strand	157-163	7	85
β-strand	178-182	5	85
β-strand	183-184	2	83
α-helix	188-197	10
β-strand	202-203	2	85
β-strand	214-220	7	84
β-strand	225-227	3	86
α-helix	229-233	5
α-helix	235-239	5
β-strand	268-270	3	86
β-strand	274-286	13	84
α-helix	307	1
β-strand	311	1	87
β-strand	315	1	87
β-strand	321-325	5	84
β-strand	335-340	6	84
β-strand	356-359	4	84
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	88
α-helix	27-36	10
β-strand	41-44	4	88
α-helix	50-62	13
β-strand	66-69	4	88
α-helix	74-80	7
β-strand	89-94	6	88

Chain AC: 23 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	6-11	6	90
β-strand	13-20	8	90
α-helix	32-42	11
α-helix	47-49	3
β-strand	63-64	2	91
β-strand	75-76	2	91
β-strand	88	1	91
α-helix	98-99	2
α-helix	115-128	14
α-helix	132-138	7
β-strand	150-152	3	90
α-helix	154-158	5
α-helix	162-172	11
α-helix	175-180	6
β-strand	186-187	2	92
α-helix	188	1
α-helix	191-194	4
β-strand	199-200	2	92
β-strand	206-209	4	90
α-helix	215-218	4
β-strand	226-229	4	90
α-helix	235-238	4
α-helix	240-242	3
β-strand	248-251	4	90
α-helix	252-262	11
α-helix	276-279	4
α-helix	287-290	4
α-helix	293-296	4
α-helix	300-302	3
α-helix	314-316	3
β-strand	317	1	93
β-strand	319	1	93
α-helix	321-326	6
α-helix	330-336	7
α-helix	342-345	4
α-helix	353-360	8

Chain Ad: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	8-15	8	94
α-helix	25-27	3
α-helix	28-44	17
β-strand	49-51	3	94
α-helix	53-59	7
α-helix	60-62	3
β-strand	70-79	10	94
β-strand	89-95	7	94
β-strand	107-109	3	94
α-helix	110	1

Chain AD: 18 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	10-15	6
α-helix	30-37	8
α-helix	46-49	4
β-strand	50-56	7	97
β-strand	59-67	9	97
β-strand	72-79	8	97
α-helix	80-85	6
α-helix	95-112	18
α-helix	133-135	3
α-helix	139-142	4
β-strand	143	1	98
β-strand	145-147	3	97
α-helix	159-168	10
β-strand	172	1	98
α-helix	192-199	8
α-helix	202-214	13
α-helix	216-221	6
α-helix	224-228	5
α-helix	233-235	3
α-helix	236-249	14
α-helix	262-269	8
α-helix	270-272	3
α-helix	273-276	4
α-helix	279-294	16

67 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
40S ribosomal protein S0-A	BA	protein	206	Saccharomyces cerevisiae	P32905 (AlphaFold model)
40S ribosomal protein S1-A	BB	protein	214	Saccharomyces cerevisiae	P33442 (AlphaFold model)
40S ribosomal protein S2	BC	protein	217	Saccharomyces cerevisiae	P25443 (AlphaFold model)
40S ribosomal protein S3	BD	protein	223	Saccharomyces cerevisiae	P05750 (AlphaFold model)
40S ribosomal protein S4-A	BE	protein	260	Saccharomyces cerevisiae	P0CX35
40S ribosomal protein S5	BF	protein	206	Saccharomyces cerevisiae	P26783
40S ribosomal protein S6-A	BG	protein	226	Saccharomyces cerevisiae	P0CX37
40S ribosomal protein S7-A	BH	protein	184	Saccharomyces cerevisiae	P26786
40S ribosomal protein S8-A	BI	protein	188	Saccharomyces cerevisiae	P0CX39
40S ribosomal protein S9-A	BJ	protein	185	Saccharomyces cerevisiae	O13516
40S ribosomal protein S10-A	BK	protein	96	Saccharomyces cerevisiae	Q08745
40S ribosomal protein S11-A	BL	protein	155	Saccharomyces cerevisiae	P0CX47

67 more molecules are not listed.

Sequence of entity 1 (BA), FASTA

>7MPJ_1 40S ribosomal protein S0-A (chains BA)
SLPATFDLTPEDAQLLLAANTHLGARNVQVHQEPYVFNARPDGVHVINVGKTWEKLVLAA
RIIAAIPNPEDVVAISSRTFGQRAVLKFAAHTGATPIAGRFTPGSFTNYITRSFKEPRLV
IVTDPRSDAQAIKEASYVNIPVIALTDLDSPSEFVDVAIPCNNRGKHSIGLIWYLLAREV
LRLRGALVDRTQPWSIMPDLYFYRDP

Sequence of entity 2 (BB), FASTA

>7MPJ_2 40S ribosomal protein S1-A (chains BB)
VVDPFTRKEWFDIKAPSTFENRNVGKTLVNKSTGLKSASDALKGRVVEVCLADLQGSEDH
SFRKIKLRVDEVQGKNLLTNFHGMDFTTDKLRSMVRKWQTLIEANVTVKTSDDYVLRIFA
IAFTRKQANQVKRHSYAQSSHIRAIRKVISEILTKEVQGSTLAQLTSKLIPEVINKEIEN
ATKDIFPLQNIHVRKVKLLKQPKFDVGALMALHG

Sequence of entity 3 (BC), FASTA

>7MPJ_3 40S ribosomal protein S2 (chains BC)
GWVPVTKLGRLVKAGKITTIEEIFLHSLPVKEFQIIDTLLPGLQDEVMNIKPVQKQTRAG
QRTRFKAVVVVGDSNGHVGLGIKTAKEVAGAIRAGIIIAKLSVIPIRRGYWGTNLGQPHS
LATKTTGKCGSVTVRLIPAPRGSGIVASPAVKKLLQLAGVEDVYTQSNGKTRTLENTLKA
AFVAIGNTYGFLTPNLWAEQPLPVSPLDIYSDEASAQ

Sequence of entity 4 (BD), FASTA

>7MPJ_4 40S ribosomal protein S3 (chains BD)
ALISKKRKLVADGVFYAELNEFFTRELAEEGYSGVEVRVTPTKTEVIIRATRTQDVLGEN
GRRINELTLLVQKRFKYAPGTIVLYAERVQDRGLSAVAQAESMKFKLLNGLAIRRAAYGV
VRYVMESGAKGCEVVVSGKLRAARAKAMKFADGFLIHSGQPVNDFIDTATRHVLMRQGVL
GIKVKIMRDPAKSRTGPKALPDAVTIIEPKEEEPILAPSVKDY

Sequence of entity 5 (BE), FASTA

>7MPJ_5 40S ribosomal protein S4-A (chains BE)
ARGPKKHLKRLAAPHHWLLDKLSGCYAPRPSAGPHKLRESLPLIVFLRNRLKYALNGREV
KAILMQRHVKVDGKVRTDTTYPAGFMDVITLDATNENFRLVYDVKGRFAVHRITDEEASY
KLGKVKKVQLGKKGVPYVVTHDGRTIRYPDPNIKVNDTVKIDLASGKITDFIKFDAGKLV
YVTGGRNLGRIGTIVHKERHDGGFDLVHIKDSLDNTFVTRLNNVFVIGEQGKPYISLPKG
KGIKLSIAEERDRRRAQQGL

Sequence of entity 6 (BF), FASTA

>7MPJ_6 40S ribosomal protein S5 (chains BF)
FTPVVLATPIPEEVQQAQTEIKLFNKWSFEEVEVKDASLVDYVQVRQPIFVAHTAGRYAN
KRFRKAQCPIIERLTNSLMMNGRNNGKKLKAVRIIKHTLDIINVLTDQNPIQVVVDAITN
TGPREDTTRVGGGGAARRQAVDVSPLRRVNQAIALLTIGAREAAFRNIKTIAETLAEELI
NAAKGSSTSYAIKKKDELERVAKSNR

Sequence of entity 7 (BG), FASTA

>7MPJ_7 40S ribosomal protein S6-A (chains BG)
MKLNISYPVNGSQKTFEIDDEHRIRVFFDKRIGQEVDGEAVGDEFKGYVFKISGGNDKQG
FPMKQGVLLPTRIKLLLTKNVSCYRPRRDGERKRKSVRGAIVGPDLAVLALVIVKKGEQE
LEGLTDTTVPKRLGPKRANNIRKFFGLSKEDDVRDFVIRREVTKGEKTYTKAPKIQRLVT
PQRLQRKRHQRALKVRNAQAQREAAAEYAQLLAKRLSERKAEKAEI

Sequence of entity 8 (BH), FASTA

>7MPJ_8 40S ribosomal protein S7-A (chains BH)
PQAKILSQAPTELELQVAQAFVELENSSPELKAELRPLQFKSIREIDVAGGKKALAIFVP
VPSLAGFHKVQTKLTRELEKKFQDRHVIFLAERRILPKPSRTSRQVQKRPRSRTLTAVHD
KILEDLVFPTEIVGKRVRYLVGGNKIQKVLLDSKDVQQIDYKLESFQAVYNKLTGKQIVF
EIPS

Sequence of entity 9 (BI), FASTA

>7MPJ_9 40S ribosomal protein S8-A (chains BI)
GISRDSRHKRSATGAKRAQFRKKRKFELGRQPANTKIGAKRIHSVRTRGGNKKYRALRIE
TGNFSWASEGISKKTRIAGVVYHPSNNELVRTNTLTKAAIVQIDATPFRQWFEAHYGQTL
GKKSKNAERKWAARAASAKIESSVESQFSAGRLYACISSRPGQSGRCDGYILEGEELAFY
LRRLTAKK

Sequence of entity 10 (BJ), FASTA

>7MPJ_10 40S ribosomal protein S9-A (chains BJ)
PRAPRTYSKTYSTPKRPYESSRLDAELKLAGEFGLKNKKEIYRISFQLSKIRRAARDLLT
RDEKDPKRLFEGNALIRRLVRVGVLSEDKKKLDYVLALKVEDFLERRLQTQVYKLGLAKS
VHHARVLITQRHIAVGKQIVNIPSFMVRLDSEKHIDFAPTSPFGGARPGRVARRNAARKA
EASGE

Sequence of entity 11 (BK), FASTA

>7MPJ_11 40S ribosomal protein S10-A (chains BK)
MLMPKEDRNKIHQYLFQEGVVVAKKDFNQAKHEEIDTKNLYVIKALQSLTSKGYVKTQFS
WQYYYYTLTEEGVEYLREYLNLPEHIVPGTYIQERN

Sequence of entity 12 (BL), FASTA

>7MPJ_12 40S ribosomal protein S11-A (chains BL)
STELTVQSERAFQKQPHIFNNPKVKTSKRTKRWYKNAGLGFKTPKTAIEGSYIDKKCPFT
GLVSIRGKILTGTVVSTKMHRTIVIRRAYLHYIPKYNRYEKRHKNVPVHVSPAFRVQVGD
IVTVGQCRPISKTVRFNVVKVSAAAGKANKQFAKF

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
MG	Magnesium ion	Mg	745

Primary citation

CryoEM structures of pseudouridine-free ribosome suggest impacts of chemical modifications on ribosome conformations. Zhao, Y., Rai, J., Yu, H. et al. Structure (2022) 30:983. DOI 10.1016/j.str.2022.04.002 · 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

Browse structure collections

About this viewer

MolViewer shows 7MPJ directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.