4V88: Eukaryotic ribosome

Name: PDB 4V88: The structure of the eukaryotic ribosome at 3.0 A resolution.
Published: 2014-07-09
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

The structure of the eukaryotic ribosome at 3.0 A resolution. Determined by X-ray diffraction at 3.0 Å resolution. Released 9 Jul 2014.

Method: X-ray diffraction
Resolution: 3.0 Å
Organism: Saccharomyces cerevisiae
Chains: 162
Atoms: 416,785
Mol. weight: 6757.34 kDa
Ligands: OHX, MG, ZN
Released: 9 Jul 2014

Explore 4V88 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4V88 contains 1,031 α-helices and 1,065 β-strands across 154 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: 3 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	20-22	3	10
β-strand	29-31	3	10
α-helix	32-34	3
β-strand	37-42	6	11
α-helix	50-55	6
β-strand	67-72	6	11
α-helix	76-80	5

Chain AA: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	11-20	10
β-strand	24-25	2	8
β-strand	37-41	5	8
β-strand	45-48	4	8
α-helix	50-64	15
α-helix	70-72	3
β-strand	73-77	5	9
α-helix	80-92	13
β-strand	96-99	4	9
β-strand	120-123	4	9
α-helix	130-137	8
β-strand	143-147	5	9
β-strand	159-161	3	9
α-helix	169-182	14
α-helix	199-201	3

Chain Ab: 2 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	12-16	5
β-strand	32-36	5	24
β-strand	44-47	4	24
β-strand	49	1	25
α-helix	54-56	3
β-strand	64-65	2	26
β-strand	70	1	25
β-strand	72-73	2	26
β-strand	78-80	3	24

Chain AB: 8 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	29-33	5	21
β-strand	42-47	6	21
α-helix	57-60	4
β-strand	65-69	5	22
α-helix	71-74	4
β-strand	83-87	5	22
β-strand	91-92	2	21
β-strand	95-96	2	21
β-strand	99-103	5	22
α-helix	107-113	7
β-strand	120-122	3	23
β-strand	125-128	4	22
β-strand	134-137	4	22
β-strand	140-142	3	23
α-helix	159-175	17
α-helix	180-188	9
α-helix	192-202	11
β-strand	208-211	4	23
β-strand	215-219	5	22
α-helix	225-228	4
α-helix	229-231	3

Chain Ac: 0 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	8-19	12	39
β-strand	25-32	8	39
β-strand	39-43	5	39
β-strand	53-56	4	39

Chain AC: 9 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	40-46	7
α-helix	53-58	6
α-helix	66-72	7
β-strand	77	1	36
β-strand	80-90	11	36
β-strand	93-105	13	36
β-strand	110-118	9	36
α-helix	121-134	14
β-strand	137-138	2	36
β-strand	141-142	2	37
β-strand	153-154	2	37
β-strand	158-162	5	38
β-strand	165-171	7	38
β-strand	178-179	2	38
α-helix	182-190	9
β-strand	196-201	6	38
α-helix	207-219	13
α-helix	220-223	4
α-helix	227-229	3
α-helix	239-242	4

Chain Ad: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	16-18	3
β-strand	30-31	2	57
α-helix	33-35	3
β-strand	38-39	2	57
α-helix	40-50	11
β-strand	53	1	281

Chain AD: 10 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	7-28	22
α-helix	30-32	3
β-strand	34-41	8	53
β-strand	46-52	7	53
α-helix	55-59	5
α-helix	66-77	12
β-strand	85-89	5	53
α-helix	94-96	3
α-helix	98-110	13
α-helix	116-128	13
β-strand	133-140	8	54
β-strand	148-155	8	54
α-helix	162-167	6
β-strand	168-176	9	54
β-strand	181-189	9	54
α-helix	192-194	3
β-strand	207-208	2	55
α-helix	209	1
β-strand	222-224	3	56

143 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	A2	RNA	1800	Saccharomyces cerevisiae
40S ribosomal protein S0-A	AA, CA	protein	252	Saccharomyces cerevisiae	P32905 (AlphaFold model)
40S ribosomal protein S1-A	AB, CB	protein	255	Saccharomyces cerevisiae	P33442 (AlphaFold model)
40S ribosomal protein S2	AC, CC	protein	254	Saccharomyces cerevisiae	P25443 (AlphaFold model)
40S ribosomal protein S3	AD, CD	protein	240	Saccharomyces cerevisiae	P05750 (AlphaFold model)
40S ribosomal protein S4-A	AE, CE	protein	261	Saccharomyces cerevisiae	P0CX35
40S ribosomal protein S5	AF, CF	protein	225	Saccharomyces cerevisiae	P26783
40S ribosomal protein S6-A	AG, CG	protein	236	Saccharomyces cerevisiae	P0CX37
40S ribosomal protein S7-A	AH, CH	protein	190	Saccharomyces cerevisiae	P26786
40S ribosomal protein S8-A	AI, CI	protein	200	Saccharomyces cerevisiae	P0CX39
40S ribosomal protein S9-A	AJ, CJ	protein	197	Saccharomyces cerevisiae	O13516
40S ribosomal protein S10-A	AK, CK	protein	105	Saccharomyces cerevisiae	Q08745

73 more molecules are not listed.

Sequence of entity 1 (A2), FASTA

>4V88_1 18S RIBOSOMAL RNA (chains A2)
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
AUCUGCUUAGAGANNNNNNNNNNNNNNUCUCAGAGCGGAGAAUUUGGACAAACUUGGUCA
UUUAGAGGAACUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA

Sequence of entity 2 (AA, CA), FASTA

>4V88_2 40S ribosomal protein S0-A (chains AA, CA)
MSLPATFDLTPEDAQLLLAANTHLGARNVQVHQEPYVFNARPDGVHVINVGKTWEKLVLA
ARIIAAIPNPEDVVAISSRTFGQRAVLKFAAHTGATPIAGRFTPGSFTNYITRSFKEPRL
VIVTDPRSDAQAIKEASYVNIPVIALTDLDSPSEFVDVAIPCNNRGKHSIGLIWYLLARE
VLRLRGALVDRTQPWSIMPDLYFYRDPEEVEQQVAEEATTEEAGEEEAKEEVTEEQAEAT
EWAEENADNVEW

Sequence of entity 3 (AB, CB), FASTA

>4V88_3 40S ribosomal protein S1-A (chains AB, CB)
MAVGKNKRLSKGKKGQKKRVVDPFTRKEWFDIKAPSTFENRNVGKTLVNKSTGLKSASDA
LKGRVVEVCLADLQGSEDHSFRKIKLRVDEVQGKNLLTNFHGMDFTTDKLRSMVRKWQTL
IEANVTVKTSDDYVLRIFAIAFTRKQANQVKRHSYAQSSHIRAIRKVISEILTKEVQGST
LAQLTSKLIPEVINKEIENATKDIFPLQNIHVRKVKLLKQPKFDVGALMALHGEGSGEEK
GKKVTGFKDEVLETV

Sequence of entity 4 (AC, CC), FASTA

>4V88_4 40S ribosomal protein S2 (chains AC, CC)
MSAPEAQQQKRGGFGGRNRGRPNRRGPRNTEEKGWVPVTKLGRLVKAGKITTIEEIFLHS
LPVKEFQIIDTLLPGLQDEVMNIKPVQKQTRAGQRTRFKAVVVVGDSNGHVGLGIKTAKE
VAGAIRAGIIIAKLSVIPIRRGYWGTNLGQPHSLATKTTGKCGSVTVRLIPAPRGSGIVA
SPAVKKLLQLAGVEDVYTQSNGKTRTLENTLKAAFVAIGNTYGFLTPNLWAEQPLPVSPL
DIYSDEASAQKKRF

Sequence of entity 5 (AD, CD), FASTA

>4V88_5 40S ribosomal protein S3 (chains AD, CD)
MVALISKKRKLVADGVFYAELNEFFTRELAEEGYSGVEVRVTPTKTEVIIRATRTQDVLG
ENGRRINELTLLVQKRFKYAPGTIVLYAERVQDRGLSAVAQAESMKFKLLNGLAIRRAAY
GVVRYVMESGAKGCEVVVSGKLRAARAKAMKFADGFLIHSGQPVNDFIDTATRHVLMRQG
VLGIKVKIMRDPAKSRTGPKALPDAVTIIEPKEEEPILAPSVKDYRPAEETEAQAEPVEA

Sequence of entity 6 (AE, CE), FASTA

>4V88_6 40S ribosomal protein S4-A (chains AE, CE)
MARGPKKHLKRLAAPHHWLLDKLSGCYAPRPSAGPHKLRESLPLIVFLRNRLKYALNGRE
VKAILMQRHVKVDGKVRTDTTYPAGFMDVITLDATNENFRLVYDVKGRFAVHRITDEEAS
YKLGKVKKVQLGKKGVPYVVTHDGRTIRYPDPNIKVNDTVKIDLASGKITDFIKFDAGKL
VYVTGGRNLGRIGTIVHKERHDGGFDLVHIKDSLDNTFVTRLNNVFVIGEQGKPYISLPK
GKGIKLSIAEERDRRRAQQGL

Sequence of entity 7 (AF, CF), FASTA

>4V88_7 40S ribosomal protein S5 (chains AF, CF)
MSDTEAPVEVQEDFEVVEEFTPVVLATPIPEEVQQAQTEIKLFNKWSFEEVEVKDASLVD
YVQVRQPIFVAHTAGRYANKRFRKAQCPIIERLTNSLMMNGRNNGKKLKAVRIIKHTLDI
INVLTDQNPIQVVVDAITNTGPREDTTRVGGGGAARRQAVDVSPLRRVNQAIALLTIGAR
EAAFRNIKTIAETLAEELINAAKGSSTSYAIKKKDELERVAKSNR

Sequence of entity 8 (AG, CG), FASTA

>4V88_8 40S ribosomal protein S6-A (chains AG, CG)
MKLNISYPVNGSQKTFEIDDEHRIRVFFDKRIGQEVDGEAVGDEFKGYVFKISGGNDKQG
FPMKQGVLLPTRIKLLLTKNVSCYRPRRDGERKRKSVRGAIVGPDLAVLALVIVKKGEQE
LEGLTDTTVPKRLGPKRANNIRKFFGLSKEDDVRDFVIRREVTKGEKTYTKAPKIQRLVT
PQRLQRKRHQRALKVRNAQAQREAAAEYAQLLAKRLSERKAEKAEIRKRRASSLKA

Sequence of entity 9 (AH, CH), FASTA

>4V88_9 40S ribosomal protein S7-A (chains AH, CH)
MSAPQAKILSQAPTELELQVAQAFVELENSSPELKAELRPLQFKSIREIDVAGGKKALAI
FVPVPSLAGFHKVQTKLTRELEKKFQDRHVIFLAERRILPKPSRTSRQVQKRPRSRTLTA
VHDKILEDLVFPTEIVGKRVRYLVGGNKIQKVLLDSKDVQQIDYKLESFQAVYNKLTGKQ
IVFEIPSETH

Sequence of entity 10 (AI, CI), FASTA

>4V88_10 40S ribosomal protein S8-A (chains AI, CI)
MGISRDSRHKRSATGAKRAQFRKKRKFELGRQPANTKIGAKRIHSVRTRGGNKKYRALRI
ETGNFSWASEGISKKTRIAGVVYHPSNNELVRTNTLTKAAIVQIDATPFRQWFEAHYGQT
LGKKKNVKEEETVAKSKNAERKWAARAASAKIESSVESQFSAGRLYACISSRPGQSGRCD
GYILEGEELAFYLRRLTAKK

Sequence of entity 11 (AJ, CJ), FASTA

>4V88_11 40S ribosomal protein S9-A (chains AJ, CJ)
MPRAPRTYSKTYSTPKRPYESSRLDAELKLAGEFGLKNKKEIYRISFQLSKIRRAARDLL
TRDEKDPKRLFEGNALIRRLVRVGVLSEDKKKLDYVLALKVEDFLERRLQTQVYKLGLAK
SVHHARVLITQRHIAVGKQIVNIPSFMVRLDSEKHIDFAPTSPFGGARPGRVARRNAARK
AEASGEAADEADEADEE

Sequence of entity 12 (AK, CK), FASTA

>4V88_12 40S ribosomal protein S10-A (chains AK, CK)
MLMPKEDRNKIHQYLFQEGVVVAKKDFNQAKHEEIDTKNLYVIKALQSLTSKGYVKTQFS
WQYYYYTLTEEGVEYLREYLNLPEHIVPGTYIQERNPTQRPQRRY

Ligands and cofactors

ID	Name	Formula	Copies
OHX	osmium (III) hexammine	H12 N6 Os	1345
MG	Magnesium ion	Mg	2205
ZN	Zinc ion	Zn	16

Primary citation

The structure of the eukaryotic ribosome at 3.0 angstrom resolution. Ben-Shem, A., Garreau de Loubresse, N., Melnikov, S. et al. Science (2011) 334:1524-1529. 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

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