6P4G: Mammalian small ribosomal subunit

Name: PDB 6P4G: Structure of a mammalian small ribosomal subunit in complex with the Israeli Acute Paralysis Virus IRES (Class 1)
Published: 2019-09-18
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Structure of a mammalian small ribosomal subunit in complex with the Israeli Acute Paralysis Virus IRES (Class 1). Determined by electron microscopy at 3.1 Å resolution. Released 18 Sept 2019.

Method: Electron microscopy
Resolution: 3.1 Å
Organisms: Oryctolagus cuniculus, Israeli acute paralysis virus
Chains: 36
Atoms: 79,374
Mol. weight: 1316.42 kDa
Released: 18 Sept 2019

Explore 6P4G in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6P4G contains 208 α-helices and 257 β-strands across 34 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: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	47	1	1
β-strand	50	1	66
α-helix	52-61	10
α-helix	62-64	3
β-strand	68	1	2
α-helix	70-76	7
β-strand	79	1	1
α-helix	81-93	13
β-strand	98-102	5	2
β-strand	107-110	4	2

Chain b: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	20-22	3	5
β-strand	29-31	3	5
β-strand	38-43	6	6
α-helix	50-55	6
β-strand	57	1	59
α-helix	63-65	3
β-strand	66-71	6	6
α-helix	75-80	6
α-helix	97-98	2

Chain B: 10 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	12-21	10
β-strand	25	1	3
α-helix	32-34	3
β-strand	40	1	3
α-helix	46-47	2
β-strand	48	1	3
α-helix	49	1
α-helix	51-67	17
β-strand	75-78	4	4
α-helix	81-94	14
β-strand	97-100	4	4
β-strand	122-124	3	4
α-helix	131-137	7
β-strand	144-148	5	4
β-strand	159-162	4	4
α-helix	168-186	19
α-helix	199-201	3
α-helix	207-213	7

Chain c: 2 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	12-17	6
β-strand	32-36	5	9
β-strand	44-47	4	9
β-strand	55	1	10
β-strand	62	1	10
β-strand	64-65	2	11
β-strand	72-73	2	11
α-helix	74	1
β-strand	78-82	5	9

Chain C: 9 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	24-26	3
β-strand	28-34	7	7
β-strand	43-50	8	7
β-strand	66-70	5	7
α-helix	71-73	3
β-strand	82-91	10	7
β-strand	95-105	11	7
α-helix	107-113	7
β-strand	120-128	9	7
β-strand	134-142	9	7
β-strand	143	1	8
α-helix	144-146	3
α-helix	158-174	17
α-helix	181-188	8
α-helix	193-200	8
β-strand	207	1	8
β-strand	211-214	4	7
β-strand	217-219	3	7
α-helix	223-224	2
α-helix	225-230	6

Chain d: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	10-17	8	15
β-strand	21	1	15
β-strand	27-34	8	15
β-strand	41-47	7	15
α-helix	54	1
β-strand	55-58	4	15
α-helix	65-67	3

Chain D: 10 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	65-71	7
α-helix	78-83	6
α-helix	92-97	6
β-strand	103-114	12	12
β-strand	121-132	12	12
β-strand	136-144	9	12
α-helix	147-161	15
β-strand	163-164	2	12
β-strand	168	1	13
β-strand	179	1	13
β-strand	184-188	5	14
β-strand	191-196	6	14
β-strand	204-205	2	14
α-helix	208-216	9
β-strand	222-227	6	14
α-helix	233-245	13
α-helix	246-249	4
α-helix	253-256	4
α-helix	265-268	4
α-helix	270-276	7

Chain e: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	3-6	4
β-strand	30-31	2	21
α-helix	33-35	3
β-strand	38-39	2	21
α-helix	42-50	9
β-strand	54	1	73

26 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 rRNA	2	RNA	1869	Oryctolagus cuniculus
uS2	B	protein	295	Oryctolagus cuniculus	G1TLT8 (AlphaFold model)
eS1	C	protein	264	Oryctolagus cuniculus	G1SS70 (AlphaFold model)
uS5	D	protein	255	Oryctolagus cuniculus	G1SWM1 (AlphaFold model)
uS3	E	protein	281	Oryctolagus cuniculus	G1TNM3 (AlphaFold model)
eS4	F	protein	263	Oryctolagus cuniculus	G1TK17
uS7	G	protein	204	Oryctolagus cuniculus	G1TFM5
eS6	H	protein	249	Oryctolagus cuniculus	G1TM55
eS7	I	protein	194	Oryctolagus cuniculus	G1SVB0
eS8	J	protein	208	Oryctolagus cuniculus	G1TJW1
uS4	K	protein	194	Oryctolagus cuniculus	B7NZS8
eS10	L	protein	149	Oryctolagus cuniculus	G1TPV3

24 more molecules are not listed.

Sequence of entity 1 (2), FASTA

>6P4G_1 18S rRNA (chains 2)
UACCUGGUUGAUCCUGCCAGUAGCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUA
AGUACGCACGGCCGGUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUGGUUCCUU
UGGUCGCUCGCUCCUCUCCCACUUGGAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCCG
ACGGGCGCUGACCCCCUUCGCGGGGGGGAUGCGUGCAUUUAUCAGAUCAAAACCAACCCG
GUCAGCCCCUCUCCGGCCCCGGCCGGGGGGCGGGCGCCGGCGGCUUUGGUGACUCUAGAU
AACCUCGGGCCGAUCGCACGCCCCCCGUGGCGGCGACGACCCAUUCGAACGUCUGCCCUA
UCAACUUUCGAUGGUAGUCGCCGUGCCUACCAUGGUGACCACGGGUGACGGGGAAUCAGG
GUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCG
CGCAAAUUACCCACUCCCGACCCGGGGAGGUAGUGACGAAAAAUAACAAUACAGGACUCU
UUCGAGGCCCUGUAAUUGGAAUGAGUCCACUUUAAAUCCUUUAACGAGGAUCCAUUGGAG
GGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGC
UGCAGUUAAAAAGCUCGUAGUUGGAUCUUGGGAGCGGGCGGGCGGUCCGCCGCGAGGCGA
GCCACCGCCCGUCCCCGCCCCUUGCCUCUCGGCGCCCCCUCGAUGCUCUUAGCUGAGUGU
CCCGCGGGGCCCGAAGCGUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCCCGAGCC
GCCUGGAUACCGCAGCUAGGAAUAAUGGAAUAGGACCGCGGUUCUAUUUUGUUGGUUUUC
GGAACUGAGGCCAUGAUUAAGAGGGACGGCCGGGGGCAUUCGUAUUGCGCCGCUAGAGGU
GAAAUUCUUGGACCGGCGCAAGACGGACCAGAGCGAAAGCAUUUGCCAAGAAUGUUUUCA
UUAAUCAAGAACGAAAGUCGGAGGUUCGAAGACGAUCAGAUACCGUCGUAGUUCCGACCA
UAAACGAUGCCGACCGGCGAUGCGGCGGCGUUAUUCCCAUGACCCGCCGGGCAGCUUCCG
GGAAACCAAAGUCUUUGGGUUCCGGGGGGAGUAUGGUUGCAAAGCUGAAACUUAAAGGAA
UUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAA
CCUCACCCGGCCCGGACACGGACAGGAUUGACAGAUUGAUAGCUCUUUCUCGAUUCCGUG
GGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGAUAAC
GAACGAGACUCUGGCAUGCUAACUAGUUACGCGACCCCCGAGCGGUCGGCGUCCCCCAAC
UUCUUAGAGGGACAAGUGGCGUUCAGCCACCCGAGAUUGAGCAAUAACAGGUCUGUGAUG
CCCUUAGAUGUCCGGGGCUGCACGCGCGCUACACUGACUGGCUCAGCGUGUGCCUACCCU
ACGCCGGCAGGCGCGGGUAACCCGUUGAACCCCAUUCGUGAUGGGGAUCGGGGAUUGCAA
UUAUUCCCCAUGAACGAGGAAUUCCCAGUAAGUGCGGGUCAUAAGCUUGCGUUGAUUAAG
UCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGGAUGGUUUAGUGAGGCCC
UCGGAUCGGCCCCGCCGGGGUCGGCCCACGGCCCUGGCGGAGCGCUGAGAAGACGGUCGA
ACUUGACUAUCUAGAGGAAGUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAA
GGAUCAUUA

Sequence of entity 2 (B), FASTA

>6P4G_2 uS2 (chains B)
MSGALDVLQMKEEDVLKFLAAGTHLGGTNLDFQMEQYIYKRKSDGIYIINLKRTWEKLLL
AARAIVAIENPADVSVISSRNTGQRAVLKFAAATGATPIAGRFTPGTFTNQIQAAFREPR
LLVVTDPQADHQPLMEASYVNLPTIALCNTDSPLHYVDIAIPCNNKGAHSVGLMWWMLAQ
EVLRMRGTISREHPWEVMPDLYFYRDPEEIEKEEQAAAEKAVTKEEFQGEWTAPEPEFTA
TQPEVADWSEGMQVPSVPIQQFPTEDWSAQPATEDWSAAPTAQATEWMGTTTEWS

Sequence of entity 3 (C), FASTA

>6P4G_3 eS1 (chains C)
MAVGKNKRLTKGGKKGAKKKVVDPFSKKDWYDVKAPAMFNIRNIGKTLVTRTQGTKIASD
GLKGRVFEVSLADLQNDEVAFRKFKLITEDVQGKNCLTNFHGMDLTRDKMCSMVKKWQTM
IEAHVDVKTTDGYLLRLFCVGFTKKRNNQIRKTSYAQHQQVRQIRKKMMEIMTREVQTND
LKEVVNKLIPDSIGKDIEKACQSIYPLHDVFVRKVKMLKKPKFELGKLMELHGEGSSSGK
ATGDETGAKVERADGYEPPVQESV

Sequence of entity 4 (D), FASTA

>6P4G_4 uS5 (chains D)
MADDAGAAGGPGGPGGPGNKEWLPVTKLGRLVKDMKIKSLEEIYLFSLPIKESEIIDFCL
GAALKDEVLKIMPVQKQTRAGQRTRFKAFVAIGDYNGHVGLGLKCSKEVATAIRGAIILA
KLSIVPVRRGYWGNKIGKPHTVPCKVTGRCGSVLVRLIPAPRGTGIVSAPVPKKLLLMAG
IDDCYTSARGCTATLGNFAKATFDAISKTYSYLTPDLWKETVFTKSPYQEFTNHLMKTHT
RVSVQRTQAPAVATT

Sequence of entity 5 (E), FASTA

>6P4G_5 uS3 (chains E)
MSARRRRRRAAFRRRAEPFIPISVREPLPFLSAARGGKMAVQISKKRKFVADGIFKAELN
EFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLGEKGRRIRELTAVVQKRFGFPEG
SVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFIMESGAKGCEVVVSGKL
RGQRAKSMKFVDGLMIHSGDPVNYYVDTAVRHVLLRQGVLGIKVKIMLPWDPSGKIGPKK
PLPDHVSIVEPKDEILPTTPISEQKGGKPEPPAMPQPVPTA

Sequence of entity 6 (F), FASTA

>6P4G_6 eS4 (chains F)
MARGPKKHLKRVAAPKHWMLDKLTSVFAPRPSTGPHKLRECLPLIIFLRNKLKYALTGDE
VKKICMQRFIKIDGKVRADITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRITPEEAK
YKLCKVRKIFVGTKGIPHLVTHDARTIRYPDPLIKMNDTIQIDLETGKITDFIKFDTGNL
CMVTGGANLGRIGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGKGNKPWISLPR
GKGIRLTIAEERDKRLAAKQSSG

Sequence of entity 7 (G), FASTA

>6P4G_7 uS7 (chains G)
MTEWETAAPAVAETPDIKLFGKWSTDDVQINDISLQDYIAVKEKYAKYLPHSAGRYAAKR
FRKAQCPIVERLTNSMMMHGRNNGKKLMTVRIVKHAFEIIHLLTGENPLQVLVNAIINSG
PREDSTRIGRAGTVRRQAVDVSPLRRVNQAIWLLCTGAREAAFRNIKTIAECLADELINA
AKGSSNSYAIKKKDELERVAKSNR

Sequence of entity 8 (H), FASTA

>6P4G_8 eS6 (chains H)
MKLNISFPATGCQKLIEVDDERKLRTFYEKRMATEVAADALGEEWKGYVVRISGGNDKQG
FPMKQGVLTHGRVRLLLSKGHSCYRPRRTGERKRKSVRGCIVDANLSVLNLVIVKKGEKD
IPGLTDTTVPRRLGPKRASRIRKLFNLSKEDDVRQYVVRKPLNKEGKKPRTKAPKIQRLV
TPRVLQHKRRRIALKKQRTKKNKEEAAEYAKLLAKRMKEAKEKRQEQIAKRRRLSSLRAS
TSKSESSQK

Sequence of entity 9 (I), FASTA

>6P4G_9 eS7 (chains I)
MFSSSAKIVKPNGEKPDEFESGISQALLELEMNSDLKAQLRELNITAAKEIEVGGGRKAI
IIFVPVPQLKSFQKIQVRLVRELEKKFSGKHVVFIAQRRILPKPTRKSRTKNKQKRPRSR
TLTAVHDAILEDLVFPSEIVGKRIRVKLDGSRLIKVHLDKAQQNNVEHKVETFSGVYKKL
TGKDVNFEFPEFQL

Sequence of entity 10 (J), FASTA

>6P4G_10 eS8 (chains J)
MGISRDNWHKRRKTGGKRKPYHKKRKYELGRPAANTKIGPRRIHTVRVRGGNKKYRALRL
DVGNFSWGSECCTRKTRIIDVVYNASNNELVRTKTLVKNCIVLIDSTPYRQWYESHYALP
LGRKKGAKLTPEEEEILNKKRSKKIQKKYDERKKNAKISSLLEEQFQQGKLLACIASRPG
QCGRADGYVLEGKELEFYLRKIKARKGK

Sequence of entity 11 (K), FASTA

>6P4G_11 uS4 (chains K)
MPVARSWVCRKTYVTPRRPFEKSRLDQELKLIGEYGLRNKREVWRVKFTLAKIRKAAREL
LTLDEKDPRRLFEGNALLRRLVRIGVLDEGKMKLDYILGLKIEDFLERRLQTQVFKLGLA
KSIHHARVLIRQRHIRVRKQVVNIPSFIVRLDSQKHIDFSLRSPYGGGRPGRVKRKNAKK
GQGGAGAGDDEEED

Sequence of entity 12 (L), FASTA

>6P4G_12 eS10 (chains L)
MLMPKKNRIAIYELLFKEGVMVAKKDVHMPKHPELADKNVPNLHVMKAMQSLKSRGYVKE
QFAWRHFYWYLTNEGIQYLRDYLHLPPEIVPATLRRSRPETGRPRPKGLEGERPARLTRG
EADRDTYRRSAVPPGADKKAEAGAGSATE

Primary citation

The Israeli acute paralysis virus IRES captures host ribosomes by mimicking a ribosomal state with hybrid tRNAs. Acosta-Reyes, F., Neupane, R., Frank, J. et al. EMBO J (2019) 38:e102226-e102226. DOI 10.15252/embj.2019102226 · PubMed

Other PDB entries of the same protein (UniProt G1TLT8 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7O7Y 2.2 Å, Rabbit 80S ribosome stalled close to the mutated SARS-CoV-2 slippery site by a…
7OYD 2.3 Å, Cryo-EM structure of a rabbit 80S ribosome with zebrafish Dap1b
7O7Z 2.4 Å, Rabbit 80S ribosome stalled close to the mutated SARS-CoV-2 slippery site by a…
8SCB 2.5 Å, Terminating ribosome with SRI-41315
9MR4 2.65 Å, NAC: Ribosome nascent chain complex(Oxa1L)
9RHU 2.65 Å, Rabbit 80S ribosome in complex with eRF1-AAQ, stalled at the Stop codon in mutated F2A…
7JQB 2.7 Å, SARS-CoV-2 Nsp1 and rabbit 40S ribosome complex
8VVQ 2.7 Å, Codon sampling state of elongation inhibitor-treated mammalian ribosomes obtained from…
7ZJW 2.8 Å, Rabbit 80S ribosome as it decodes the Sec-UGA codon
9QQA 2.8 Å, Ternary complex of translating ribosome, NAC and NMT1
9Q7Q 2.86 Å, ABCE1-eRF1-rnc-AMD1C
7O80 2.9 Å, Rabbit 80S ribosome in complex with eRF1 and ABCE1 stalled at the STOP codon in the…

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