6P4H: Mammalian small ribosomal subunit

Name: PDB 6P4H: Structure of a mammalian small ribosomal subunit in complex with the Israeli Acute Paralysis Virus IRES (Class 2)
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 2). Determined by electron microscopy at 3.2 Å resolution. Released 18 Sept 2019.

Method: Electron microscopy
Resolution: 3.2 Å
Organisms: Oryctolagus cuniculus, Israeli acute paralysis virus
Chains: 36
Atoms: 79,374
Mol. weight: 1316.29 kDa
Released: 18 Sept 2019

Explore 6P4H in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6P4H contains 210 α-helices and 250 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	4
β-strand	50	1	65
α-helix	53-61	9
α-helix	62-64	3
β-strand	68	1	5
α-helix	70-76	7
β-strand	79	1	4
α-helix	81-93	13
β-strand	97-101	5	5
β-strand	108-111	4	5

Chain b: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	19	1
β-strand	20-22	3	8
β-strand	29-31	3	8
β-strand	36-40	5	9
β-strand	43	1	10
α-helix	50-56	7
β-strand	57	1	59
α-helix	62-65	4
β-strand	66	1	10
β-strand	69-73	5	9
α-helix	75-80	6
α-helix	91-93	3
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	2
α-helix	32-37	6
β-strand	40-41	2	2
α-helix	42	1
β-strand	47-48	2	2
α-helix	51-67	17
β-strand	74-78	5	3
α-helix	81-94	14
β-strand	97-100	4	3
β-strand	121-124	4	3
α-helix	131-139	9
β-strand	144-148	5	3
β-strand	159-162	4	3
α-helix	168-186	19
α-helix	194-195	2
α-helix	199-202	4
α-helix	207-216	10

Chain c: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	12-17	6
β-strand	32-36	5	14
β-strand	44-47	4	14
β-strand	54-55	2	15
β-strand	62-65	4	15
α-helix	71	1
β-strand	72-73	2	15
α-helix	74	1
β-strand	78-81	4	14

Chain C: 9 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	24-27	4
β-strand	28-34	7	6
β-strand	43-50	8	6
α-helix	58-61	4
β-strand	66-70	5	6
α-helix	71-74	4
β-strand	82-91	10	6
β-strand	95-105	11	6
α-helix	107-113	7
β-strand	120-128	9	6
β-strand	134-142	9	6
β-strand	143	1	7
α-helix	144-146	3
α-helix	158-177	20
α-helix	181-188	8
α-helix	192-200	9
β-strand	207	1	7
β-strand	211-214	4	6
β-strand	217-219	3	6
α-helix	225-231	7

Chain d: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	10-21	12	21
β-strand	27-34	8	21
β-strand	41-47	7	21
β-strand	55-58	4	21
α-helix	65-67	3

Chain D: 12 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	65-71	7
α-helix	79-83	5
α-helix	92-97	6
α-helix	99-101	3
β-strand	103-115	13	11
β-strand	120-132	13	11
β-strand	136-144	9	11
α-helix	147-160	14
β-strand	163-164	2	11
α-helix	165-166	2
β-strand	168	1	12
β-strand	179	1	12
β-strand	184-188	5	13
β-strand	191-196	6	13
β-strand	204-205	2	13
α-helix	208-216	9
β-strand	221	1	12
β-strand	222-224	3	13
β-strand	227	1	13
α-helix	233-245	13
α-helix	253-255	3
α-helix	262-264	3
α-helix	265-268	4
α-helix	270-276	7

Chain e: 2 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	30-31	2	22
α-helix	33-35	3
β-strand	38-39	2	22
α-helix	40-50	11
β-strand	53	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)
Iapv-ires	1	RNA	253	Israeli acute paralysis virus
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	207	Oryctolagus cuniculus	G1TJW1
uS4	K	protein	194	Oryctolagus cuniculus	B7NZS8

24 more molecules are not listed.

Sequence of entity 1 (2), FASTA

>6P4H_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

>6P4H_2 uS2 (chains B)
MSGALDVLQMKEEDVLKFLAAGTHLGGTNLDFQMEQYIYKRKSDGIYIINLKRTWEKLLL
AARAIVAIENPADVSVISSRNTGQRAVLKFAAATGATPIAGRFTPGTFTNQIQAAFREPR
LLVVTDPQADHQPLMEASYVNLPTIALCNTDSPLHYVDIAIPCNNKGAHSVGLMWWMLAQ
EVLRMRGTISREHPWEVMPDLYFYRDPEEIEKEEQAAAEKAVTKEEFQGEWTAPEPEFTA
TQPEVADWSEGMQVPSVPIQQFPTEDWSAQPATEDWSAAPTAQATEWMGTTTEWS

Sequence of entity 3 (C), FASTA

>6P4H_3 eS1 (chains C)
MAVGKNKRLTKGGKKGAKKKVVDPFSKKDWYDVKAPAMFNIRNIGKTLVTRTQGTKIASD
GLKGRVFEVSLADLQNDEVAFRKFKLITEDVQGKNCLTNFHGMDLTRDKMCSMVKKWQTM
IEAHVDVKTTDGYLLRLFCVGFTKKRNNQIRKTSYAQHQQVRQIRKKMMEIMTREVQTND
LKEVVNKLIPDSIGKDIEKACQSIYPLHDVFVRKVKMLKKPKFELGKLMELHGEGSSSGK
ATGDETGAKVERADGYEPPVQESV

Sequence of entity 4 (D), FASTA

>6P4H_4 uS5 (chains D)
MADDAGAAGGPGGPGGPGNKEWLPVTKLGRLVKDMKIKSLEEIYLFSLPIKESEIIDFCL
GAALKDEVLKIMPVQKQTRAGQRTRFKAFVAIGDYNGHVGLGLKCSKEVATAIRGAIILA
KLSIVPVRRGYWGNKIGKPHTVPCKVTGRCGSVLVRLIPAPRGTGIVSAPVPKKLLLMAG
IDDCYTSARGCTATLGNFAKATFDAISKTYSYLTPDLWKETVFTKSPYQEFTNHLMKTHT
RVSVQRTQAPAVATT

Sequence of entity 5 (E), FASTA

>6P4H_5 uS3 (chains E)
MSARRRRRRAAFRRRAEPFIPISVREPLPFLSAARGGKMAVQISKKRKFVADGIFKAELN
EFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLGEKGRRIRELTAVVQKRFGFPEG
SVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFIMESGAKGCEVVVSGKL
RGQRAKSMKFVDGLMIHSGDPVNYYVDTAVRHVLLRQGVLGIKVKIMLPWDPSGKIGPKK
PLPDHVSIVEPKDEILPTTPISEQKGGKPEPPAMPQPVPTA

Sequence of entity 6 (1), FASTA

>6P4H_6 IAPV-IRES (chains 1)
GAGCGGUUUCUGGAAUACUAUAUGUAAGUAUAGUGUUCUGGAGGCAUCAUUCUAUGGUUA
CCCAUCAUUAGAGGAAAUUUCCAAUAAACUCUGGUGUAAGGCUUAGAGUGAUGGUCGAGG
UGCCCUAUUUAGGGUGAGGAGCCUCGGUGGCAGCCCCACCAAAUCCUCUAUUGGAUAGGA
ACAGCUGUACUGGGCAGUUACAGCAGUCGUAUGGUAACACAUGCGGCGUUCCGAAAUACC
AUGCCUGGCGAUG

Sequence of entity 7 (F), FASTA

>6P4H_7 eS4 (chains F)
MARGPKKHLKRVAAPKHWMLDKLTSVFAPRPSTGPHKLRECLPLIIFLRNKLKYALTGDE
VKKICMQRFIKIDGKVRADITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRITPEEAK
YKLCKVRKIFVGTKGIPHLVTHDARTIRYPDPLIKMNDTIQIDLETGKITDFIKFDTGNL
CMVTGGANLGRIGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGKGNKPWISLPR
GKGIRLTIAEERDKRLAAKQSSG

Sequence of entity 8 (G), FASTA

>6P4H_8 uS7 (chains G)
MTEWETAAPAVAETPDIKLFGKWSTDDVQINDISLQDYIAVKEKYAKYLPHSAGRYAAKR
FRKAQCPIVERLTNSMMMHGRNNGKKLMTVRIVKHAFEIIHLLTGENPLQVLVNAIINSG
PREDSTRIGRAGTVRRQAVDVSPLRRVNQAIWLLCTGAREAAFRNIKTIAECLADELINA
AKGSSNSYAIKKKDELERVAKSNR

Sequence of entity 9 (H), FASTA

>6P4H_9 eS6 (chains H)
MKLNISFPATGCQKLIEVDDERKLRTFYEKRMATEVAADALGEEWKGYVVRISGGNDKQG
FPMKQGVLTHGRVRLLLSKGHSCYRPRRTGERKRKSVRGCIVDANLSVLNLVIVKKGEKD
IPGLTDTTVPRRLGPKRASRIRKLFNLSKEDDVRQYVVRKPLNKEGKKPRTKAPKIQRLV
TPRVLQHKRRRIALKKQRTKKNKEEAAEYAKLLAKRMKEAKEKRQEQIAKRRRLSSLRAS
TSKSESSQK

Sequence of entity 10 (I), FASTA

>6P4H_10 eS7 (chains I)
MFSSSAKIVKPNGEKPDEFESGISQALLELEMNSDLKAQLRELNITAAKEIEVGGGRKAI
IIFVPVPQLKSFQKIQVRLVRELEKKFSGKHVVFIAQRRILPKPTRKSRTKNKQKRPRSR
TLTAVHDAILEDLVFPSEIVGKRIRVKLDGSRLIKVHLDKAQQNNVEHKVETFSGVYKKL
TGKDVNFEFPEFQL

Sequence of entity 11 (J), FASTA

>6P4H_11 eS8 (chains J)
MGISRDNWHKRRKTGGKRKPYHKKRKYELGRPAANTKIGPRRIHTVRVRGGNKKYRALRL
DVGNFSWGSECCTRKTRIIDVVYNASNNELVRTKTLVKNCIVLIDSTPYRQWYESHYALP
LGRKKGAKLTPEEEEILNKKRSKKIQKKYDERKKNAKISSLLEEQFQQGKLLACIASRPG
QCGRADGYVLEGKELEFYLRKIKARKG

Sequence of entity 12 (K), FASTA

>6P4H_12 uS4 (chains K)
MPVARSWVCRKTYVTPRRPFEKSRLDQELKLIGEYGLRNKREVWRVKFTLAKIRKAAREL
LTLDEKDPRRLFEGNALLRRLVRIGVLDEGKMKLDYILGLKIEDFLERRLQTQVFKLGLA
KSIHHARVLIRQRHIRVRKQVVNIPSFIVRLDSQKHIDFSLRSPYGGGRPGRVKRKNAKK
GQGGAGAGDDEEED

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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