8P09: PDB entry 8P09

Name: PDB 8P09: 48S late-stage initiation complex with non methylated mRNA
Published: 2024-03-20
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: translation

48S late-stage initiation complex with non methylated mRNA. Determined by electron microscopy at 3.3 Å resolution. Released 20 Mar 2024.

Method: Electron microscopy
Resolution: 3.3 Å
Organism: Oryctolagus cuniculus
Chains: 40
Atoms: 86,284
Mol. weight: 1336.47 kDa
Ligands: MG
Released: 20 Mar 2024

Explore 8P09 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8P09 contains 229 α-helices and 297 β-strands across 37 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: 6 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	7-15	9	6
β-strand	20-27	8	6
α-helix	34-36	3
α-helix	37-48	12
β-strand	55-62	8	6
β-strand	69-76	8	6
α-helix	80-85	6
α-helix	88-93	6
α-helix	104-114	11
α-helix	123-126	4

Chain A: 13 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	14-15	2
β-strand	19-27	9	7
β-strand	32-34	3	7
β-strand	44-46	3	7
α-helix	48-50	3
α-helix	59-61	3
β-strand	68-77	10	7
β-strand	82-86	5	7
α-helix	92-111	20
α-helix	115-118	4
α-helix	125-131	7
α-helix	132-136	5
α-helix	137-142	6
α-helix	149-158	10
α-helix	172-183	12
β-strand	196	1	8
α-helix	204-212	9
β-strand	226-228	3	9
β-strand	234	1	8
β-strand	236-238	3	9
α-helix	249-252	4
α-helix	254-264	11

Chain b: 5 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	20-22	3	10
β-strand	28	1	85
β-strand	29-31	3	10
β-strand	36-43	8	11
α-helix	50-53	4
β-strand	57	1	84
α-helix	64-65	2
β-strand	66-73	8	11
α-helix	75-80	6
α-helix	90-92	3
α-helix	97-99	3

Chain c: 0 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	32-34	3	14
β-strand	45-47	3	14
β-strand	64-65	2	15
β-strand	72-73	2	15
β-strand	80-81	2	14

Chain C: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	10-11	2
α-helix	12-21	10
β-strand	25	1	12
β-strand	38-41	4	12
β-strand	47-49	3	12
α-helix	51-66	16
β-strand	76-78	3	13
α-helix	81-93	13
β-strand	98-100	3	13
β-strand	123-125	3	13
α-helix	131-137	7
β-strand	145-148	4	13
β-strand	159-162	4	13
α-helix	169-186	18
α-helix	199-202	4

Chain d: 0 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	10	1	18
β-strand	13	1	19
β-strand	14-17	4	20
β-strand	28-32	5	20
β-strand	42-46	5	20
β-strand	55	1	19
β-strand	58	1	18

Chain D: 9 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	28-34	7	16
β-strand	43-50	8	16
α-helix	51-52	2
α-helix	58-61	4
β-strand	66-69	4	16
α-helix	72-75	4
β-strand	84-91	8	16
β-strand	95-103	9	16
α-helix	107-111	5
β-strand	120-128	9	17
β-strand	134-142	9	17
α-helix	158-177	20
α-helix	181-188	8
α-helix	192-200	9
α-helix	201-203	3
β-strand	209-219	11	17
α-helix	225-231	7

Chain e: 2 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	30-31	2	25
α-helix	33-35	3
β-strand	38-39	2	25
α-helix	40-46	7
β-strand	53-54	2	96

29 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
initiator methionylated tRNA	1	RNA	75	Oryctolagus cuniculus
18S ribosomal RNA	2	RNA	1863	Oryctolagus cuniculus
mRNA	3	RNA	9	Oryctolagus cuniculus
Eukaryotic translation initiation factor 2 subunit 1	A	protein	284	Oryctolagus cuniculus	G1T2G4 (AlphaFold model)
40S ribosomal protein SA	C	protein	207	Oryctolagus cuniculus	G1TLT8 (AlphaFold model)
ribosomal protein eS1	D	protein	215	Oryctolagus cuniculus	G1TN72 (AlphaFold model)
40S ribosomal protein S2	E	protein	270	Oryctolagus cuniculus	G1TUT9
Ribosomal protein S3	F	protein	227	Oryctolagus cuniculus	G1TNM3
40S ribosomal protein S4	G	protein	263	Oryctolagus cuniculus	G1TK17
Ribosomal protein S5	H	protein	191	Oryctolagus cuniculus	U3KMN4
40S ribosomal protein S6	I	protein	237	Oryctolagus cuniculus	A0A5K1UJS7
ribosomal protein eS7	J	protein	190	Oryctolagus cuniculus	G1SVB0

28 more molecules are not listed.

Sequence of entity 1 (1), FASTA

>8P09_1 initiator methionylated tRNA (chains 1)
AGCAGAGUGGCGCAGCGGAAGCGUGCUGGGCCCAUAACCCAGAGGUCGAUGGAUCGAAAC
CAUCCUCUGCUACCA

Sequence of entity 2 (2), FASTA

>8P09_2 18S ribosomal RNA (chains 2)
UACCUGGUUGAUCCUGCCAGUAGCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUA
AGUACGCACGGCCGGUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUGGUUCCUU
UGGUCGCUCGCUCCUCUCCUACUUGGAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCCG
ACGGCGCUGACUCCCUUUGUGUGGGAUGCGUGCAUUUAUCAGAUCAAAACCAACCCGGUC
AGCCUCCCCGCCGGCCGGGGGGGUGGGGCGGCGGCUUUGGUGACUCUAGAUAACCUCGGG
CCGAUCGCAGCCCUCCGUGGCGGCGACGACCCAUUCGAACGUCUGCCCUAUCAACUUUCG
AUGGUAGUCGCCGUGCCUACCAUGGUGACCACGGGUGACGGGGAAUCAGGGUUCGAUUCC
GGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUAC
CCACUCCCGACCCGGGGAGGUAGUGACGAAAAAUAACAAUACAGGACUCUUUCGAGGCCC
UGUAAUUGGAAUGAGUCCACUUUAAAUCCUUUAACGAGGAUCCAUUGGAGGGCAAGUCUG
GUCGCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGCUGCAGUUAAA
AAGCUCGUAGUUGGAUCUUGUGGAGGGUGCGUAGCGGGCGGUCCGCCGCGAGGCGAGCCA
CCGCCCGUCCCCGCCCCUUGCCUCUCGGCGCCCCCUCGAUGCUCUUAGCUGAGUGUCCCG
CGGGGCCCGAAGCGUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCCCGAGCCGCCU
GGAUACCGCAGCUAGGAAUAAUGGAAUAGGACCGCGGUUCUAUUUUGUUGGUUUUCGGAA
CUGAGGCCAUGAUUAAGAGGGACGGCCGGGGGCAUUCGUAUUGCGCCGCUAGAGGUGAAA
UUCUUGGACCGGCGCAAGACGGACCAGAGCGAAAGCAUUUGCCAAGAAUGUUUUCAUUAA
UCAAGAACGAAAGUCGGAGGUUCGAAGACGAUCAGAUACCGUCGUAGUUCCGACCAUAAA
CGAUGCCGACUGGCGAUGCGGCGGCGUUAUUCCCAUGACCCGCCGGGCAGCUUCCGGGAA
ACCAAAGUCUUUGGGUUCCGGGGGGAGUAUGGUUGCAAAGCUGAAACUUAAAGGAAUUGA
CGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACXCAACACGGGAAACCUC
ACCCGGCCCGGACACGGACAGGAUUGACAGAUUGAUAGCUCUUUCUCGAUUCUGUGGGUG
GUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGAUAACGAAC
GAGACUCUGGCAUGCUAACUAGUUACGCGACCCCCGAGCGGUCGGCGUCCCCCAACUUCU
UAGAGGGACAAGUGGCGUUCAGCCACCCGAGAUUGAGCAAUAACAGGUCUGUGAUGCCCU
UAGAUGUCGGGGCUGCACGCGCGCUACACUGACUGGCUCAGCGUGUGCCUACCCUACGCC
GGCAGGCGCGGGUAACCCGUUGAACCCCAUUCGUGAUGGGGAUCGGGGAUUGCAAUUAUU
CCCCAUGAACGAGGAAUUCCCAGUAAGUGCGGGUCAUAAGCUUGCGUUGAUUAAGUCCCU
GCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGGAUGGUUUAGUGAGGCCCUCGGA
UCGGCCCGCCGGGGUCGGCCCACGGCCCUGGCGGAGCGCUGAGAAGACGGUCGAACUUGA
CUAUCUAGAGGAAGUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCA
UUA

Sequence of entity 3 (3), FASTA

>8P09_3 mRNA (chains 3)
ACACCAUGG

Sequence of entity 4 (A), FASTA

>8P09_4 Eukaryotic translation initiation factor 2 subunit 1 (chains A)
MPGLSCRFYQHKFPEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSIN
KLIRIGRNECVVVIRVDKEKGYIDLSKRRVSPEEAIKCEDKFTKSKTVYSILRHVAEVLE
YTKDEQLESLFQRTAWVFDDKYKRPGYGAYDAFKHAVSDPSILDSLDLNEDEREVLINNI
NRRLTPQAVKIRADIEVACYGYEGIDAVKEALRAGLNCSTETMPIKINLIAPPRYVMTTT
TLERTEGLSVLNQAMAVIKEKIEEKRGVFNVQMEQVWKTPRRKT

Sequence of entity 5 (C), FASTA

>8P09_5 40S ribosomal protein SA (chains C)
GALDVLQMKEEDVLKFLAAGTHLGGTNLDFQMEQYIYKRKSDGIYIINLKRTWEKLLLAA
RAIVAIENPADVSVISSRNTGQRAVLKFAAATGATPIAGRFTPGTFTNQIQAAFREPRLL
VVTDPRADHQPLTEASYVNLPTIALCNTDSPLRYVDIAIPCNNKGAHSVGLMWWMLAREV
LRMRGTISREHPWEVMPDLYFYRDPEE

Sequence of entity 6 (D), FASTA

>8P09_6 ribosomal protein eS1 (chains D)
KKVVDPFSKKDWYDVKAPAMFNIRNIGKTLVTRTQGTKIASDGLKGRVFEVSLADLQNDE
VAFRKFKLITEDVQGKNCLTNFHGMDLTRDKMCSMVKKWQTMIEAHVDVKTTDGYLLHLF
CVGFTKKCNNQIRKTSYAQHQQVRQIRKKMMEIMTREVQTNDLKEVVNKLIPDSIGKDIE
KACQSIYPLHDVFVRKVKMLKKPKFELGKLMELHG

Sequence of entity 7 (E), FASTA

>8P09_7 40S ribosomal protein S2 (chains E)
LGFGGAEGGGGGRLLGLGSGRGRGRGARGGKAEDKEWLPVTKLGRLVKDVKIKSLEEIYL
FSLPIKESEIIDFFLGAALKDEVLKIMPVQKQTRAAQRTRFKAFVAIGDYNGHVGLGVKC
SKEVATAIRGAIILAKLSIVPVRRGYWGNKIGKPHTVPCKVTGRCGSVLVHLIPAPRGTG
IVSAPVPKKLLLMAGIDDCYTSAWSCTATLGNFAKATFDAISKTYSYLTPDLWKETVFTK
SPYQEFTDHLVKTHTRVSVQRTQAPAVATT

Sequence of entity 8 (F), FASTA

>8P09_8 Ribosomal protein S3 (chains F)
MAVQISKKRKFVADGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLG
EKGRRIRELTAVVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRRACY
GVLRFIMESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPVNYYVDTAVRHVLLRQG
VLGIKVKIMLPWDPSGKIGPKKPLPDHVSIVEPKDEILPTTPISEQK

Sequence of entity 9 (G), FASTA

>8P09_9 40S ribosomal protein S4 (chains G)
MARGPKKHLKRVAAPKHWMLDKLTSVFAPRPSTGPHKLRECLPLIIFLRNKLKYALTGDE
VKKICMQRFIKIDGKVRADITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRITPEEAK
YKLCKVRKIFVGTKGIPHLVTHDARTIRYPDPLIKMNDTIQIDLETGKITDFIKFDTGNL
CMVTGGANLGRIGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGKGNKPWISLPR
GKGIRLTIAEERDKRLAAKQSSG

Sequence of entity 10 (H), FASTA

>8P09_10 Ribosomal protein S5 (chains H)
TPDIKLFGKWSTDDVQINDISLQDYIAVKEKYAKYLPHSAGRYAAKRFRKAQCPIVERLT
NSMMMHGRNNGKKLMTVRIVKHAFEIIHLLTGENPLQVLVNAIINSGPREDSTRIGRAGT
VRRQAVDVSPLRRVNQAIWLLCTGAREAAFRNIKTIAECLADELINAAKGSSNSYAIKKK
DELERVAKSNR

Sequence of entity 11 (I), FASTA

>8P09_11 40S ribosomal protein S6 (chains I)
MKLNISFPATGCQKLIEVDDERKLRTFYEKRMATEVAADALGEEWKGYVVRISGGNDKQG
FPMKQGVLTHGRVRLLLSKGHSCYRPRRTGERKRKSVRGCIVDANLSVLNLVIVKKGEKD
IPGLTDTTVTRRLGPKRASRIRKLFNLSKEDDVRQYVVRKPLNKEGKKPRTKAPKIQRLV
TPRVLQHKRRRIALKKQRTKKNKEEAAEYAKLLAKRMKEAKEKRQEQIAKRRRLSSL

Sequence of entity 12 (J), FASTA

>8P09_12 ribosomal protein eS7 (chains J)
SAKIVKPNGEKPDEFESGISQALLELEMNSDLKAQLRELNITAAKEIEVGGGRKAIIIFV
PVPQLKSFQKIQVRLVRELEKKFSGKHVVFIAQRRILPKPTRKSRTKNKQKRPRSRTLTA
VHDAILEDLVFPSEIVGKRIRVKLDGSRLIKVHLDKAQQNNVEHKVETFSGVYKKLTGKD
VNFEFPEFQL

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	230

Primary citation

N 6 -methyladenosine in 5' UTR does not promote translation initiation. Guca, E., Alarcon, R., Palo, M.Z. et al. Mol Cell (2024) 84:584-595.e6. DOI 10.1016/j.molcel.2023.12.028 · PubMed

Other PDB entries of the same protein (UniProt G1T2G4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9H6Y 2.9 Å, Late-stage 48S Initiation Complex (LS48S IC) guided by the trans-RNA
9H74 2.9 Å, Late-stage 48S Initiation Complex with eIF3 (LS48S-eIF3 IC) guided by the trans-RNA
6YAL 3.0 Å, Mammalian 48S late-stage initiation complex with beta-globin mRNA
8P03 3.04 Å, 48S late-stage initiation complex with m6A mRNA
6YAN 3.48 Å, Mammalian 48S late-stage translation initiation complex with histone 4 mRNA
6YAM 3.6 Å, Mammalian 48S late-stage translation initiation complex (LS48S+eIF3 IC) with beta-globin…
5K0Y 5.8 Å, m48S late-stage initiation complex, purified from rabbit reticulocytes lysates,…
9CPA 6.0 Å, Structure of a Mammalian DHX29-bound 43S Pre-initiation Complex

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