9H6Y: PDB entry 9H6Y

Name: PDB 9H6Y: Late-stage 48S Initiation Complex (LS48S IC) guided by the trans-RNA
Published: 2025-12-10
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: translation

Late-stage 48S Initiation Complex (LS48S IC) guided by the trans-RNA. Determined by electron microscopy at 2.9 Å resolution. Released 10 Dec 2025.

Method: Electron microscopy
Resolution: 2.9 Å
Organism: Oryctolagus cuniculus
Chains: 42
Atoms: 90,469
Mol. weight: 1522.59 kDa
Ligands: SF4
Released: 10 Dec 2025

Explore 9H6Y in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9H6Y contains 293 α-helices and 303 β-strands across 39 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: 7 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	6-15	10	9
β-strand	20-28	9	9
α-helix	34-36	3
α-helix	37-48	12
α-helix	52-54	3
β-strand	55-62	8	9
β-strand	68-76	9	9
α-helix	79-85	7
α-helix	88-92	5
α-helix	104-114	11
α-helix	122-124	3

Chain A: 13 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	14-15	2
β-strand	19-27	9	7
β-strand	31-36	6	7
β-strand	43-47	5	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	92-115	24
α-helix	124-130	7
α-helix	131-135	5
α-helix	136-137	2
α-helix	140-142	3
α-helix	149-158	10
α-helix	161-164	4
α-helix	170-184	15
β-strand	192-195	4	8
α-helix	204-211	8
β-strand	227-231	5	8
β-strand	234-238	5	8
α-helix	248-263	16

Chain b: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	20-22	3	15
β-strand	29-31	3	15
β-strand	36-43	8	16
α-helix	50-55	6
β-strand	57	1	76
α-helix	64-65	2
β-strand	66-73	8	16
α-helix	75-80	6
α-helix	91-93	3
α-helix	97-99	3

Chain B: 13 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	55-60	6	10
α-helix	68-73	6
β-strand	95-98	4	10
β-strand	101-103	3	11
α-helix	135-137	3
β-strand	138-141	4	11
β-strand	143-147	5	10
α-helix	152-154	3
α-helix	155-164	10
β-strand	167-173	7	10
α-helix	182-192	11
β-strand	198-204	7	10
α-helix	210-223	14
α-helix	224-226	3
β-strand	234-236	3	10
α-helix	245-254	10
α-helix	256-260	5
α-helix	266-267	2
β-strand	268-274	7	12
β-strand	291-298	8	12
β-strand	301-302	2	13
β-strand	306-314	9	12
α-helix	315	1
β-strand	324-330	7	12
β-strand	333-336	4	12
β-strand	339-341	3	12
β-strand	343-344	2	13
β-strand	349-353	5	12
α-helix	358-360	3
β-strand	369-373	5	12
β-strand	380-390	11	14
α-helix	407-411	5
β-strand	416-421	6	14
β-strand	426-434	9	14
β-strand	437-447	11	14
β-strand	454-458	5	14
β-strand	465-472	8	14

Chain c: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	12-15	4
β-strand	32-35	4	19
β-strand	44-47	4	19
β-strand	64-65	2	20
β-strand	72-73	2	20
α-helix	80	1
β-strand	81	1	19
α-helix	82	1

Chain C: 14 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	6-8	3
α-helix	9-11	3
α-helix	12-19	8
β-strand	25	1	17
α-helix	35-37	3
β-strand	38-41	4	17
β-strand	47-49	3	17
α-helix	50	1
α-helix	51-65	15
α-helix	71-73	3
β-strand	74-78	5	18
α-helix	81-83	3
α-helix	84-93	10
β-strand	97-100	4	18
α-helix	102-104	3
β-strand	121-124	4	18
α-helix	131-137	7
β-strand	144-148	5	18
β-strand	159-162	4	18
α-helix	169-185	17
α-helix	194-195	2
α-helix	199-202	4

Chain d: 0 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	10-21	12	24
β-strand	27-34	8	24
β-strand	41-46	6	24
β-strand	55-58	4	24

Chain D: 11 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	24-27	4
β-strand	28-34	7	21
β-strand	43-50	8	21
α-helix	51-52	2
β-strand	53	1	22
β-strand	56	1	22
α-helix	58-62	5
β-strand	66-70	5	21
α-helix	71-74	4
β-strand	82-92	11	21
β-strand	95-105	11	21
α-helix	107-113	7
β-strand	118	1	23
β-strand	120-128	9	21
β-strand	134-143	10	21
β-strand	154	1	23
α-helix	155-157	3
α-helix	158-177	20
α-helix	181-188	8
α-helix	192-200	9
α-helix	201-203	3
β-strand	207-219	13	21
α-helix	225-230	6

31 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	76	Oryctolagus cuniculus
18S ribosomal RNA	2	RNA	1863	Oryctolagus cuniculus
Linear mRNA	3	RNA	160	Oryctolagus cuniculus
Eukaryotic translation initiation factor 2 subunit 1	A	protein	284	Oryctolagus cuniculus	G1T2G4 (AlphaFold model)
Eukaryotic translation initiation factor 2 subunit 3	B	protein	485	Oryctolagus cuniculus	P81795 (AlphaFold model)
Small ribosomal subunit protein uS2	C	protein	295	Oryctolagus cuniculus	G1TLT8 (AlphaFold model)
Small ribosomal subunit protein eS1	D	protein	264	Oryctolagus cuniculus	G1TN72 (AlphaFold model)
Small ribosomal subunit protein uS5	E	protein	270	Oryctolagus cuniculus	A0AAA9WW19
Small ribosomal subunit protein uS3	F	protein	243	Oryctolagus cuniculus	G1TNM3
Small ribosomal subunit protein eS4	G	protein	263	Oryctolagus cuniculus	G1TK17
Small ribosomal subunit protein uS7	H	protein	204	Oryctolagus cuniculus	G1TFM5
Small ribosomal subunit protein eS6	I	protein	249	Oryctolagus cuniculus	G1TM55

30 more molecules are not listed.

Sequence of entity 1 (1), FASTA

>9H6Y_1 Initiator methionylated tRNA (chains 1)
GAGCAGAGUGGCGCAGCGGAAGCGUGCUGGGCCCAUAACCCAGAGGUCGAUGGAUCGAAA
CCAUCCUCUGCUACCA

Sequence of entity 2 (2), FASTA

>9H6Y_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

>9H6Y_3 Linear mRNA (chains 3)
GGGACAUUUGCUUCUGACACAACAUGGAAUCGAUCAUCAACUUCGAAAAGCUAUAGUAAU
GUGUUCACUAGCAACCUCAAACAGACACCGCCACCAUGGUGAGCGGCUGGCGGCUGUUCA
AGAAGAUUAGCCCGCUCGAGAUGGUGAGCAAGGGCGAGGA

Sequence of entity 4 (A), FASTA

>9H6Y_4 Eukaryotic translation initiation factor 2 subunit 1 (chains A)
MPGLSCRFYQHKFPEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSIN
KLIRIGRNECVVVIRVDKEKGYIDLSKRRVSPEEAIKCEDKFTKSKTVYSILRHVAEVLE
YTKDEQLESLFQRTAWVFDDKYKRPGYGAYDAFKHAVSDPSILDSLDLNEDEREVLINNI
NRRLTPQAVKIRADIEVACYGYEGIDAVKEALRAGLNCSTETMPIKINLIAPPRYVMTTT
TLERTEGLSVLNQAMAVIKEKIEEKRGVFNVQMEQVWKTPRRKT

Sequence of entity 5 (B), FASTA

>9H6Y_5 Eukaryotic translation initiation factor 2 subunit 3 (chains B)
MRLPGQLPSSPGKMAGGEAGVTLGQPHLSRQDLATLDVTKLTPLSHEVISRQATINIGTI
GHVAHGKSTVVKAISGVHTVRFKNELERNITIKLGYANAKIYKLDDPSCPRPECYRSCGS
STPDEFPTDIPGTKGNFKLVRHVSFVDCPGHDILMATMLNGAAVMDAALLLIAGNESCPQ
PQTSEHLAAIEIMKLKHILILQNKIDLVKESQAKEQYEQILAFVQGTVAEGAPIIPISAQ
LKYNIEVVCEYIVKKIPVPPRDFTSEPRLIVIRSFDVNKPGCEVDDLKGGVAGGSILKGV
LKVGQEIEVRPGIVSKDSEGKLMCKPIFSKIVSLFAEHNDLQYAAPGGLIGVGTKIDPTL
CRADRMVGQVLGAVGALPEIFTELEISYFLLRRLLGVRTEGDKKAAKVQKLSKNEVLMVN
IGSLSTGGRVSAVKADLGKIVLTNPVCTEVGEKIALSRRVEKHWRLIGWGQIRRGVTIKP
TVDDD

Sequence of entity 6 (C), FASTA

>9H6Y_6 Small ribosomal subunit protein uS2 (chains C)
MSGALDVLQMKEEDVLKFLAAGTHLGGTNLDFQMEQYIYKRKSDGIYIINLKRTWEKLLL
AARAIVAIENPADVSVISSRNTGQRAVLKFAAATGATPIAGRFTPGTFTNQIQAAFREPR
LLVVTDPRADHQPLTEASYVNLPTIALCNTDSPLRYVDIAIPCNNKGAHSVGLMWWMLAR
EVLRMRGTISREHPWEVMPDLYFYRDPEEIEKEEQAAAEKAVTKEEFQGEWTAPAPEFTA
TQPEVADWSEGVQVPSVPIQQFPTEDWSAQPATEDWSAAPTAQATEWVGTTTEWS

Sequence of entity 7 (D), FASTA

>9H6Y_7 Small ribosomal subunit protein eS1 (chains D)
MAVGKNKRLTKGGKKGAKKKVVDPFSKKDWYDVKAPAMFNIRNIGKTLVTRTQGTKIASD
GLKGRVFEVSLADLQNDEVAFRKFKLITEDVQGKNCLTNFHGMDLTRDKMCSMVKKWQTM
IEAHVDVKTTDGYLLHLFCVGFTKKCNNQIRKTSYAQHQQVRQIRKKMMEIMTREVQTND
LKEVVNKLIPDSIGKDIEKACQSIYPLHDVFVRKVKMLKKPKFELGKLMELHGEGSSSGK
ATGDETGAKVERADGYEPPVQESV

Sequence of entity 8 (E), FASTA

>9H6Y_8 Small ribosomal subunit protein uS5 (chains E)
LGFGGAEGGGGGRLLGLGSGRGRGRGARGGKAEDKEWLPVTKLGRLVKDVKIKSLEEIYL
FSLPIKESEIIDFFLGAALKDEVLKIMPVQKQTRAAQRTRFKAFVAIGDYNGHVGLGVKC
SKEVATAIRGAIILAKLSIVPVRRGYWGNKIGKPHTVPCKVTGRCGSVLVHLIPAPRGTG
IVSAPVPKKLLLMAGIDDCYTSAWSCTATLGNFAKATFDAISKTYSYLTPDLWKETVFTK
SPYQEFTDHLVKTHTRVSVQRTQAPAVATT

Sequence of entity 9 (F), FASTA

>9H6Y_9 Small ribosomal subunit protein uS3 (chains F)
MAVQISKKRKFVADGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLG
EKGRRIRELTAVVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRRACY
GVLRFIMESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPVNYYVDTAVRHVLLRQG
VLGIKVKIMLPWDPSGKIGPKKPLPDHVSIVEPKDEILPTTPISEQKGGKPEPPAMPQPV
PTA

Sequence of entity 10 (G), FASTA

>9H6Y_10 Small ribosomal subunit protein eS4 (chains G)
MARGPKKHLKRVAAPKHWMLDKLTSVFAPRPSTGPHKLRECLPLIIFLRNKLKYALTGDE
VKKICMQRFIKIDGKVRADITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRITPEEAK
YKLCKVRKIFVGTKGIPHLVTHDARTIRYPDPLIKMNDTIQIDLETGKITDFIKFDTGNL
CMVTGGANLGRIGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGKGNKPWISLPR
GKGIRLTIAEERDKRLAAKQSSG

Sequence of entity 11 (H), FASTA

>9H6Y_11 Small ribosomal subunit protein uS7 (chains H)
MTEWETAAPAVAETPDIKLFGKWSTDDVQINDISLQDYIAVKEKYAKYLPHSAGRYAAKR
FRKAQCPIVERLTNSMMMHGRNNGKKLMTVRIVKHAFEIIHLLTGENPLQVLVNAIINSG
PREDSTRIGRAGTVRRQAVDVSPLRRVNQAIWLLCTGAREAAFRNIKTIAECLADELINA
AKGSSNSYAIKKKDELERVAKSNR

Sequence of entity 12 (I), FASTA

>9H6Y_12 Small ribosomal subunit protein eS6 (chains I)
MKLNISFPATGCQKLIEVDDERKLRTFYEKRMATEVAADALGEEWKGYVVRISGGNDKQG
FPMKQGVLTHGRVRLLLSKGHSCYRPRRTGERKRKSVRGCIVDANLSVLNLVIVKKGEKD
IPGLTDTTVTRRLGPKRASRIRKLFNLSKEDDVRQYVVRKPLNKEGKKPRTKAPKIQRLV
TPRVLQHKRRRIALKKQRTKKNKEEAAEYAKLLAKRMKEAKEKRQEQIAKRRRLSSLRAS
TSKSESSQK

Ligands and cofactors

ID	Name	Formula	Copies
SF4	Iron/sulfur cluster	Fe4 S4	2

Primary citation

Programmable initiation of mRNA translation by trans-RNA. Jia, L., Nguyen, T.T., Uematsu, S. et al. Nat Biotechnol (2025). DOI 10.1038/s41587-025-02897-1 · PubMed

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

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
8P09 3.3 Å, 48S late-stage initiation complex with non methylated 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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