9KN6: PDB entry 9KN6

Structure of the HCV IRES-dependent pre-48S translation initiation complex with eIF1A, eIF5B, and eIF3. Determined by electron microscopy at 3.3 Å resolution. Released 3 Dec 2025.

Method: Electron microscopy
Resolution: 3.3 Å
Organisms: Homo sapiens, Hepacivirus hominis
Chains: 48
Atoms: 115,376
Mol. weight: 2044.89 kDa
Ligands: ZN, GTP, MG
Released: 3 Dec 2025

Explore 9KN6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9KN6 contains 414 α-helices and 341 β-strands across 44 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 1A: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	23-25	3
α-helix	27-29	3
β-strand	34-40	7	1
β-strand	46-51	6	1
β-strand	56-61	6	1
β-strand	76-81	6	1
β-strand	89-94	6	1
α-helix	97-106	10

Chain 3a: 34 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	8-21	14
α-helix	24-36	13
α-helix	47-61	15
α-helix	64-78	15
α-helix	83-115	33
α-helix	124-129	6
α-helix	137-145	9
α-helix	147-164	18
α-helix	171-187	17
α-helix	191-211	21
α-helix	223-243	21
α-helix	246-261	16
α-helix	266-268	3
α-helix	269-285	17
α-helix	289-306	18
α-helix	312-327	16
α-helix	337-341	5
α-helix	347-356	10
α-helix	367-370	4
α-helix	371-375	5
α-helix	385-387	3
α-helix	390-395	6
α-helix	403-415	13
α-helix	422-426	5
α-helix	428-446	19
β-strand	447	1	71
β-strand	449-451	3	77
α-helix	452-458	7
α-helix	464-472	9
α-helix	473-477	5
β-strand	482-485	4	77
β-strand	490-493	4	77
α-helix	500-502	3
α-helix	515-520	6
α-helix	522-537	16
α-helix	540-559	20
α-helix	563-586	24
α-helix	588-594	7

Chain 3c: 31 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	329-339	11
α-helix	347-363	17
α-helix	369-384	16
α-helix	392-394	3
α-helix	395-414	20
β-strand	418-419	2	83
β-strand	438-439	2	83
α-helix	444-461	18
α-helix	467-473	7
α-helix	476-493	18
α-helix	496-508	13
α-helix	516-521	6
α-helix	544-555	12
α-helix	563-578	16
α-helix	583-591	9
α-helix	594-597	4
α-helix	598-600	3
α-helix	603-621	19
α-helix	626-637	12
α-helix	642-646	5
α-helix	661-666	6
α-helix	671-672	2
α-helix	673-675	3
α-helix	679-700	22
α-helix	707-709	3
α-helix	712-723	12
α-helix	733-746	14
α-helix	750-756	7
α-helix	759-764	6
α-helix	772-794	23
β-strand	799	1	77
β-strand	802-803	2	79
α-helix	804-810	7
α-helix	815-827	13
β-strand	833-836	4	79
β-strand	841-844	4	79
α-helix	851-876	26

Chain 3e: 23 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	8-11	4
α-helix	19-29	11
α-helix	34-47	14
α-helix	51-61	11
α-helix	70-95	26
α-helix	99-106	8
α-helix	110-121	12
α-helix	125-141	17
α-helix	144-157	14
α-helix	165-178	14
α-helix	182-198	17
α-helix	204-224	21
α-helix	228-236	9
α-helix	240-249	10
α-helix	253-263	11
α-helix	270-283	14
α-helix	291-300	10
α-helix	305-321	17
α-helix	329-347	19
β-strand	348	1	79
β-strand	351-352	2	80
α-helix	353-357	5
α-helix	364-377	14
β-strand	382-384	3	80
β-strand	390-393	4	80
α-helix	397-399	3
α-helix	400-427	28

Chain 3f: 8 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	91-94	4	74
α-helix	96-107	12
β-strand	117-124	8	74
β-strand	128-137	10	74
β-strand	139-141	3	75
β-strand	146-148	3	75
α-helix	150-163	14
β-strand	168-175	8	74
α-helix	181-190	10
β-strand	198-202	5	74
β-strand	213-217	5	74
β-strand	234	1	74
β-strand	236-237	2	74
α-helix	243-253	11
β-strand	262-264	3	76
α-helix	268-295	28
α-helix	299-301	3
α-helix	304-313	10
α-helix	320-356	37

Chain 3h: 11 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	38-41	4	76
α-helix	43-55	13
β-strand	63	1	85
β-strand	65-68	4	85
β-strand	71-72	2	76
β-strand	75-78	4	76
β-strand	80-83	4	85
α-helix	96-107	12
β-strand	116-122	7	85
α-helix	131-141	11
β-strand	149-152	4	85
α-helix	154-159	6
β-strand	164-169	6	85
α-helix	171-179	9
α-helix	184-190	7
β-strand	198-201	4	85
β-strand	203-206	4	76
α-helix	209-218	10
α-helix	236-282	47
α-helix	284-291	8
α-helix	301-304	4
α-helix	313-348	36

Chain 3k: 14 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	4-15	12
α-helix	23-38	16
α-helix	44-56	13
α-helix	58-60	3
α-helix	63-75	13
α-helix	81-88	8
α-helix	92-95	4
α-helix	97-110	14
α-helix	114-123	10
α-helix	125-128	4
α-helix	134-149	16
β-strand	150	1	91
β-strand	152-154	3	92
α-helix	155-162	8
α-helix	167-177	11
β-strand	180-181	2	92
β-strand	186-188	3	92
α-helix	208-210	3

Chain 3l: 31 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	50-75	26
α-helix	81-93	13
α-helix	94-98	5
α-helix	99-105	7
α-helix	111-114	4
α-helix	115-117	3
α-helix	119-122	4
α-helix	126-142	17
α-helix	150-168	19
α-helix	180-202	23
α-helix	209-217	9
α-helix	224-238	15
α-helix	240-249	10
α-helix	253-256	4
α-helix	260-262	3
α-helix	264-284	21
α-helix	288-292	5
α-helix	302-303	2
α-helix	309-326	18
α-helix	329-345	17
α-helix	347-349	3
α-helix	354-375	22
α-helix	384-403	20
α-helix	406-414	9
α-helix	425-426	2
α-helix	435-437	3
α-helix	438-454	17
α-helix	457-464	8
β-strand	467	1	80
β-strand	469-471	3	91
α-helix	472-478	7
α-helix	483-497	15
β-strand	499-501	3	95
β-strand	512-514	3	95
β-strand	521-524	4	91
β-strand	527-530	4	91
α-helix	536-562	27

36 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
Eukaryotic translation initiation factor 1A, X-chromosomal	1A	protein	144	Homo sapiens	P47813 (AlphaFold model)
Eukaryotic translation initiation factor 5B	5B	protein	621	Homo sapiens	O60841 (AlphaFold model)
Small ribosomal subunit protein uS2	SA	protein	295	Homo sapiens	P08865 (AlphaFold model)
40S ribosomal protein S3a	SB	protein	264	Homo sapiens	P61247 (AlphaFold model)
40S ribosomal protein S2	SC	protein	293	Homo sapiens	P15880
40S ribosomal protein S3	SD	protein	243	Homo sapiens	P23396
40S ribosomal protein S4, X isoform	SE	protein	263	Homo sapiens	P62701
40S ribosomal protein S5	SF	protein	204	Homo sapiens	P46782
40S ribosomal protein S6	SG	protein	249	Homo sapiens	P62753
40S ribosomal protein S7	SH	protein	194	Homo sapiens	P62081
40S ribosomal protein S8	SI	protein	208	Homo sapiens	P62241
40S ribosomal protein S9	SJ	protein	194	Homo sapiens	P46781

36 more molecules are not listed.

Sequence of entity 1 (1A), FASTA

>9KN6_1 Eukaryotic translation initiation factor 1A, X-chromosomal (chains 1A)
MPKNKGKGGKNRRRGKNENESEKRELVFKEDGQEYAQVIKMLGNGRLEAMCFDGVKRLCH
IRGKLRKKVWINTSDIILVGLRDYQDNKADVILKYNADEARSLKAYGELPEHAKINETDT
FGPGDDDEIQFDDIGDDDEDIDDI

Sequence of entity 2 (5B), FASTA

>9KN6_2 Eukaryotic translation initiation factor 5B (chains 5B)
TKEERAYDKAKRRIEKRRLEHSKNVNTEKLRAPIICVLGHVDTGKTKILDKLRHTHVQDG
EAGGITQQIGATNVPLEAINEQTKMIKNFDRENVRIPGMLIIDTPGHESFSNLRNRGSSL
CDIAILVVDIMHGLEPQTIESINLLKSKKCPFIVALNKIDRLYDWKKSPDSDVAATLKKQ
KKNTKDEFEERAKAIIVEFAQQGLNAALFYENKDPRTFVSLVPTSAHTGDGMGSLIYLLV
ELTQTMLSKRLAHCEELRAQVMEVKALPGMGTTIDVILINGRLKEGDTIIVPGVEGPIVT
QIRGLLLPPPMKELRVKNQYEKHKEVEAAQGVKILGKDLEKTLAGLPLLVAYKEDEIPVL
KDELIHELKQTLNAIKLEEKGVYVQASTLGSLEALLEFLKTSEVPYAGINIGPVHKKDVM
KASVMLEHDPQYAVILAFDVRIERDAQEMADSLGVRIFSAEIIYHLFDAFTKYRQDYKKQ
KQEEFKHIAVFPCKIKILPQYIFNSRDPIVMGVTVEAGQVKQGTPMCVPSKNFVDIGIVT
SIEINHKQVDVAKKGQEVCVKIEPIPGESPKMFGRHFEATDILVSKISRQSIDALKDWFR
DEMQKSDWQLIVELKKVFEII

Sequence of entity 3 (SA), FASTA

>9KN6_3 Small ribosomal subunit protein uS2 (chains SA)
MSGALDVLQMKEEDVLKFLAAGTHLGGTNLDFQMEQYIYKRKSDGIYIINLKRTWEKLLL
AARAIVAIENPADVSVISSRNTGQRAVLKFAAATGATPIAGRFTPGTFTNQIQAAFREPR
LLVVTDPRADHQPLTEASYVNLPTIALCNTDSPLRYVDIAIPCNNKGAHSVGLMWWMLAR
EVLRMRGTISREHPWEVMPDLYFYRDPEEIEKEEQAAAEKAVTKEEFQGEWTAPAPEFTA
TQPEVADWSEGVQVPSVPIQQFPTEDWSAQPATEDWSAAPTAQATEWVGATTDWS

Sequence of entity 4 (SB), FASTA

>9KN6_4 40S ribosomal protein S3a (chains SB)
MAVGKNKRLTKGGKKGAKKKVVDPFSKKDWYDVKAPAMFNIRNIGKTLVTRTQGTKIASD
GLKGRVFEVSLADLQNDEVAFRKFKLITEDVQGKNCLTNFHGMDLTRDKMCSMVKKWQTM
IEAHVDVKTTDGYLLRLFCVGFTKKRNNQIRKTSYAQHQQVRQIRKKMMEIMTREVQTND
LKEVVNKLIPDSIGKDIEKACQSIYPLHDVFVRKVKMLKKPKFELGKLMELHGEGSSSGK
ATGDETGAKVERADGYEPPVQESV

Sequence of entity 5 (SC), FASTA

>9KN6_5 40S ribosomal protein S2 (chains SC)
MADDAGAAGGPGGPGGPGMGNRGGFRGGFGSGIRGRGRGRGRGRGRGRGARGGKAEDKEW
MPVTKLGRLVKDMKIKSLEEIYLFSLPIKESEIIDFFLGASLKDEVLKIMPVQKQTRAGQ
RTRFKAFVAIGDYNGHVGLGVKCSKEVATAIRGAIILAKLSIVPVRRGYWGNKIGKPHTV
PCKVTGRCGSVLVRLIPAPRGTGIVSAPVPKKLLMMAGIDDCYTSARGCTATLGNFAKAT
FDAISKTYSYLTPDLWKETVFTKSPYQEFTDHLVKTHTRVSVQRTQAPAVATT

Sequence of entity 6 (SD), FASTA

>9KN6_6 40S ribosomal protein S3 (chains SD)
MAVQISKKRKFVADGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLG
EKGRRIRELTAVVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRRACY
GVLRFIMESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPVNYYVDTAVRHVLLRQG
VLGIKVKIMLPWDPTGKIGPKKPLPDHVSIVEPKDEILPTTPISEQKGGKPEPPAMPQPV
PTA

Sequence of entity 7 (SE), FASTA

>9KN6_7 40S ribosomal protein S4, X isoform (chains SE)
MARGPKKHLKRVAAPKHWMLDKLTGVFAPRPSTGPHKLRECLPLIIFLRNRLKYALTGDE
VKKICMQRFIKIDGKVRTDITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRITPEEAK
YKLCKVRKIFVGTKGIPHLVTHDARTIRYPDPLIKVNDTIQIDLETGKITDFIKFDTGNL
CMVTGGANLGRIGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGKGNKPWISLPR
GKGIRLTIAEERDKRLAAKQSSG

Sequence of entity 8 (SF), FASTA

>9KN6_8 40S ribosomal protein S5 (chains SF)
MTEWETAAPAVAETPDIKLFGKWSTDDVQINDISLQDYIAVKEKYAKYLPHSAGRYAAKR
FRKAQCPIVERLTNSMMMHGRNNGKKLMTVRIVKHAFEIIHLLTGENPLQVLVNAIINSG
PREDSTRIGRAGTVRRQAVDVSPLRRVNQAIWLLCTGAREAAFRNIKTIAECLADELINA
AKGSSNSYAIKKKDELERVAKSNR

Sequence of entity 9 (SG), FASTA

>9KN6_9 40S ribosomal protein S6 (chains SG)
MKLNISFPATGCQKLIEVDDERKLRTFYEKRMATEVAADALGEEWKGYVVRISGGNDKQG
FPMKQGVLTHGRVRLLLSKGHSCYRPRRTGERKRKSVRGCIVDANLSVLNLVIVKKGEKD
IPGLTDTTVPRRLGPKRASRIRKLFNLSKEDDVRQYVVRKPLNKEGKKPRTKAPKIQRLV
TPRVLQHKRRRIALKKQRTKKNKEEAAEYAKLLAKRMKEAKEKRQEQIAKRRRLSSLRAS
TSKSESSQK

Sequence of entity 10 (SH), FASTA

>9KN6_10 40S ribosomal protein S7 (chains SH)
MFSSSAKIVKPNGEKPDEFESGISQALLELEMNSDLKAQLRELNITAAKEIEVGGGRKAI
IIFVPVPQLKSFQKIQVRLVRELEKKFSGKHVVFIAQRRILPKPTRKSRTKNKQKRPRSR
TLTAVHDAILEDLVFPSEIVGKRIRVKLDGSRLIKVHLDKAQQNNVEHKVETFSGVYKKL
TGKDVNFEFPEFQL

Sequence of entity 11 (SI), FASTA

>9KN6_11 40S ribosomal protein S8 (chains SI)
MGISRDNWHKRRKTGGKRKPYHKKRKYELGRPAANTKIGPRRIHTVRVRGGNKKYRALRL
DVGNFSWGSECCTRKTRIIDVVYNASNNELVRTKTLVKNCIVLIDSTPYRQWYESHYALP
LGRKKGAKLTPEEEEILNKKRSKKIQKKYDERKKNAKISSLLEEQFQQGKLLACIASRPG
QCGRADGYVLEGKELEFYLRKIKARKGK

Sequence of entity 12 (SJ), FASTA

>9KN6_12 40S ribosomal protein S9 (chains SJ)
MPVARSWVCRKTYVTPRRPFEKSRLDQELKLIGEYGLRNKREVWRVKFTLAKIRKAAREL
LTLDEKDPRRLFEGNALLRRLVRIGVLDEGKMKLDYILGLKIEDFLERRLQTQVFKLGLA
KSIHHARVLIRQRHIRVRKQVVNIPSFIVRLDSQKHIDFSLRSPYGGGRPGRVKRKNAKK
GQGGAGAGDDEEED

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	1
MG	Magnesium ion	Mg	8

Primary citation

Structural insights into the role of eIF3 in translation mediated by the HCV IRES. Iwasaki, W., Kashiwagi, K., Sakamoto, A. et al. Proc Natl Acad Sci U S A (2025) 122:e2505538122-e2505538122. DOI 10.1073/pnas.2505538122 · PubMed

Other PDB entries of the same protein (UniProt P47813 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8PPL 2.65 Å, MERS-CoV Nsp1 bound to the human 43S pre-initiation complex
28ZX 2.8 Å, human 48S PIC with mRNA (Kozak_1)
28ZV 2.9 Å, human 48S PIC with mRNA (non-Kozak)
6ZP4 2.9 Å, SARS-CoV-2 Nsp1 bound to a human 43S preinitiation ribosome complex - state 2
8PJ5 2.9 Å, Structure of human 48S translation initiation complex after eIF2 release prior 60S…
8PJ6 2.9 Å, Structure of human 48S translation initiation complex with initiator tRNA, eIF1A and…
9H74 2.9 Å, Late-stage 48S Initiation Complex with eIF3 (LS48S-eIF3 IC) guided by the trans-RNA
28ZY 3.0 Å, human 48S PIC with mRNA (Kozak_2)
6YBW 3.1 Å, Structure of a human 48S translational initiation complex - 40S body
8SUP 3.1 Å, Structure of the 48S translation initiation complex assembled on the…
28ZU 3.2 Å, human 48S PIC with Kozak mRNA and eIF1A W70A mutant
7TQL 3.2 Å, CryoEM structure of the human 40S small ribosomal subunit in complex with translation…

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