9KN5: Human 40S ribosome

Name: PDB 9KN5: Structure of the human 40S ribosome complexed with HCV IRES, eIF1A and eIF3
Published: 2025-12-03
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Structure of the human 40S ribosome complexed with HCV IRES, eIF1A and eIF3. Determined by electron microscopy at 3.2 Å resolution. Released 3 Dec 2025.

Method: Electron microscopy
Resolution: 3.2 Å
Organisms: Homo sapiens, Hepacivirus hominis
Chains: 46
Atoms: 108,797
Mol. weight: 1950.04 kDa
Ligands: ZN, MG
Released: 3 Dec 2025

Explore 9KN5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9KN5 contains 400 α-helices and 284 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
β-strand	34-40	7	1
β-strand	46-51	6	1
β-strand	56-61	6	1
α-helix	63-65	3
β-strand	76-81	6	1
β-strand	88-95	8	1
α-helix	97-105	9

Chain 3a: 37 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	9-19	11
α-helix	24-36	13
α-helix	47-60	14
α-helix	64-78	15
α-helix	83-107	25
α-helix	108-112	5
α-helix	113-115	3
α-helix	124-127	4
α-helix	137-144	8
α-helix	146-163	18
α-helix	171-187	17
α-helix	191-210	20
α-helix	217-219	3
α-helix	223-242	20
α-helix	247-261	15
α-helix	266-268	3
α-helix	269-272	4
α-helix	275-286	12
α-helix	289-306	18
α-helix	312-326	15
α-helix	338-341	4
α-helix	347-359	13
α-helix	367-370	4
α-helix	371-375	5
α-helix	379-381	3
α-helix	385-387	3
α-helix	391-395	5
α-helix	403-415	13
α-helix	422-424	3
α-helix	428-446	19
β-strand	447	1	51
β-strand	449-451	3	58
α-helix	452-458	7
α-helix	464-476	13
β-strand	483-485	3	58
β-strand	490-492	3	58
α-helix	515-518	4
α-helix	522-536	15
α-helix	541-559	19
α-helix	562-586	25
α-helix	588-594	7

Chain 3c: 31 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	329-339	11
α-helix	347-363	17
α-helix	368-383	16
α-helix	392-394	3
α-helix	395-414	20
β-strand	418-421	4	63
β-strand	438-441	4	63
α-helix	444-461	18
α-helix	467-473	7
α-helix	475-493	19
α-helix	496-508	13
α-helix	516-521	6
α-helix	544-557	14
α-helix	563-578	16
α-helix	583-592	10
α-helix	594-596	3
α-helix	603-621	19
α-helix	626-638	13
α-helix	642-645	4
α-helix	661-665	5
α-helix	671-672	2
α-helix	673-675	3
α-helix	679-700	22
α-helix	707-709	3
α-helix	712-722	11
α-helix	733-744	12
α-helix	750-756	7
α-helix	759-761	3
α-helix	762-766	5
α-helix	772-795	24
β-strand	799-803	5	58
α-helix	804-810	7
α-helix	815-827	13
β-strand	833-836	4	58
β-strand	841-844	4	58
α-helix	851-877	27

Chain 3d: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	5-7	3

Chain 3e: 26 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3
α-helix	8-11	4
α-helix	20-29	10
α-helix	34-46	13
α-helix	51-61	11
α-helix	70-87	18
α-helix	89-95	7
α-helix	98-106	9
α-helix	110-121	12
α-helix	125-140	16
α-helix	144-157	14
α-helix	164-178	15
α-helix	182-198	17
α-helix	204-224	21
α-helix	228-238	11
α-helix	240-249	10
α-helix	252-263	12
α-helix	267-283	17
α-helix	291-300	10
α-helix	305-320	16
α-helix	329-347	19
β-strand	348-349	2	58
β-strand	351-352	2	59
α-helix	353-357	5
α-helix	364-377	14
β-strand	383	1	60
β-strand	384	1	61
α-helix	387-389	3
β-strand	390-391	2	59
β-strand	392	1	60
α-helix	403-424	22
α-helix	425-429	5

Chain 3f: 8 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	91-94	4	53
α-helix	96-107	12
β-strand	117-121	5	54
β-strand	124	1	53
β-strand	128-131	4	53
β-strand	134-137	4	54
β-strand	139-141	3	55
β-strand	146-148	3	55
α-helix	150-163	14
β-strand	169-175	7	54
α-helix	182-190	9
β-strand	198-202	5	54
β-strand	213-217	5	54
β-strand	236-239	4	53
α-helix	243-254	12
α-helix	255-257	3
β-strand	262-264	3	56
α-helix	268-295	28
α-helix	304-314	11
α-helix	320-356	37

Chain 3h: 15 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	38-41	4	56
α-helix	43-55	13
α-helix	61-63	3
β-strand	64-72	9	56
β-strand	75-83	9	56
α-helix	96-110	15
β-strand	116-122	7	56
α-helix	124-126	3
α-helix	131-143	13
β-strand	149-152	4	56
α-helix	154-159	6
β-strand	164-169	6	56
α-helix	174-179	6
α-helix	184-189	6
β-strand	198-201	4	56
β-strand	203-206	4	56
α-helix	209-220	12
α-helix	236-246	11
α-helix	250-287	38
α-helix	301-304	4
α-helix	310-312	3
α-helix	314-344	31
α-helix	345-349	5

Chain 3k: 13 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	4-16	13
α-helix	23-38	16
α-helix	44-56	13
α-helix	63-75	13
α-helix	82-87	6
α-helix	91-93	3
α-helix	97-110	14
α-helix	114-123	10
α-helix	125-128	4
α-helix	134-149	16
β-strand	150	1	68
β-strand	152-154	3	69
α-helix	155-162	8
α-helix	167-176	10
β-strand	180-181	2	69
β-strand	186-188	3	69
α-helix	211-214	4

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)
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 (AlphaFold model)
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
40S ribosomal protein S10	SK	protein	165	Homo sapiens	P46783

34 more molecules are not listed.

Sequence of entity 1 (1A), FASTA

>9KN5_1 Eukaryotic translation initiation factor 1A, X-chromosomal (chains 1A)
MPKNKGKGGKNRRRGKNENESEKRELVFKEDGQEYAQVIKMLGNGRLEAMCFDGVKRLCH
IRGKLRKKVWINTSDIILVGLRDYQDNKADVILKYNADEARSLKAYGELPEHAKINETDT
FGPGDDDEIQFDDIGDDDEDIDDI

Sequence of entity 2 (SA), FASTA

>9KN5_2 Small ribosomal subunit protein uS2 (chains SA)
MSGALDVLQMKEEDVLKFLAAGTHLGGTNLDFQMEQYIYKRKSDGIYIINLKRTWEKLLL
AARAIVAIENPADVSVISSRNTGQRAVLKFAAATGATPIAGRFTPGTFTNQIQAAFREPR
LLVVTDPRADHQPLTEASYVNLPTIALCNTDSPLRYVDIAIPCNNKGAHSVGLMWWMLAR
EVLRMRGTISREHPWEVMPDLYFYRDPEEIEKEEQAAAEKAVTKEEFQGEWTAPAPEFTA
TQPEVADWSEGVQVPSVPIQQFPTEDWSAQPATEDWSAAPTAQATEWVGATTDWS

Sequence of entity 3 (SB), FASTA

>9KN5_3 40S ribosomal protein S3a (chains SB)
MAVGKNKRLTKGGKKGAKKKVVDPFSKKDWYDVKAPAMFNIRNIGKTLVTRTQGTKIASD
GLKGRVFEVSLADLQNDEVAFRKFKLITEDVQGKNCLTNFHGMDLTRDKMCSMVKKWQTM
IEAHVDVKTTDGYLLRLFCVGFTKKRNNQIRKTSYAQHQQVRQIRKKMMEIMTREVQTND
LKEVVNKLIPDSIGKDIEKACQSIYPLHDVFVRKVKMLKKPKFELGKLMELHGEGSSSGK
ATGDETGAKVERADGYEPPVQESV

Sequence of entity 4 (SC), FASTA

>9KN5_4 40S ribosomal protein S2 (chains SC)
MADDAGAAGGPGGPGGPGMGNRGGFRGGFGSGIRGRGRGRGRGRGRGRGARGGKAEDKEW
MPVTKLGRLVKDMKIKSLEEIYLFSLPIKESEIIDFFLGASLKDEVLKIMPVQKQTRAGQ
RTRFKAFVAIGDYNGHVGLGVKCSKEVATAIRGAIILAKLSIVPVRRGYWGNKIGKPHTV
PCKVTGRCGSVLVRLIPAPRGTGIVSAPVPKKLLMMAGIDDCYTSARGCTATLGNFAKAT
FDAISKTYSYLTPDLWKETVFTKSPYQEFTDHLVKTHTRVSVQRTQAPAVATT

Sequence of entity 5 (SD), FASTA

>9KN5_5 40S ribosomal protein S3 (chains SD)
MAVQISKKRKFVADGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLG
EKGRRIRELTAVVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRRACY
GVLRFIMESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPVNYYVDTAVRHVLLRQG
VLGIKVKIMLPWDPTGKIGPKKPLPDHVSIVEPKDEILPTTPISEQKGGKPEPPAMPQPV
PTA

Sequence of entity 6 (SE), FASTA

>9KN5_6 40S ribosomal protein S4, X isoform (chains SE)
MARGPKKHLKRVAAPKHWMLDKLTGVFAPRPSTGPHKLRECLPLIIFLRNRLKYALTGDE
VKKICMQRFIKIDGKVRTDITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRITPEEAK
YKLCKVRKIFVGTKGIPHLVTHDARTIRYPDPLIKVNDTIQIDLETGKITDFIKFDTGNL
CMVTGGANLGRIGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGKGNKPWISLPR
GKGIRLTIAEERDKRLAAKQSSG

Sequence of entity 7 (SF), FASTA

>9KN5_7 40S ribosomal protein S5 (chains SF)
MTEWETAAPAVAETPDIKLFGKWSTDDVQINDISLQDYIAVKEKYAKYLPHSAGRYAAKR
FRKAQCPIVERLTNSMMMHGRNNGKKLMTVRIVKHAFEIIHLLTGENPLQVLVNAIINSG
PREDSTRIGRAGTVRRQAVDVSPLRRVNQAIWLLCTGAREAAFRNIKTIAECLADELINA
AKGSSNSYAIKKKDELERVAKSNR

Sequence of entity 8 (SG), FASTA

>9KN5_8 40S ribosomal protein S6 (chains SG)
MKLNISFPATGCQKLIEVDDERKLRTFYEKRMATEVAADALGEEWKGYVVRISGGNDKQG
FPMKQGVLTHGRVRLLLSKGHSCYRPRRTGERKRKSVRGCIVDANLSVLNLVIVKKGEKD
IPGLTDTTVPRRLGPKRASRIRKLFNLSKEDDVRQYVVRKPLNKEGKKPRTKAPKIQRLV
TPRVLQHKRRRIALKKQRTKKNKEEAAEYAKLLAKRMKEAKEKRQEQIAKRRRLSSLRAS
TSKSESSQK

Sequence of entity 9 (SH), FASTA

>9KN5_9 40S ribosomal protein S7 (chains SH)
MFSSSAKIVKPNGEKPDEFESGISQALLELEMNSDLKAQLRELNITAAKEIEVGGGRKAI
IIFVPVPQLKSFQKIQVRLVRELEKKFSGKHVVFIAQRRILPKPTRKSRTKNKQKRPRSR
TLTAVHDAILEDLVFPSEIVGKRIRVKLDGSRLIKVHLDKAQQNNVEHKVETFSGVYKKL
TGKDVNFEFPEFQL

Sequence of entity 10 (SI), FASTA

>9KN5_10 40S ribosomal protein S8 (chains SI)
MGISRDNWHKRRKTGGKRKPYHKKRKYELGRPAANTKIGPRRIHTVRVRGGNKKYRALRL
DVGNFSWGSECCTRKTRIIDVVYNASNNELVRTKTLVKNCIVLIDSTPYRQWYESHYALP
LGRKKGAKLTPEEEEILNKKRSKKIQKKYDERKKNAKISSLLEEQFQQGKLLACIASRPG
QCGRADGYVLEGKELEFYLRKIKARKGK

Sequence of entity 11 (SJ), FASTA

>9KN5_11 40S ribosomal protein S9 (chains SJ)
MPVARSWVCRKTYVTPRRPFEKSRLDQELKLIGEYGLRNKREVWRVKFTLAKIRKAAREL
LTLDEKDPRRLFEGNALLRRLVRIGVLDEGKMKLDYILGLKIEDFLERRLQTQVFKLGLA
KSIHHARVLIRQRHIRVRKQVVNIPSFIVRLDSQKHIDFSLRSPYGGGRPGRVKRKNAKK
GQGGAGAGDDEEED

Sequence of entity 12 (SK), FASTA

>9KN5_12 40S ribosomal protein S10 (chains SK)
MLMPKKNRIAIYELLFKEGVMVAKKDVHMPKHPELADKNVPNLHVMKAMQSLKSRGYVKE
QFAWRHFYWYLTNEGIQYLRDYLHLPPEIVPATLRRSRPETGRPRPKGLEGERPARLTRG
EADRDTYRRSAVPPGADKKAEAGAGSATEFQFRGGFGRGRGQPPQ

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
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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