9KKF: Human 40S ribosome

Name: PDB 9KKF: Structure of the human 40S ribosome complexed with HCV IRES 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 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: 45
Atoms: 108,043
Mol. weight: 1933.55 kDa
Ligands: MG, ZN
Released: 3 Dec 2025

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

Secondary structure: helices and β-sheets

9KKF contains 402 α-helices and 283 β-strands across 43 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 3a: 33 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	8-20	13
α-helix	24-35	12
α-helix	47-59	13
α-helix	64-78	15
α-helix	83-108	26
α-helix	112-115	4
α-helix	124-128	5
α-helix	137-163	27
α-helix	171-187	17
α-helix	191-210	20
α-helix	223-242	20
α-helix	247-261	15
α-helix	266-267	2
α-helix	269-283	15
α-helix	289-306	18
α-helix	312-327	16
α-helix	338-341	4
α-helix	347-357	11
α-helix	367-370	4
α-helix	371-375	5
α-helix	379-381	3
α-helix	390-395	6
α-helix	403-415	13
α-helix	425-427	3
α-helix	428-446	19
β-strand	449-451	3	58
α-helix	452-458	7
α-helix	464-476	13
β-strand	482-485	4	58
β-strand	490-493	4	58
α-helix	499-501	3
α-helix	515-520	6
α-helix	522-537	16
α-helix	540-559	20
α-helix	562-583	22
α-helix	588-594	7

Chain 3c: 32 helices, 6 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	419-421	3	62
β-strand	439-441	3	62
α-helix	444-461	18
α-helix	467-474	8
α-helix	476-490	15
α-helix	499-508	10
α-helix	516-521	6
α-helix	544-557	14
α-helix	563-578	16
α-helix	582-592	11
α-helix	594-597	4
α-helix	603-621	19
α-helix	626-638	13
α-helix	642-646	5
α-helix	661-665	5
α-helix	670-672	3
α-helix	673-675	3
α-helix	676-678	3
α-helix	679-700	22
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	772-794	23
β-strand	801	1	58
β-strand	802-803	2	59
α-helix	804-810	7
α-helix	815-827	13
β-strand	833-836	4	59
β-strand	841-844	4	59
α-helix	848-850	3
α-helix	851-877	27

Chain 3d: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	5-7	3

Chain 3e: 28 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	8-12	5
α-helix	20-29	10
α-helix	34-47	14
α-helix	51-61	11
α-helix	70-87	18
α-helix	89-95	7
α-helix	99-106	8
α-helix	111-121	11
α-helix	125-141	17
α-helix	144-157	14
α-helix	164-179	16
α-helix	182-197	16
α-helix	204-224	21
α-helix	228-237	10
α-helix	240-248	9
α-helix	253-263	11
α-helix	267-283	17
α-helix	291-297	7
α-helix	298-302	5
α-helix	305-320	16
α-helix	329-347	19
β-strand	348	1	59
β-strand	351-352	2	60
α-helix	353-357	5
α-helix	364-377	14
β-strand	383-384	2	60
α-helix	387-389	3
β-strand	390-392	3	60
α-helix	397-399	3
α-helix	400-407	8
α-helix	409-424	16
α-helix	425-429	5

Chain 3f: 7 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	91-94	4	51
α-helix	96-107	12
β-strand	117-120	4	52
β-strand	124	1	51
β-strand	128-131	4	51
β-strand	134-137	4	52
β-strand	139-141	3	53
β-strand	146-148	3	53
α-helix	150-163	14
β-strand	171-175	5	52
α-helix	181-193	13
β-strand	198-202	5	52
β-strand	213-217	5	52
β-strand	234	1	52
β-strand	236-239	4	51
α-helix	243-256	14
β-strand	262-264	3	54
α-helix	268-295	28
α-helix	304-314	11
α-helix	320-355	36

Chain 3h: 15 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	38-41	4	54
α-helix	43-55	13
β-strand	64-72	9	54
β-strand	75-83	9	54
α-helix	96-108	13
β-strand	116-122	7	54
α-helix	131-141	11
β-strand	149-153	5	54
α-helix	154-159	6
β-strand	163-169	7	54
α-helix	171-179	9
α-helix	184-190	7
α-helix	194-196	3
β-strand	198-201	4	54
β-strand	203-206	4	54
α-helix	209-218	10
α-helix	238-282	45
α-helix	284-287	4
α-helix	288-290	3
α-helix	301-304	4
α-helix	307-312	6
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	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	68
β-strand	152-154	3	69
α-helix	155-161	7
α-helix	167-177	11
β-strand	180-181	2	69
β-strand	186-188	3	69
α-helix	211-215	5

Chain 3l: 28 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	50-75	26
α-helix	81-92	12
α-helix	93-99	7
α-helix	100-105	6
α-helix	111-112	2
α-helix	119-122	4
α-helix	126-143	18
α-helix	150-169	20
α-helix	180-202	23
α-helix	209-217	9
α-helix	224-236	13
α-helix	240-249	10
α-helix	253-256	4
α-helix	264-284	21
α-helix	287-293	7
α-helix	304-307	4
α-helix	309-325	17
α-helix	329-345	17
α-helix	347-349	3
α-helix	354-376	23
α-helix	384-403	20
α-helix	406-415	10
α-helix	425-426	2
α-helix	438-453	16
α-helix	455-466	12
β-strand	467	1	60
β-strand	469-471	3	68
α-helix	472-478	7
α-helix	483-497	15
β-strand	499-501	3	73
β-strand	512-514	3	73
β-strand	519-524	6	68
β-strand	527-532	6	68
α-helix	536-561	26

35 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
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 (AlphaFold model)
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
40S ribosomal protein S11	SL	protein	158	Homo sapiens	P62280

33 more molecules are not listed.

Sequence of entity 1 (SA), FASTA

>9KKF_1 Small ribosomal subunit protein uS2 (chains SA)
MSGALDVLQMKEEDVLKFLAAGTHLGGTNLDFQMEQYIYKRKSDGIYIINLKRTWEKLLL
AARAIVAIENPADVSVISSRNTGQRAVLKFAAATGATPIAGRFTPGTFTNQIQAAFREPR
LLVVTDPRADHQPLTEASYVNLPTIALCNTDSPLRYVDIAIPCNNKGAHSVGLMWWMLAR
EVLRMRGTISREHPWEVMPDLYFYRDPEEIEKEEQAAAEKAVTKEEFQGEWTAPAPEFTA
TQPEVADWSEGVQVPSVPIQQFPTEDWSAQPATEDWSAAPTAQATEWVGATTDWS

Sequence of entity 2 (SB), FASTA

>9KKF_2 40S ribosomal protein S3a (chains SB)
MAVGKNKRLTKGGKKGAKKKVVDPFSKKDWYDVKAPAMFNIRNIGKTLVTRTQGTKIASD
GLKGRVFEVSLADLQNDEVAFRKFKLITEDVQGKNCLTNFHGMDLTRDKMCSMVKKWQTM
IEAHVDVKTTDGYLLRLFCVGFTKKRNNQIRKTSYAQHQQVRQIRKKMMEIMTREVQTND
LKEVVNKLIPDSIGKDIEKACQSIYPLHDVFVRKVKMLKKPKFELGKLMELHGEGSSSGK
ATGDETGAKVERADGYEPPVQESV

Sequence of entity 3 (SC), FASTA

>9KKF_3 40S ribosomal protein S2 (chains SC)
MADDAGAAGGPGGPGGPGMGNRGGFRGGFGSGIRGRGRGRGRGRGRGRGARGGKAEDKEW
MPVTKLGRLVKDMKIKSLEEIYLFSLPIKESEIIDFFLGASLKDEVLKIMPVQKQTRAGQ
RTRFKAFVAIGDYNGHVGLGVKCSKEVATAIRGAIILAKLSIVPVRRGYWGNKIGKPHTV
PCKVTGRCGSVLVRLIPAPRGTGIVSAPVPKKLLMMAGIDDCYTSARGCTATLGNFAKAT
FDAISKTYSYLTPDLWKETVFTKSPYQEFTDHLVKTHTRVSVQRTQAPAVATT

Sequence of entity 4 (SD), FASTA

>9KKF_4 40S ribosomal protein S3 (chains SD)
MAVQISKKRKFVADGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLG
EKGRRIRELTAVVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRRACY
GVLRFIMESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPVNYYVDTAVRHVLLRQG
VLGIKVKIMLPWDPTGKIGPKKPLPDHVSIVEPKDEILPTTPISEQKGGKPEPPAMPQPV
PTA

Sequence of entity 5 (SE), FASTA

>9KKF_5 40S ribosomal protein S4, X isoform (chains SE)
MARGPKKHLKRVAAPKHWMLDKLTGVFAPRPSTGPHKLRECLPLIIFLRNRLKYALTGDE
VKKICMQRFIKIDGKVRTDITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRITPEEAK
YKLCKVRKIFVGTKGIPHLVTHDARTIRYPDPLIKVNDTIQIDLETGKITDFIKFDTGNL
CMVTGGANLGRIGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGKGNKPWISLPR
GKGIRLTIAEERDKRLAAKQSSG

Sequence of entity 6 (SF), FASTA

>9KKF_6 40S ribosomal protein S5 (chains SF)
MTEWETAAPAVAETPDIKLFGKWSTDDVQINDISLQDYIAVKEKYAKYLPHSAGRYAAKR
FRKAQCPIVERLTNSMMMHGRNNGKKLMTVRIVKHAFEIIHLLTGENPLQVLVNAIINSG
PREDSTRIGRAGTVRRQAVDVSPLRRVNQAIWLLCTGAREAAFRNIKTIAECLADELINA
AKGSSNSYAIKKKDELERVAKSNR

Sequence of entity 7 (SG), FASTA

>9KKF_7 40S ribosomal protein S6 (chains SG)
MKLNISFPATGCQKLIEVDDERKLRTFYEKRMATEVAADALGEEWKGYVVRISGGNDKQG
FPMKQGVLTHGRVRLLLSKGHSCYRPRRTGERKRKSVRGCIVDANLSVLNLVIVKKGEKD
IPGLTDTTVPRRLGPKRASRIRKLFNLSKEDDVRQYVVRKPLNKEGKKPRTKAPKIQRLV
TPRVLQHKRRRIALKKQRTKKNKEEAAEYAKLLAKRMKEAKEKRQEQIAKRRRLSSLRAS
TSKSESSQK

Sequence of entity 8 (SH), FASTA

>9KKF_8 40S ribosomal protein S7 (chains SH)
MFSSSAKIVKPNGEKPDEFESGISQALLELEMNSDLKAQLRELNITAAKEIEVGGGRKAI
IIFVPVPQLKSFQKIQVRLVRELEKKFSGKHVVFIAQRRILPKPTRKSRTKNKQKRPRSR
TLTAVHDAILEDLVFPSEIVGKRIRVKLDGSRLIKVHLDKAQQNNVEHKVETFSGVYKKL
TGKDVNFEFPEFQL

Sequence of entity 9 (SI), FASTA

>9KKF_9 40S ribosomal protein S8 (chains SI)
MGISRDNWHKRRKTGGKRKPYHKKRKYELGRPAANTKIGPRRIHTVRVRGGNKKYRALRL
DVGNFSWGSECCTRKTRIIDVVYNASNNELVRTKTLVKNCIVLIDSTPYRQWYESHYALP
LGRKKGAKLTPEEEEILNKKRSKKIQKKYDERKKNAKISSLLEEQFQQGKLLACIASRPG
QCGRADGYVLEGKELEFYLRKIKARKGK

Sequence of entity 10 (SJ), FASTA

>9KKF_10 40S ribosomal protein S9 (chains SJ)
MPVARSWVCRKTYVTPRRPFEKSRLDQELKLIGEYGLRNKREVWRVKFTLAKIRKAAREL
LTLDEKDPRRLFEGNALLRRLVRIGVLDEGKMKLDYILGLKIEDFLERRLQTQVFKLGLA
KSIHHARVLIRQRHIRVRKQVVNIPSFIVRLDSQKHIDFSLRSPYGGGRPGRVKRKNAKK
GQGGAGAGDDEEED

Sequence of entity 11 (SK), FASTA

>9KKF_11 40S ribosomal protein S10 (chains SK)
MLMPKKNRIAIYELLFKEGVMVAKKDVHMPKHPELADKNVPNLHVMKAMQSLKSRGYVKE
QFAWRHFYWYLTNEGIQYLRDYLHLPPEIVPATLRRSRPETGRPRPKGLEGERPARLTRG
EADRDTYRRSAVPPGADKKAEAGAGSATEFQFRGGFGRGRGQPPQ

Sequence of entity 12 (SL), FASTA

>9KKF_12 40S ribosomal protein S11 (chains SL)
MADIQTERAYQKQPTIFQNKKRVLLGETGKEKLPRYYKNIGLGFKTPKEAIEGTYIDKKC
PFTGNVSIRGRILSGVVTKMKMQRTIVIRRDYLHYIRKYNRFEKRHKNMSVHLSPCFRDV
QIGDIVTVGECRPLSKTVRFNVLKVTKAAGTKKQFQKF

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	8
ZN	Zinc ion	Zn	2

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 P08865 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8GLP 1.67 Å, mRNA decoding in human is kinetically and structurally distinct from bacteria (Consensus…
8QOI 1.9 Å, Structure of the human 80S ribosome at 1.9 A resolution - the molecular role of chemical…
9O3W 1.9 Å, Human 80S ribosome bound to IDB-001 stalled on MYC nascent chain
8YOO 2.0 Å, Cryo-EM structure of the human 80S ribosome with 100 um Tigecycline
9C3H 2.0 Å, Structure of the CNOT3-bound human 80S ribosome with tRNA-ARG in the P-site.
29IZ 2.08 Å, Dormant 80S:eEF2:SERBP1:tRNA complex from human cells treated with toxin NT-2
9TV2 2.1 Å, 80S ribosomes from primary B-cells infected with delta v-snoRNA1 EBV
3BCH 2.15 Å, Crystal Structure of the Human Laminin Receptor Precursor
7R4X 2.15 Å, Cryo-EM reconstruction of the human 40S ribosomal subunit - Full map
9I2D 2.19 Å, NMT1-NAC bound human RNC with 10 amino acid ARF1-linker
9PBE 2.19 Å, In situ human 80S ribosome (composite map)
8YOP 2.2 Å, Cryo-EM structure of the human 80S ribosome with 4 um Tigecycline

Browse structure collections

About this viewer

MolViewer shows 9KKF directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.