9Q1S: NediV IRES

Name: PDB 9Q1S: NediV IRES (P site) in complex with Rabbit 80S ribosome
Published: 2026-06-17
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

NediV IRES (P site) in complex with Rabbit 80S ribosome. Determined by electron microscopy at 3.0 Å resolution. Released 17 Jun 2026.

Method: Electron microscopy
Resolution: 3.0 Å
Organisms: Oryctolagus cuniculus, Nedicistrovirus TFN-2012
Chains: 78
Atoms: 208,701
Mol. weight: 3093.61 kDa
Ligands: ZN, MG
Released: 17 Jun 2026

Explore 9Q1S in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9Q1S contains 506 α-helices and 483 β-strands across 73 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: 8 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	7-10	4
α-helix	42-48	7
α-helix	65-68	4
β-strand	72-74	3	113
α-helix	75-77	3
α-helix	84-92	9
β-strand	98	1	79
α-helix	99	1
β-strand	100-102	3	114
α-helix	103-106	4
β-strand	110-112	3	113
β-strand	123-126	4	114
β-strand	128-129	2	113
α-helix	131-140	10
β-strand	143-146	4	114

Chain A: 12 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
α-helix	6-10	5
α-helix	14-16	3
α-helix	29-32	4
α-helix	34-38	5
β-strand	40-49	10	11
α-helix	57	1
β-strand	58-64	7	11
β-strand	71-77	7	11
β-strand	79	1	12
β-strand	83	1	13
β-strand	86-91	6	11
α-helix	94-96	3
β-strand	100-103	4	14
β-strand	113-114	2	14
β-strand	116	1	15
β-strand	126	1	15
β-strand	134	1	14
β-strand	135-140	6	16
α-helix	142-144	3
β-strand	145-149	5	16
β-strand	155-159	5	16
β-strand	163-166	4	14
β-strand	169	1	12
α-helix	174-176	3
α-helix	178-179	2
α-helix	182-190	9
β-strand	224-225	2	17
α-helix	229-230	2
β-strand	237-238	2	17

Chain aa: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	20-22	3	88
β-strand	29-31	3	88
β-strand	36-43	8	89
α-helix	49-56	8
β-strand	57	1	58
α-helix	62-65	4
β-strand	66-73	8	89
α-helix	75-80	6
α-helix	96-99	4

Chain AA: 14 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	6-8	3
α-helix	12-21	10
β-strand	25	1	133
α-helix	32-37	6
β-strand	38-41	4	134
α-helix	43-45	3
β-strand	47-49	3	134
α-helix	51-67	17
α-helix	71-73	3
β-strand	74-78	5	135
α-helix	81-94	14
α-helix	96	1
β-strand	97-100	4	135
β-strand	121-124	4	135
α-helix	131-139	9
β-strand	144-148	5	135
β-strand	159-162	4	135
α-helix	168-186	19
α-helix	194-195	2
α-helix	199-202	4
α-helix	204-206	3
α-helix	207-217	11

Chain b: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	12-19	8
α-helix	37-49	13
α-helix	52-54	3
α-helix	55-75	21
α-helix	91-100	10
α-helix	106-116	11

Chain B: 17 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	9-10	2
α-helix	14-16	3
α-helix	32-35	4
β-strand	42-43	2	24
β-strand	45-59	15	25
β-strand	71-80	10	25
β-strand	84-94	11	26
β-strand	99-106	8	26
α-helix	112-115	4
α-helix	116-118	3
α-helix	133-137	5
α-helix	140-156	17
β-strand	159-165	7	26
α-helix	177-179	3
β-strand	180-184	5	26
β-strand	185-186	2	24
α-helix	190-199	10
β-strand	204-205	2	26
β-strand	216-222	7	25
α-helix	223-224	2
β-strand	225-229	5	27
α-helix	231-235	5
α-helix	237-241	5
α-helix	262-263	2
β-strand	270-273	4	27
β-strand	276-288	13	25
α-helix	289	1
β-strand	293-294	2	28
β-strand	297-298	2	28
β-strand	320	1	29
β-strand	324	1	29
β-strand	330-335	6	25
β-strand	344-349	6	25
α-helix	357-360	4
α-helix	361-363	3
β-strand	365-368	4	25
α-helix	382-389	8

Chain bb: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	12-17	6
β-strand	32-36	5	92
β-strand	44-47	4	92
β-strand	54-55	2	93
β-strand	62-65	4	93
α-helix	71	1
β-strand	72-73	2	93
α-helix	74	1
β-strand	78-82	5	92

Chain BB: 9 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	24-27	4
β-strand	28-34	7	140
β-strand	43-50	8	140
α-helix	58-62	5
β-strand	66-70	5	140
α-helix	71-74	4
β-strand	82-91	10	140
β-strand	95-105	11	140
α-helix	107-113	7
β-strand	120-128	9	140
β-strand	134-143	10	140
α-helix	144-146	3
α-helix	158-177	20
α-helix	181-188	8
α-helix	193-201	9
β-strand	207-217	11	140
α-helix	225-231	7

65 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
18S rRNA	9	RNA	1670	Oryctolagus cuniculus
60S ribosomal protein L8	A	protein	248	Oryctolagus cuniculus	G1TT27 (AlphaFold model)
60S ribosomal protein L3	B	protein	394	Oryctolagus cuniculus	G1TL06 (AlphaFold model)
60S ribosomal protein L4	C	protein	362	Oryctolagus cuniculus	A0A5F9DCT1 (AlphaFold model)
Large ribosomal subunit protein eL6	E	protein	251	Oryctolagus cuniculus	G1SKF7 (AlphaFold model)
Large ribosomal subunit protein eL8	G	protein	240	Oryctolagus cuniculus	G1STW0
60S ribosomal protein L9	H	protein	190	Oryctolagus cuniculus	G1SWI6
Ribosomal protein L10	I	protein	213	Oryctolagus cuniculus	B7NZQ2
60S ribosomal protein L11	J	protein	170	Oryctolagus cuniculus	G1TUB8
Large ribosomal subunit protein eL13	L	protein	210	Oryctolagus cuniculus	G1TKB3
60S ribosomal protein L15	N	protein	203	Oryctolagus cuniculus	G1T0C1
Large ribosomal subunit protein uL13	O	protein	199	Oryctolagus cuniculus	G1TVS8

66 more molecules are not listed.

Sequence of entity 1 (9), FASTA

>9Q1S_1 18S rRNA (chains 9)
UACCUGGUUGAUCCUGCCAGUAGCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUA
AGUACGCACGGCCGGUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUGGUUCCUU
UGGUCGCUCGACUUGGAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCCGACGGGCGCUG
ACCCCCUUCGCGGGGGGGAUGCGUGCAUUUAUCAGUGGUGACUCUAGAUAACCUCGGGCC
GAUCGCACGCCCGGCGGCGACGACCCAUUCGAACGUCUGCCCUAUCAACUUUCGAUGGUA
GUCGCCGUGCCUACCAUGGUGACCACGGGUGACGGGGAAUCAGGGUUCGAUUCCGGAGAG
GGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCACUC
CCGACCCGGGGAGGUAGUGACGAAAAAUAACAAUACAGGACUCUUUCGAGGCCCUGUAAU
UGGAAUGAGUCCACUUUAAAUCCUUUAACGAGGAUCCAUUGGAGGGCAAGUCUGGUGCCA
GCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGCUGCAGUUAAAAAGCUC
GUAGUUGGAUCUUGGGAGCGGCCGUCCCCUGCUCGGGGCCCGAAGCGUUUACUUUGAAAA
AAUUAGAGUGUUCAAAGCAGGCCGCCUGGAUACCGCAGCUAGGAAUAAUGGAAUAGGACC
GCGGUUCUAUUUUGUUGGUUUUCGGAACUGAGGCCAUGAUUAAGAGGGACGGCCGGGGGC
AUUCGUAUUGCGCCGCUAGAGGUGAAAUUCUUGGACCGGCGCAAGACGGACCAGAGCGAA
AGCAUUUGCCAAGAAUGUUUUCAUUAAUCAAGAACGAAAGUCGGAGGUUCGAAGACGAUC
AGAUACCGUCGUAGUUCCGACCAUAAACGAUGCCGACCGGCGAUGCGGCGGCGUUAUUCC
CAUGACCCGCCGGGCAGCUUCCGGGAAACCAAAGUCUUUGGGUUCCGGGGGGAGUAUGGU
UGCAAAGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGC
UUAAUUUGACUCAACACGGGAAACCUCACCCGGCCCGGACACGGACAGGAUUGACAGAUU
GAUAGCUCUUUCUCGAUUCCGUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGA
UUUGUCUGGUUAAUUCCGAUAACGAACGAGACUCUGGCAUGCUAACUAGUUAUCUUAGAG
GGACAAGUGGCGUUCAGCCACCCGAGAUUGAGCAAUAACAGGUCUGUGAUGCCCUUAGAU
GUCCGGGGCUGCACGCGCGCUACACUGACUGGCUCAGCGUGUGCCUACCCUACGCCGGCA
GGCGCGGGUAACCCGUUGAACCCCAUUCGUGAUGGGGAUCGGGGAUUGCAAUUAUUCCCC
AUGAACGAGGAAUUCCCAGUAAGUGCGGGUCAUAAGCUUGCGUUGAUUAAGUCCCUGCCC
UUGUACACACCGCCCGUCGCUACUACCGAUUGGAUGGUUUAGUGAGGCCCUCGGAUCGGC
CCCGCCGGGGUGCCCUGGCGGAGCGCUGAGAAGACGGUCGAACUUGACUAUCUAGAGGAA
GUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA

Sequence of entity 2 (A), FASTA

>9Q1S_2 60S ribosomal protein L8 (chains A)
GRVIRGQRKGAGSVFRAHVKHRKGAARLRAVDFAERHGYIKGIVKDIIHDPGRGAPLAKV
VFRDPYRFKKRTELFIAAEGIHTGQFVYCGKKAQLNIGNVLPVGTMPEGTIVCCLEEKPG
DRGKLARASGNYATVISHNPETKKTRVKLPSGSKKVISSANRAVVGVVAGGGRIDKPILK
AGRAYHKYKAKRNCWPRVRGVAMNPVEHPFGGGNHQHIGKPSTIRRDAPAGRKVGLIAAR
RTGRLRGT

Sequence of entity 3 (B), FASTA

>9Q1S_3 60S ribosomal protein L3 (chains B)
SHRKFSAPRHGSLGFLPRKRSSRHRGKVKSFPKDDPSKPVHLTAFLGYKAGMTHIVREVD
RPGSKVNKKEVVEAVTIVETPPMVVVGIVGYVETPRGLRTFKTVFAEHISDECKRRFYKN
WHKSKKKAFTKYCKKWQDDAGKRQLDKDFSSMKKYCQVIRVLAHTQMRLLPLRQKKAHLM
EIQVNGGTVAEKLDWARERLEQQVPVSQVFGQDEMIDVIGVTKGKGYKGVTSRWHTKKLP
RKTHRGLRKVACIGAWHPARVAFSVARAGQKGYHHRTEINKKIYKIGQGYLIKDGKLIKN
NASTDYDLSDKSINPLGGFVHYGEVTNDFVMLKGCVVGTKKRVLTLRKSLLVQTKRRALE
KIDLKFIDTTSKFGHGRFQTVEEKKAFMGPLKKD

Sequence of entity 4 (C), FASTA

>9Q1S_4 60S ribosomal protein L4 (chains C)
ACARPLISVYSEKGESSGKNVTLPAVFKAPIRPDIVNFVHTNLRKNNRQPYAVSELAGHQ
TSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRGGRMFAPTKTWRRWHRRVNTTQKR
YAICSALAASALPALVMSKGHRIEEVPELPLVVEDKVEGYKKTKEAVLLLKKLKAWNDIK
KVYASQRMRAGKGKMRNRRRIQRRGPCVIYNEDNGIVKAFRNIPGITLLNVTKLNILKLA
PGGHVGRFCIWTESAFRKLDDLYGTWRKAASLKSNYNLPMHKMLNTDLSRILKSPEIQRA
LRAPRKKIHRRVLKKNPLKNLRIMLKLNPYAKTMRRNTILRQARNHKLRVERAAAALAAK
SD

Sequence of entity 5 (E), FASTA

>9Q1S_5 Large ribosomal subunit protein eL6 (chains E)
KGKPHCSRNPVLVRGIGRYSRSAMYSRKALYKRKYAAPKSRIERKKKREKVLATVTKPVG
GDKNGGTRVVKLRKMPRYYPTEDVPRKLLSHGKKPFSQHVRKLRASITPGTILIILTGRH
RGKRVVFLKQLSSGLLLVTGPLSLNRVPLRRTHQKFVIATSTKIDISGVKIPKHLTDAYF
KKKKLRKPRHQEGEIFDTEKEKYEITEQRKVDQKAVDSQILPKIKAVPQLQGYLRSVFAL
TNGVYPHKLVF

Sequence of entity 6 (G), FASTA

>9Q1S_6 Large ribosomal subunit protein eL8 (chains G)
VVNPLFEKRPKNFGIGQDIQPKRDLTRFVKWPRYIRLQRQRAILYKRLKVPPAINQFTQV
LDRQTATQLLKLAHKYRPETKQEKKQRLLARAEKKAAGKGDVPTKRPPVLRAGVNTVTTL
VENKKAQLVVIAHDVDPIELVVFLPALCRKMGVPYCILKGKARLGRLVHRKTCTTVAFTQ
VNSEDKGALAKLVEAIRTNYNDRYDEIRRHWGGNVLGPKSVARIAKLEKAKAKELATKLG

Sequence of entity 7 (H), FASTA

>9Q1S_7 60S ribosomal protein L9 (chains H)
MKTILSNQTVDIPENVDISLKGRTVIVKGPRGTLRRDFNHINVELSLLGKKKKRLRVDKW
WGNRKELATVRTICSHVQNMIKGVTLGFRYKMRSVYAHFPINVVIQENGSLVEIRNFLGE
KYIRRVRMRPGVACSVSQAQKDELVLEGNDIELVSNSAALIQQATTVKNKDIRKFLDGIY
VSEKGTVQQA

Sequence of entity 8 (I), FASTA

>9Q1S_8 Ribosomal protein L10 (chains I)
GRRPARCYRYCKNKPYPKSRFCRGVPDAKIRIFDLGRKKAKVDEFPLCGHMVSDEYEQLS
SEALEAARICANKYMVKSCGKDGFHIRVRLHPFHVIRINKMLSCAGADRLQTGMRGAFGK
PQGTVARVHIGQVIMSIRTKLQNKEHVVEALRRAKFKFPGRQKIHISKKWGFTKFNADEF
EDMVAEKRLIPDGCGVKYIPNRGPLDKWRALHS

Sequence of entity 9 (J), FASTA

>9Q1S_9 60S ribosomal protein L11 (chains J)
KENPMRELRIRKLCLNICVGESGDRLTRAAKVLEQLTGQTPVFSKARYTVRSFGIRRNEK
IAVHCTVRGAKAEEILEKGLKVREYELRKNNFSDTGNFGFGIQEHIDLGIKYDPSIGIYG
LDFYVVLGRPGFSIADKKRRTGCIGAKHRISKEEAMRWFQQKYDGIILPG

Sequence of entity 10 (L), FASTA

>9Q1S_10 Large ribosomal subunit protein eL13 (chains L)
APSRNGMILKPHFHKDWQRRVATWFNQPARKIRRRKARQARARRIAPRPAAGPIRPIVRC
PTVRYHTKVRAGRGFSLEELRVAGIHKKVARTIGISVDPRRRNKSTESLQANVQRLKEYR
SKLVLFPRKPSAPKKGDSSAEELKLATQLTGPVMPIRNVFKKEKARVITEEEKNFKAFAS
LRMARANARLFGIRAKRAKEAAEQDVEKKK

Sequence of entity 11 (N), FASTA

>9Q1S_11 60S ribosomal protein L15 (chains N)
GAYKYIQELWRKKQSDVMRFLLRVRCWQYRQLSALHRAPRPTRPDKARRLGYKAKQGYVI
YRIRVRRGGRKRPVPKGATYGKPVHHGVNQLKFARSLQSVAEERAGRHCGALRVLNSYWV
GEDSTYKFFEVILIDPFHKAIRRNPDTQWITKPVHKHREMRGLTSAGRKSRGLGKGHKFH
HTIGGSRRAAWRRRNTLQLHRYR

Sequence of entity 12 (O), FASTA

>9Q1S_12 Large ribosomal subunit protein uL13 (chains O)
QVLVLDGRGHLLGRLAAIVAKQVLLGRKVVVVRCEGINISGNFYRNKLKYLAFLRKRMNT
NPSRGPYHFRAPSRIFWRTVRGMLPHKTKRGQAALDRLKVFDGIPPPYDKKKRMVVPAAL
KVVRLKPTRKFAYLGRLAHEVGWKYQAVTATLEEKRKEKAKIHYRKKKQLMRLRKQAEKN
VEKKISKFTDVLKTHGLLV

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	7
MG	Magnesium ion	Mg	206

Primary citation

Structural studies of nedicistrovirus IRES-driven, initiation factor-independent translation shed light on key steps of eukaryotic translation elongation. De, S., Altomare, C.G., Abaeva, I.S. et al. Nucleic Acids Res (2026) 54. DOI 10.1093/nar/gkag510 · PubMed

Other PDB entries of the same protein (UniProt G1TT27 (AlphaFold model), which also has an AlphaFold model), best resolution first:

11IQ 2.4 Å, Rabbit 80S with eEF2,eIF5A and SERBP1
8SCB 2.5 Å, Terminating ribosome with SRI-41315
9MR4 2.65 Å, NAC: Ribosome nascent chain complex(Oxa1L)
9RHU 2.65 Å, Rabbit 80S ribosome in complex with eRF1-AAQ, stalled at the Stop codon in mutated F2A…
8RJB 2.69 Å, Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in…
8VVQ 2.7 Å, Codon sampling state of elongation inhibitor-treated mammalian ribosomes obtained from…
8RJD 2.79 Å, Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in…
8B6C 2.79 Å, Cryo-EM structure of ribosome-Sec61 in complex with cyclotriazadisulfonamide derivative…
6SGC 2.8 Å, Rabbit 80S ribosome stalled on a poly(A) tail
7UCK 2.8 Å, 80S translation initiation complex with ac4c(-1) mRNA and Harringtonine
9BDL 2.8 Å, 80S ribosome with angiogenin
9QQA 2.8 Å, Ternary complex of translating ribosome, NAC and NMT1

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