9Q1Q: NediV IRES

Name: PDB 9Q1Q: NediV IRES (A site) in complex with Rabbit 80S ribosome
Published: 2026-06-17
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

NediV IRES (A site) in complex with Rabbit 80S ribosome. Determined by electron microscopy at 3.5 Å resolution. Released 17 Jun 2026.

Method: Electron microscopy
Resolution: 3.5 Å
Organism: Oryctolagus cuniculus
Chains: 83
Atoms: 216,047
Mol. weight: 3232.67 kDa
Ligands: MG, ZN
Released: 17 Jun 2026

Explore 9Q1Q in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9Q1Q contains 472 α-helices and 557 β-strands across 78 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: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	29	1	1
β-strand	31	1	1
α-helix	42-48	7
β-strand	72-74	3	2
α-helix	75-77	3
α-helix	84-92	9
β-strand	97-98	2	89
β-strand	100-102	3	3
α-helix	103-106	4
β-strand	110-112	3	2
β-strand	122-126	5	3
α-helix	131-140	10
β-strand	142-146	5	3

Chain A: 11 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	6-10	5
α-helix	14-16	3
β-strand	18	1	8
α-helix	30-32	3
α-helix	34-37	4
β-strand	41-47	7	9
β-strand	58-62	5	9
β-strand	73-77	5	9
α-helix	78	1
β-strand	79	1	10
β-strand	82-83	2	11
α-helix	86	1
β-strand	87-90	4	9
α-helix	94-96	3
β-strand	100-103	4	9
β-strand	112-114	3	9
β-strand	116	1	12
β-strand	126	1	12
β-strand	134-140	7	9
α-helix	142-144	3
β-strand	145-149	5	9
β-strand	155-159	5	9
β-strand	163-166	4	9
α-helix	168	1
β-strand	169	1	10
α-helix	178-179	2
α-helix	182-188	7
β-strand	193	1	8
β-strand	224-225	2	13
β-strand	237-238	2	13

Chain aa: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	20-22	3	178
β-strand	28	1	151
β-strand	29-31	3	178
β-strand	36-43	8	179
α-helix	49-55	7
β-strand	57	1	149
α-helix	62-65	4
β-strand	66-73	8	179
α-helix	75-78	4
α-helix	97-99	3

Chain AA: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	25-26	2	76
β-strand	47-48	2	76
α-helix	51-65	15
α-helix	71-73	3
β-strand	74-78	5	77
α-helix	84-94	11
β-strand	97-100	4	77
β-strand	121-124	4	77
α-helix	132-135	4
β-strand	144-148	5	77
β-strand	159-162	4	77
α-helix	168-186	19
α-helix	199-202	4

Chain b: 5 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	12-18	7
β-strand	22	1	144
α-helix	37-48	12
α-helix	55-74	20
α-helix	91-100	10
α-helix	106-116	11

Chain B: 11 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	9-10	2
α-helix	32-34	3
β-strand	42	1	19
β-strand	45-60	16	20
β-strand	70-80	11	20
α-helix	82-83	2
β-strand	84-95	12	21
β-strand	98-106	9	21
α-helix	112-115	4
α-helix	134-137	4
α-helix	140-156	17
β-strand	159-166	8	21
β-strand	180-184	5	21
β-strand	186	1	19
α-helix	190-199	10
β-strand	204-205	2	21
α-helix	207-210	4
β-strand	216-222	7	20
α-helix	223-225	3
β-strand	228-229	2	22
α-helix	237-240	4
β-strand	270-271	2	22
β-strand	276-287	12	20
β-strand	292-294	3	23
β-strand	297-299	3	23
β-strand	330-334	5	20
β-strand	344-349	6	20
β-strand	365-368	4	20
α-helix	382-389	8

Chain bb: 1 helix, 8 β-strands

Element	Residues	Length	Sheet
α-helix	12-16	5
β-strand	32-35	4	181
β-strand	36	1	182
β-strand	44-47	4	181
β-strand	54-55	2	183
β-strand	62-64	3	183
β-strand	73	1	183
β-strand	78	1	182
β-strand	81-82	2	181

Chain BB: 10 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	24-27	4
β-strand	28-34	7	82
β-strand	43-50	8	82
α-helix	62-64	3
β-strand	66-70	5	82
α-helix	71-74	4
β-strand	82-91	10	82
β-strand	95-105	11	82
α-helix	107-113	7
β-strand	120-128	9	82
β-strand	134-143	10	82
α-helix	155-157	3
α-helix	158-172	15
α-helix	174-178	5
α-helix	181-188	8
α-helix	194-200	7
β-strand	207-217	11	82
α-helix	226-231	6

70 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
5S rRNA	7	RNA	119	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)
60S ribosomal protein L5	D	protein	293	Oryctolagus cuniculus	P19949 (AlphaFold model)
Large ribosomal subunit protein eL6	E	protein	251	Oryctolagus cuniculus	G1SKF7
60S ribosomal protein L7	F	protein	225	Oryctolagus cuniculus	G1SV32
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

71 more molecules are not listed.

Sequence of entity 1 (7), FASTA

>9Q1Q_1 5S rRNA (chains 7)
GUCUACGGCCAUACCACCCUGAACGCGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGG
GUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCGGGUGCUGUAGGCU

Sequence of entity 2 (A), FASTA

>9Q1Q_2 60S ribosomal protein L8 (chains A)
GRVIRGQRKGAGSVFRAHVKHRKGAARLRAVDFAERHGYIKGIVKDIIHDPGRGAPLAKV
VFRDPYRFKKRTELFIAAEGIHTGQFVYCGKKAQLNIGNVLPVGTMPEGTIVCCLEEKPG
DRGKLARASGNYATVISHNPETKKTRVKLPSGSKKVISSANRAVVGVVAGGGRIDKPILK
AGRAYHKYKAKRNCWPRVRGVAMNPVEHPFGGGNHQHIGKPSTIRRDAPAGRKVGLIAAR
RTGRLRGT

Sequence of entity 3 (B), FASTA

>9Q1Q_3 60S ribosomal protein L3 (chains B)
SHRKFSAPRHGSLGFLPRKRSSRHRGKVKSFPKDDPSKPVHLTAFLGYKAGMTHIVREVD
RPGSKVNKKEVVEAVTIVETPPMVVVGIVGYVETPRGLRTFKTVFAEHISDECKRRFYKN
WHKSKKKAFTKYCKKWQDDAGKRQLDKDFSSMKKYCQVIRVLAHTQMRLLPLRQKKAHLM
EIQVNGGTVAEKLDWARERLEQQVPVSQVFGQDEMIDVIGVTKGKGYKGVTSRWHTKKLP
RKTHRGLRKVACIGAWHPARVAFSVARAGQKGYHHRTEINKKIYKIGQGYLIKDGKLIKN
NASTDYDLSDKSINPLGGFVHYGEVTNDFVMLKGCVVGTKKRVLTLRKSLLVQTKRRALE
KIDLKFIDTTSKFGHGRFQTVEEKKAFMGPLKKD

Sequence of entity 4 (C), FASTA

>9Q1Q_4 60S ribosomal protein L4 (chains C)
ACARPLISVYSEKGESSGKNVTLPAVFKAPIRPDIVNFVHTNLRKNNRQPYAVSELAGHQ
TSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRGGRMFAPTKTWRRWHRRVNTTQKR
YAICSALAASALPALVMSKGHRIEEVPELPLVVEDKVEGYKKTKEAVLLLKKLKAWNDIK
KVYASQRMRAGKGKMRNRRRIQRRGPCVIYNEDNGIVKAFRNIPGITLLNVTKLNILKLA
PGGHVGRFCIWTESAFRKLDDLYGTWRKAASLKSNYNLPMHKMLNTDLSRILKSPEIQRA
LRAPRKKIHRRVLKKNPLKNLRIMLKLNPYAKTMRRNTILRQARNHKLRVERAAAALAAK
SD

Sequence of entity 5 (D), FASTA

>9Q1Q_5 60S ribosomal protein L5 (chains D)
FVKVVKNKAYFKRYQVKFRRRREGKTDYYARKRLVIQDKNKYNTPKYRMIVRVTNRDIIC
QIAYARIEGDMIVCAAYAHELPKYGVKVGLTNYAAAYCTGLLLARRLLNRFGMDKIYEGQ
VEVTGDEYNVESIDGQPGAFTCYLDAGLARTTTGNKVFGALKGAVDGGLSIPHSTKRFPG
YDSESKEFNAEVHRKHIMGQNVADYMRYLMEEDEDAYKKQFSQYIKNNVTPDMMEEMYKK
AHAAIRENPVYEKKPKREVKKKRWNRPKMSLAQKKDRVAQKKASFLRAQERAA

Sequence of entity 6 (E), FASTA

>9Q1Q_6 Large ribosomal subunit protein eL6 (chains E)
KGKPHCSRNPVLVRGIGRYSRSAMYSRKALYKRKYAAPKSRIERKKKREKVLATVTKPVG
GDKNGGTRVVKLRKMPRYYPTEDVPRKLLSHGKKPFSQHVRKLRASITPGTILIILTGRH
RGKRVVFLKQLSSGLLLVTGPLSLNRVPLRRTHQKFVIATSTKIDISGVKIPKHLTDAYF
KKKKLRKPRHQEGEIFDTEKEKYEITEQRKVDQKAVDSQILPKIKAVPQLQGYLRSVFAL
TNGVYPHKLVF

Sequence of entity 7 (F), FASTA

>9Q1Q_7 60S ribosomal protein L7 (chains F)
NFAELKIKRLRKKFAQKMLRKARRKLIYEKAKHYHKEYRQMYRTEIRMARMARKAGNFYV
PAEPKLAFVIRIRGINGVSPKVRKVLQLLRLRQIFNGTFVKLNKASINMLRIVEPYIAWG
YPNLKSVNELIYKRGYGKINKKRIALTDNTLIARSLGKYNIICMEDLIHEIYTVGKHFKE
ANNFLWPFKLSSPRGGMKKKTTHFVEGGDAGNREDQINRLIRRMN

Sequence of entity 8 (G), FASTA

>9Q1Q_8 Large ribosomal subunit protein eL8 (chains G)
VVNPLFEKRPKNFGIGQDIQPKRDLTRFVKWPRYIRLQRQRAILYKRLKVPPAINQFTQV
LDRQTATQLLKLAHKYRPETKQEKKQRLLARAEKKAAGKGDVPTKRPPVLRAGVNTVTTL
VENKKAQLVVIAHDVDPIELVVFLPALCRKMGVPYCILKGKARLGRLVHRKTCTTVAFTQ
VNSEDKGALAKLVEAIRTNYNDRYDEIRRHWGGNVLGPKSVARIAKLEKAKAKELATKLG

Sequence of entity 9 (H), FASTA

>9Q1Q_9 60S ribosomal protein L9 (chains H)
MKTILSNQTVDIPENVDISLKGRTVIVKGPRGTLRRDFNHINVELSLLGKKKKRLRVDKW
WGNRKELATVRTICSHVQNMIKGVTLGFRYKMRSVYAHFPINVVIQENGSLVEIRNFLGE
KYIRRVRMRPGVACSVSQAQKDELVLEGNDIELVSNSAALIQQATTVKNKDIRKFLDGIY
VSEKGTVQQA

Sequence of entity 10 (I), FASTA

>9Q1Q_10 Ribosomal protein L10 (chains I)
GRRPARCYRYCKNKPYPKSRFCRGVPDAKIRIFDLGRKKAKVDEFPLCGHMVSDEYEQLS
SEALEAARICANKYMVKSCGKDGFHIRVRLHPFHVIRINKMLSCAGADRLQTGMRGAFGK
PQGTVARVHIGQVIMSIRTKLQNKEHVVEALRRAKFKFPGRQKIHISKKWGFTKFNADEF
EDMVAEKRLIPDGCGVKYIPNRGPLDKWRALHS

Sequence of entity 11 (J), FASTA

>9Q1Q_11 60S ribosomal protein L11 (chains J)
KENPMRELRIRKLCLNICVGESGDRLTRAAKVLEQLTGQTPVFSKARYTVRSFGIRRNEK
IAVHCTVRGAKAEEILEKGLKVREYELRKNNFSDTGNFGFGIQEHIDLGIKYDPSIGIYG
LDFYVVLGRPGFSIADKKRRTGCIGAKHRISKEEAMRWFQQKYDGIILPG

Sequence of entity 12 (L), FASTA

>9Q1Q_12 Large ribosomal subunit protein eL13 (chains L)
APSRNGMILKPHFHKDWQRRVATWFNQPARKIRRRKARQARARRIAPRPAAGPIRPIVRC
PTVRYHTKVRAGRGFSLEELRVAGIHKKVARTIGISVDPRRRNKSTESLQANVQRLKEYR
SKLVLFPRKPSAPKKGDSSAEELKLATQLTGPVMPIRNVFKKEKARVITEEEKNFKAFAS
LRMARANARLFGIRAKRAKEAAEQDVEKKK

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	206
ZN	Zinc ion	Zn	8

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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