9M0P: Human 80S ribosome

Name: PDB 9M0P: Cryo-EM structure of human 80S ribosome in complex with montanine
Published: 2026-01-14
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Cryo-EM structure of human 80S ribosome in complex with montanine. Determined by electron microscopy at 2.78 Å resolution. Released 14 Jan 2026.

Method: Electron microscopy
Resolution: 2.78 Å
Organism: Homo sapiens
Chains: 78
Atoms: 202,018
Mol. weight: 3857.35 kDa
Ligands: A1L8F, ZN, MG
Released: 14 Jan 2026

Explore 9M0P in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9M0P contains 503 α-helices and 522 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 CA: 31 helices, 26 β-strands

Element	Residues	Length	Sheet
α-helix	114-121	8
β-strand	124-130	7	161
β-strand	134	1	161
α-helix	137-147	11
β-strand	152-158	7	161
α-helix	160-164	5
α-helix	171-191	21
β-strand	212-216	5	161
β-strand	221-223	3	161
α-helix	225-235	11
α-helix	248-258	11
β-strand	265-266	2	162
β-strand	273-274	2	162
β-strand	287	1	162
α-helix	288-289	2
α-helix	290-294	5
α-helix	295-306	12
α-helix	314-319	6
α-helix	335-343	9
β-strand	345	1	161
α-helix	346-356	11
α-helix	520-530	11
β-strand	535-538	4	163
β-strand	544-547	4	163
α-helix	551-560	10
α-helix	561-565	5
α-helix	573-576	4
β-strand	580-582	3	164
β-strand	591-594	4	165
β-strand	601-608	8	165
α-helix	609-610	2
α-helix	613-619	7
α-helix	628-639	12
α-helix	643-647	5
β-strand	649-652	4	165
α-helix	654-656	3
β-strand	657	1	165
β-strand	661-663	3	165
α-helix	673-688	16
β-strand	697	1	164
β-strand	700-708	9	165
α-helix	718-735	18
β-strand	739-742	4	164
β-strand	744-751	8	166
α-helix	753-755	3
α-helix	756-765	10
α-helix	768	1
β-strand	769-775	7	166
β-strand	782-789	8	166
α-helix	791-793	3
α-helix	796-803	8
β-strand	809	1	166
β-strand	812-814	3	166
β-strand	818-819	2	164
α-helix	830-842	13
α-helix	848-850	3
α-helix	851-854	4

Chain La: 7 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
α-helix	7-9	3
α-helix	42-48	7
α-helix	65-68	4
β-strand	72-74	3	20
α-helix	75-77	3
α-helix	84-89	6
β-strand	97-98	2	107
β-strand	100-102	3	21
β-strand	110-112	3	20
β-strand	123-126	4	21
β-strand	128-129	2	20
α-helix	131-139	9
β-strand	143-146	4	21

Chain LA: 10 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
α-helix	9-12	4
α-helix	14-16	3
α-helix	30-32	3
α-helix	34-38	5
β-strand	40-49	10	24
β-strand	58-64	7	24
β-strand	71-77	7	24
α-helix	78	1
β-strand	79	1	25
β-strand	83	1	26
β-strand	87-91	5	24
β-strand	101-103	3	24
β-strand	112-114	3	24
β-strand	116	1	27
β-strand	126	1	27
β-strand	134-140	7	24
β-strand	145-149	5	24
β-strand	155-159	5	24
β-strand	163-166	4	24
β-strand	169	1	25
α-helix	174-176	3
α-helix	182-190	9
α-helix	201-203	3
β-strand	224-225	2	28
α-helix	229-230	2
β-strand	237-238	2	28

Chain Lb: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	12-18	7
α-helix	22-25	4
α-helix	37-48	12
α-helix	49-51	3
α-helix	54-66	13

Chain LB: 16 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	14-16	3
α-helix	32-35	4
α-helix	40-41	2
β-strand	42-43	2	32
β-strand	45-60	16	33
β-strand	70-80	11	33
α-helix	82-83	2
β-strand	84-95	12	34
β-strand	98-106	9	34
α-helix	112-115	4
α-helix	116-118	3
α-helix	134-137	4
α-helix	140-156	17
β-strand	159-166	8	34
α-helix	168-170	3
β-strand	180-184	5	34
β-strand	185-186	2	32
α-helix	190-200	11
β-strand	203-205	3	34
α-helix	207-209	3
β-strand	216-222	7	33
α-helix	223-225	3
β-strand	227-229	3	35
α-helix	231-235	5
α-helix	237-241	5
β-strand	270-272	3	35
β-strand	276-287	12	33
β-strand	292	1	36
β-strand	299	1	36
β-strand	302	1	37
β-strand	312	1	37
α-helix	315-316	2
β-strand	320	1	38
β-strand	324	1	38
β-strand	330-334	5	33
β-strand	344-349	6	33
β-strand	365-368	4	33
α-helix	382-389	8

Chain Lc: 4 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	14-23	10
β-strand	25-29	5	39
α-helix	31-40	10
β-strand	45-48	4	39
α-helix	54-67	14
β-strand	70-73	4	39
α-helix	78-84	7
β-strand	93-99	7	39

Chain LC: 22 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	7-11	5	43
β-strand	17-23	7	43
α-helix	24-25	2
α-helix	26-29	4
α-helix	31-32	2
α-helix	34-44	11
α-helix	49-51	3
β-strand	65-66	2	44
β-strand	77-78	2	44
α-helix	79-81	3
β-strand	90	1	44
α-helix	117-132	16
α-helix	134-139	6
β-strand	153-154	2	43
α-helix	158-160	3
α-helix	164-173	10
α-helix	177-186	10
β-strand	188-189	2	45
α-helix	193-195	3
β-strand	201-202	2	45
β-strand	208-211	4	43
α-helix	217-221	5
β-strand	230-231	2	43
α-helix	237-240	4
α-helix	242-244	3
β-strand	250-253	4	43
α-helix	254-258	5
α-helix	289-294	6
α-helix	296-300	5
α-helix	303-305	3
α-helix	316-317	2
α-helix	322-328	7
α-helix	332-357	26

Chain Ld: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	21-27	7	46
α-helix	29-32	4
α-helix	41-57	17
β-strand	62-64	3	46
α-helix	66-72	7
β-strand	84-92	9	46
β-strand	102-108	7	46
β-strand	120-121	2	46

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
40S ribosomal protein S11	SL	protein	158	Homo sapiens	P62280 (AlphaFold model)
40S ribosomal protein S17	SR	protein	135	Homo sapiens	P08708 (AlphaFold model)
40S ribosomal protein S15	SP	protein	145	Homo sapiens	P62841 (AlphaFold model)
40S ribosomal protein S16	SQ	protein	146	Homo sapiens	P62249 (AlphaFold model)
40S ribosomal protein S21	SV	protein	83	Homo sapiens	P63220
40S ribosomal protein S23	SX	protein	143	Homo sapiens	P62266
40S ribosomal protein S26	Sa	protein	115	Homo sapiens	P62854
40S ribosomal protein S20	SU	protein	119	Homo sapiens	P60866
40S ribosomal protein S28	Sc	protein	69	Homo sapiens	P62857
40S ribosomal protein S19	ST	protein	145	Homo sapiens	P39019
Receptor of activated protein C kinase 1	Sg	protein	317	Homo sapiens	P63244
40S ribosomal protein S2	SC	protein	293	Homo sapiens	P15880

66 more molecules are not listed.

Sequence of entity 1 (SL), FASTA

>9M0P_1 40S ribosomal protein S11 (chains SL)
MADIQTERAYQKQPTIFQNKKRVLLGETGKEKLPRYYKNIGLGFKTPKEAIEGTYIDKKC
PFTGNVSIRGRILSGVVTKMKMQRTIVIRRDYLHYIRKYNRFEKRHKNMSVHLSPCFRDV
QIGDIVTVGECRPLSKTVRFNVLKVTKAAGTKKQFQKF

Sequence of entity 2 (SR), FASTA

>9M0P_2 40S ribosomal protein S17 (chains SR)
MGRVRTKTVKKAARVIIEKYYTRLGNDFHTNKRVCEEIAIIPSKKLRNKIAGYVTHLMKR
IQRGPVRGISIKLQEEERERRDNYVPEVSALDQEIIEVDPDTKEMLKLLDFGSLSNLQVT
QPTVGMNFKTPRGPV

Sequence of entity 3 (SP), FASTA

>9M0P_3 40S ribosomal protein S15 (chains SP)
MAEVEQKKKRTFRKFTYRGVDLDQLLDMSYEQLMQLYSARQRRRLNRGLRRKQHSLLKRL
RKAKKEAPPMEKPEVVKTHLRDMIILPEMVGSMVGVYNGKTFNQVEIKPEMIGHYLGEFS
ITYKPVKHGRPGIGATHSSRFIPLK

Sequence of entity 4 (SQ), FASTA

>9M0P_4 40S ribosomal protein S16 (chains SQ)
MPSKGPLQSVQVFGRKKTATAVAHCKRGNGLIKVNGRPLEMIEPRTLQYKLLEPVLLLGK
ERFAGVDIRVRVKGGGHVAQIYAIRQSISKALVAYYQKYVDEASKKEIKDILIQYDRTLL
VADPRRCESKKFGGPGARARYQKSYR

Sequence of entity 5 (SV), FASTA

>9M0P_5 40S ribosomal protein S21 (chains SV)
MQNDAGEFVDLYVPRKCSASNRIIGAKDHASIQMNVAEVDKVTGRFNGQFKTYAICGAIR
RMGESDDSILRLAKADGIVSKNF

Sequence of entity 6 (SX), FASTA

>9M0P_6 40S ribosomal protein S23 (chains SX)
MGKCRGLRTARKLRSHRRDQKWHDKQYKKAHLGTALKANPFGGASHAKGIVLEKVGVEAK
QPNSAIRKCVRVQLIKNGKKITAFVPNDGCLNFIEENDEVLVAGFGRKGHAVGDIPGVRF
KVVKVANVSLLALYKGKKERPRS

Sequence of entity 7 (Sa), FASTA

>9M0P_7 40S ribosomal protein S26 (chains Sa)
MTKKRRNNGRAKKGRGHVQPIRCTNCARCVPKDKAIKKFVIRNIVEAAAVRDISEASVFD
AYVLPKLYVKLHYCVSCAIHSKVVRNRSREARKDRTPPPRFRPAGAAPRPPPKPM

Sequence of entity 8 (SU), FASTA

>9M0P_8 40S ribosomal protein S20 (chains SU)
MAFKDTGKTPVEPEVAIHRIRITLTSRNVKSLEKVCADLIRGAKEKNLKVKGPVRMPTKT
LRITTRKTPCGEGSKTWDRFQMRIHKRLIDLHSPSEIVKQITSISIEPGVEVEVTIADA

Sequence of entity 9 (Sc), FASTA

>9M0P_9 40S ribosomal protein S28 (chains Sc)
MDTSRVQPIKLARVTKVLGRTGSQGQCTQVRVEFMDDTSRSIIRNVKGPVREGDVLTLLE
SEREARRLR

Sequence of entity 10 (ST), FASTA

>9M0P_10 40S ribosomal protein S19 (chains ST)
MPGVTVKDVNQQEFVRALAAFLKKSGKLKVPEWVDTVKLAKHKELAPYDENWFYTRAAST
ARHLYLRGGAGVGSMTKIYGGRQRNGVMPSHFSRGSKSVARRVLQALEGLKMVEKDQDGG
RKLTPQGQRDLDRIAGQVAAANKKH

Sequence of entity 11 (Sg), FASTA

>9M0P_11 Receptor of activated protein C kinase 1 (chains Sg)
MTEQMTLRGTLKGHNGWVTQIATTPQFPDMILSASRDKTIIMWKLTRDETNYGIPQRALR
GHSHFVSDVVISSDGQFALSGSWDGTLRLWDLTTGTTTRRFVGHTKDVLSVAFSSDNRQI
VSGSRDKTIKLWNTLGVCKYTVQDESHSEWVSCVRFSPNSSNPIIVSCGWDKLVKVWNLA
NCKLKTNHIGHTGYLNTVTVSPDGSLCASGGKDGQAMLWDLNEGKHLYTLDGGDIINALC
FSPNRYWLCAATGPSIKIWDLEGKIIVDELKQEVISTSSKAEPPQCTSLAWSADGQTLFA
GYTDNLVRVWQVTIGTR

Sequence of entity 12 (SC), FASTA

>9M0P_12 40S ribosomal protein S2 (chains SC)
MADDAGAAGGPGGPGGPGMGNRGGFRGGFGSGIRGRGRGRGRGRGRGRGARGGKAEDKEW
MPVTKLGRLVKDMKIKSLEEIYLFSLPIKESEIIDFFLGASLKDEVLKIMPVQKQTRAGQ
RTRFKAFVAIGDYNGHVGLGVKCSKEVATAIRGAIILAKLSIVPVRRGYWGNKIGKPHTV
PCKVTGRCGSVLVRLIPAPRGTGIVSAPVPKKLLMMAGIDDCYTSARGCTATLGNFAKAT
FDAISKTYSYLTPDLWKETVFTKSPYQEFTDHLVKTHTRVSVQRTQAPAVATT

Ligands and cofactors

ID	Name	Formula	Copies
A1L8F	(1S,13S,15S,16S)-16-methoxy-5,7-dioxa-12-azapentacyclo[10.6.1.02,10.04,8.013,18…	C17 H19 N O4	1
ZN	Zinc ion	Zn	6
MG	Magnesium ion	Mg	291

Primary citation

Modulation of translational elongation by montanine alkaloids preferentially inhibits RNA viruses. Sakai, R., Sato, K., Tsugita, A. et al. bioRxiv (2025). DOI 10.64898/2025.12.19.695327v1

Other PDB entries of the same protein (UniProt P62280 (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
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
9O3V 2.2 Å, Human 80S ribosome stalled on MYC nascent chain

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