9P8H: In situ human A/P-P/E state 80S ribosome

Name: PDB 9P8H: In situ human A/P-P/E state 80S ribosome
Published: 2025-12-24
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

In situ human A/P-P/E state 80S ribosome. Determined by electron microscopy at 2.98 Å resolution. Released 24 Dec 2025.

Method: Electron microscopy
Resolution: 2.98 Å
Organism: Homo sapiens
Chains: 84
Atoms: 220,526
Mol. weight: 3332.61 kDa
Ligands: MG, ZN, SPM, SPD
Released: 24 Dec 2025

Explore 9P8H in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9P8H contains 558 α-helices and 566 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 CH: 6 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	26-33	8
α-helix	58-63	6
α-helix	75-88	14
α-helix	92-99	8
α-helix	103-110	8
α-helix	118-128	11
β-strand	131	1	42
β-strand	139	1	42

Chain CI: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	52-62	11
α-helix	70-72	3

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
β-strand	72-74	3	81
α-helix	78-81	4
α-helix	84-92	9
β-strand	97-98	2	186
β-strand	100-102	3	82
α-helix	103-106	4
β-strand	110-112	3	81
β-strand	123-126	4	82
β-strand	128-129	2	81
α-helix	131-139	9
β-strand	143-146	4	82

Chain LA: 11 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	4-5	2
α-helix	9-11	3
β-strand	18	1	87
α-helix	29-32	4
α-helix	34-38	5
β-strand	40-50	11	88
α-helix	51	1
β-strand	57-64	8	88
β-strand	71-77	7	88
β-strand	79	1	89
β-strand	83	1	8
β-strand	87-91	5	88
β-strand	101-103	3	88
α-helix	104-106	3
β-strand	112-113	2	90
β-strand	116	1	91
β-strand	126	1	91
β-strand	134-140	7	90
α-helix	142-144	3
β-strand	145-149	5	90
β-strand	155-159	5	90
β-strand	163-165	3	88
β-strand	166	1	90
β-strand	169	1	89
α-helix	174-176	3
α-helix	182-190	9
β-strand	193	1	87
α-helix	201-203	3
β-strand	224-225	2	92
α-helix	229-230	2
β-strand	237-238	2	92

Chain Lb: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	12-18	7
α-helix	22-24	3
α-helix	37-48	12
α-helix	54-73	20
α-helix	92-100	9
α-helix	106-117	12

Chain LB: 17 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	9-10	2
α-helix	32-35	4
α-helix	40-41	2
β-strand	42-43	2	101
β-strand	45-59	15	102
β-strand	71-80	10	102
α-helix	82-83	2
β-strand	84-95	12	103
β-strand	98-106	9	103
α-helix	107	1
α-helix	112-115	4
α-helix	116-118	3
α-helix	140-156	17
β-strand	159-165	7	103
α-helix	168-170	3
β-strand	180-184	5	103
β-strand	185-186	2	101
α-helix	190-199	10
β-strand	204-205	2	103
α-helix	207-210	4
β-strand	216-222	7	102
α-helix	223-224	2
β-strand	225-229	5	104
α-helix	231-234	4
α-helix	237-241	5
β-strand	270-273	4	104
β-strand	276-287	12	102
β-strand	292-293	2	105
β-strand	297-298	2	105
α-helix	300-302	3
β-strand	320	1	106
β-strand	324	1	106
β-strand	330-334	5	102
β-strand	344-349	6	102
β-strand	365-368	4	102
α-helix	382-389	8
α-helix	393-402	10

Chain Lc: 4 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	10-21	12
β-strand	26-29	4	84
α-helix	31-40	10
β-strand	45-49	5	84
α-helix	54-67	14
β-strand	70-74	5	84
α-helix	78-85	8
β-strand	93-98	6	84

Chain LC: 23 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	7-11	5	112
β-strand	17-23	7	112
α-helix	24-25	2
α-helix	26-29	4
α-helix	34-45	12
α-helix	46-48	3
α-helix	49-51	3
β-strand	65-66	2	113
β-strand	77-78	2	113
β-strand	90	1	113
α-helix	100-101	2
α-helix	117-130	14
α-helix	134-139	6
β-strand	152-154	3	112
α-helix	156-160	5
α-helix	164-173	10
α-helix	177-186	10
β-strand	188-189	2	114
β-strand	201-202	2	114
β-strand	208-211	4	112
α-helix	217-220	4
β-strand	228-231	4	112
α-helix	232-234	3
α-helix	237-240	4
β-strand	250-253	4	112
α-helix	254-264	11
α-helix	279-282	4
α-helix	289-294	6
α-helix	296-301	6
α-helix	302-305	4
α-helix	312-314	3
α-helix	316-317	2
α-helix	322-328	7
α-helix	331-367	37

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
A/P site tRNA	AP	RNA	142	Homo sapiens
P/E site tRNA	PE	RNA	150	Homo sapiens
40S ribosomal protein S3	SD	protein	454	Homo sapiens
40S ribosomal protein S5	SF	protein	189	Homo sapiens	P46782 (AlphaFold model)
40S ribosomal protein S10	SK	protein	98	Homo sapiens	P46783 (AlphaFold model)
Small ribosomal subunit protein eS12	SM	protein	122	Homo sapiens	P25398 (AlphaFold model)
40S ribosomal protein S15	SP	protein	127	Homo sapiens	P62841 (AlphaFold model)
Small ribosomal subunit protein uS9	SQ	protein	144	Homo sapiens	P62249
Small ribosomal subunit protein eS17	SR	protein	135	Homo sapiens	P08708
40S ribosomal protein S18	SS	protein	145	Homo sapiens	P62269
40S ribosomal protein S19	ST	protein	143	Homo sapiens	P39019
40S ribosomal protein S20	SU	protein	104	Homo sapiens	P60866

72 more molecules are not listed.

Sequence of entity 1 (AP), FASTA

>9P8H_1 A/P site tRNA (chains AP)
GUCUCCGUAGUGUAGGGUAUCACGUUCGCCUAACACGCGAAAGGUCCUCGGUUCGAAACC
GGGCGGAAACAGUCUCCGUAGUGUAGGGUAUCACGUUCGCCUAACACGCGAAAGGUCCUC
GGUUCGAAACCGGGCGGAAACA

Sequence of entity 2 (PE), FASTA

>9P8H_2 P/E site tRNA (chains PE)
GCCCGGAUAGCUCAGCUGUAGAGCAUCAGACUUUUAAUCUGAGGGUCCAGGGUUCAAGUC
CCUGUUCGGGCGCCAGCCCGGAUAGCUCAGCUGUAGAGCAUCAGACUUUUAAUCUGAGGG
UCCAGGGUUCAAGUCCCUGUUCGGGCGCCA

Sequence of entity 3 (SD), FASTA

>9P8H_3 40S ribosomal protein S3 (chains SD)
MAVQISKKRKFVADGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLG
EKGRRIRELTAVVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRRACY
GVLRFIMESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPVNYYVDTAVRHVLLRQG
VLGIKVKIMLPWDPTGKIGPKKPLPDHVSIVEPKDEILPTTPISEQKMAVQISKKRKFVA
DGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLGEKGRRIRELTAVV
QKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFIMESGAKG
CEVVVSGKLRGQRAKSMKFVDGLMIHSGDPVNYYVDTAVRHVLLRQGVLGIKVKIMLPWD
PTGKIGPKKPLPDHVSIVEPKDEILPTTPISEQK

Sequence of entity 4 (SF), FASTA

>9P8H_4 40S ribosomal protein S5 (chains SF)
DIKLFGKWSTDDVQINDISLQDYIAVKEKYAKYLPHSAGRYAAKRFRKAQCPIVERLTNS
MMMHGRNNGKKLMTVRIVKHAFEIIHLLTGENPLQVLVNAIINSGPREDSTRIGRAGTVR
RQAVDVSPLRRVNQAIWLLCTGAREAAFRNIKTIAECLADELINAAKGSSNSYAIKKKDE
LERVAKSNR

Sequence of entity 5 (SK), FASTA

>9P8H_5 40S ribosomal protein S10 (chains SK)
MLMPKKNRIAIYELLFKEGVMVAKKDVHMPKHPELADKNVPNLHVMKAMQSLKSRGYVKE
QFAWRHFYWYLTNEGIQYLRDYLHLPPEIVPATLRRSR

Sequence of entity 6 (SM), FASTA

>9P8H_6 Small ribosomal subunit protein eS12 (chains SM)
VMDVNTALQEVLKTALIHDGLARGIREAAKALDKRQAHLCVLASNCDEPMYVKLVEALCA
EHQINLIKVDDNKKLGEWVGLCKIDREGKPRKVVGCSCVVVKDYGKESQAKDVIEEYFKC
KK

Sequence of entity 7 (SP), FASTA

>9P8H_7 40S ribosomal protein S15 (chains SP)
RTFRKFTYRGVDLDQLLDMSYEQLMQLYSARQRRRLNRGLRRKQHSLLKRLRKAKKEAPP
MEKPEVVKTHLRDMIILPEMVGSMVGVYNGKTFNQVEIKPEMIGHYLGEFSITYKPVKHG
RPGIGAT

Sequence of entity 8 (SQ), FASTA

>9P8H_8 Small ribosomal subunit protein uS9 (chains SQ)
SKGPLQSVQVFGRKKTATAVAHCKRGNGLIKVNGRPLEMIEPRTLQYKLLEPVLLLGKER
FAGVDIRVRVKGGGHVAQIYAIRQSISKALVAYYQKYVDEASKKEIKDILIQYDRTLLVA
DPRRCESKKFGGPGARARYQKSYR

Sequence of entity 9 (SR), FASTA

>9P8H_9 Small ribosomal subunit protein eS17 (chains SR)
MGRVRTKTVKKAARVIIEKYYTRLGNDFHTNKRVCEEIAIIPSKKLRNKIAGYVTHLMKR
IQRGPVRGISIKLQEEERERRDNYVPEVSALDQEIIEVDPDTKEMLKLLDFGSLSNLQVT
QPTVGMNFKTPRGPV

Sequence of entity 10 (SS), FASTA

>9P8H_10 40S ribosomal protein S18 (chains SS)
MSLVIPEKFQHILRVLNTNIDGRRKIAFAITAIKGVGRRYAHVVLRKADIDLTKRAGELT
EDEVERVITIMQNPRQYKIPDWFLNRQKDVKDGKYSQVLANGLDNKLREDLERLKKIRAH
RGLRHFWGLRVRGQHTKTTGRRGRT

Sequence of entity 11 (ST), FASTA

>9P8H_11 40S ribosomal protein S19 (chains ST)
PGVTVKDVNQQEFVRALAAFLKKSGKLKVPEWVDTVKLAKHKELAPYDENWFYTRAASTA
RHLYLRGGAGVGSMTKIYGGRQRNGVMPSHFSRGSKSVARRVLQALEGLKMVEKDQDGGR
KLTPQGQRDLDRIAGQVAAANKK

Sequence of entity 12 (SU), FASTA

>9P8H_12 40S ribosomal protein S20 (chains SU)
AIHRIRITLTSRNVKSLEKVCADLIRGAKEKNLKVKGPVRMPTKTLRITTRKTPCGEGSK
TWDRFQMRIHKRLIDLHSPSEIVKQITSISIEPGVEVEVTIADA

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	218
ZN	Zinc ion	Zn	6
SPM	Spermine	C10 H26 N4	7
SPD	Spermidine	C7 H19 N3	10

Primary citation

Visualizing the translation landscape in human cells at high resolution. Zheng, W., Zhang, Y., Wang, J. et al. Nat Commun (2025) 16:10757-10757. DOI 10.1038/s41467-025-65795-9 · PubMed

Other PDB entries of the same protein (UniProt P46782 (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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