9P7Y: In situ human A-P-E state 80S ribosome

Name: PDB 9P7Y: In situ human A-P-E state 80S ribosome
Published: 2025-12-24
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

In situ human A-P-E state 80S ribosome. Determined by electron microscopy at 2.75 Å resolution. Released 24 Dec 2025.

Method: Electron microscopy
Resolution: 2.75 Å
Organism: Homo sapiens
Chains: 85
Atoms: 221,484
Mol. weight: 3275.42 kDa
Ligands: SPD, SPM, ZN, MG
Released: 24 Dec 2025

Explore 9P7Y in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9P7Y contains 547 α-helices and 561 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 CI: 3 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	52-62	11
β-strand	63	1	123
α-helix	69-70	2
β-strand	71	1	123
α-helix	72	1

Chain La: 8 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
α-helix	7-10	4
α-helix	42-48	7
β-strand	72-73	2	126
α-helix	75-77	3
α-helix	84-91	8
β-strand	97-98	2	22
α-helix	99	1
β-strand	100-102	3	127
α-helix	103-106	4
β-strand	110-111	2	126
β-strand	123-126	4	127
β-strand	128-129	2	126
α-helix	131-139	9
β-strand	143-146	4	127

Chain LA: 13 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	4-5	2
α-helix	10-12	3
β-strand	28	1	133
α-helix	29-32	4
α-helix	34-38	5
β-strand	40-49	10	133
α-helix	50-51	2
β-strand	58-64	7	133
β-strand	71-77	7	133
α-helix	78	1
β-strand	79	1	134
β-strand	83	1	49
β-strand	87-91	5	133
β-strand	101-103	3	133
α-helix	104-106	3
β-strand	112-113	2	135
β-strand	116	1	136
β-strand	126	1	136
β-strand	134-140	7	135
α-helix	142-144	3
β-strand	145-149	5	135
β-strand	155-159	5	135
β-strand	163-165	3	133
β-strand	166	1	135
α-helix	168	1
β-strand	169	1	134
α-helix	174-176	3
α-helix	182-190	9
α-helix	201-203	3
β-strand	224-225	2	137
α-helix	229-230	2
β-strand	237-238	2	137

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	54-72	19
α-helix	92-99	8
α-helix	106-117	12

Chain LB: 18 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	9-10	2
α-helix	14-16	3
α-helix	32-35	4
α-helix	40-41	2
β-strand	42-43	2	139
β-strand	45-59	15	140
β-strand	71-80	10	140
α-helix	82-83	2
β-strand	84-95	12	141
β-strand	98-106	9	141
α-helix	112-115	4
α-helix	116-118	3
α-helix	134-137	4
α-helix	140-156	17
β-strand	159-165	7	141
α-helix	168-170	3
α-helix	178-179	2
β-strand	180-184	5	141
β-strand	185-186	2	139
α-helix	190-199	10
β-strand	204-205	2	141
α-helix	207-210	4
β-strand	216-222	7	140
β-strand	225-229	5	142
α-helix	231-234	4
α-helix	237-241	5
β-strand	270-273	4	142
β-strand	276-287	12	140
β-strand	292-293	2	143
β-strand	297-298	2	143
α-helix	300-302	3
β-strand	320	1	144
β-strand	324	1	144
β-strand	330-334	5	140
β-strand	344-349	6	140
β-strand	365-368	4	140
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	132
α-helix	31-40	10
β-strand	45-49	5	132
α-helix	54-67	14
β-strand	70-74	5	132
α-helix	78-84	7
β-strand	93-98	6	132

Chain LC: 22 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	7-11	5	147
α-helix	12	1
β-strand	17-23	7	147
α-helix	24-25	2
α-helix	26-29	4
α-helix	34-44	11
β-strand	65-66	2	148
β-strand	77-78	2	148
β-strand	90	1	148
α-helix	117-130	14
α-helix	134-138	5
β-strand	152-154	3	147
α-helix	156-160	5
α-helix	164-173	10
α-helix	177-185	9
β-strand	188-189	2	149
α-helix	190-191	2
β-strand	201-202	2	149
β-strand	208-211	4	147
α-helix	217-220	4
β-strand	228-231	4	147
α-helix	232-234	3
α-helix	237-240	4
β-strand	250-253	4	147
α-helix	254-264	11
α-helix	279-282	4
α-helix	289-293	5
α-helix	296-300	5
α-helix	302-305	4
α-helix	311-313	3
α-helix	316-317	2
α-helix	322-328	7
α-helix	332-365	34

Chain Ld: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	22-28	7	138
α-helix	29-33	5
α-helix	38-40	3
α-helix	41-57	17
β-strand	62-64	3	138
α-helix	66-72	7
α-helix	73-75	3
β-strand	83-92	10	138
β-strand	102-108	7	138
β-strand	120-121	2	138

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
40S ribosomal protein SA	SA	protein	221	Homo sapiens	P08865 (AlphaFold model)
40S ribosomal protein S3a	SB	protein	214	Homo sapiens	P61247 (AlphaFold model)
40S ribosomal protein S2	SC	protein	222	Homo sapiens	P15880 (AlphaFold model)
Small ribosomal subunit protein eS4, X isoform	SE	protein	262	Homo sapiens	P62701 (AlphaFold model)
40S ribosomal protein S6	SG	protein	237	Homo sapiens	P62753
Small ribosomal subunit protein eS7	SH	protein	186	Homo sapiens	P62081
40S ribosomal protein S8	SI	protein	206	Homo sapiens	P62241
40S ribosomal protein S9	SJ	protein	185	Homo sapiens	P46781
40S ribosomal protein S11	SL	protein	153	Homo sapiens	P62280
40S ribosomal protein S13	SN	protein	150	Homo sapiens	P62277
Small ribosomal subunit protein uS11	SO	protein	140	Homo sapiens	P62263
Small ribosomal subunit protein eS21	SV	protein	83	Homo sapiens	P63220

73 more molecules are not listed.

Sequence of entity 1 (SA), FASTA

>9P7Y_1 40S ribosomal protein SA (chains SA)
GALDVLQMKEEDVLKFLAAGTHLGGTNLDFQMEQYIYKRKSDGIYIINLKRTWEKLLLAA
RAIVAIENPADVSVISSRNTGQRAVLKFAAATGATPIAGRFTPGTFTNQIQAAFREPRLL
VVTDPRADHQPLTEASYVNLPTIALCNTDSPLRYVDIAIPCNNKGAHSVGLMWWMLAREV
LRMRGTISREHPWEVMPDLYFYRDPEEIEKEEQAAAEKAVT

Sequence of entity 2 (SB), FASTA

>9P7Y_2 40S ribosomal protein S3a (chains SB)
VVDPFSKKDWYDVKAPAMFNIRNIGKTLVTRTQGTKIASDGLKGRVFEVSLADLQNDEVA
FRKFKLITEDVQGKNCLTNFHGMDLTRDKMCSMVKKWQTMIEAHVDVKTTDGYLLRLFCV
GFTKKRNNQIRKTSYAQHQQVRQIRKKMMEIMTREVQTNDLKEVVNKLIPDSIGKDIEKA
CQSIYPLHDVFVRKVKMLKKPKFELGKLMELHGE

Sequence of entity 3 (SC), FASTA

>9P7Y_3 40S ribosomal protein S2 (chains SC)
EWMPVTKLGRLVKDMKIKSLEEIYLFSLPIKESEIIDFFLGASLKDEVLKIMPVQKQTRA
GQRTRFKAFVAIGDYNGHVGLGVKCSKEVATAIRGAIILAKLSIVPVRRGYWGNKIGKPH
TVPCKVTGRCGSVLVRLIPAPRGTGIVSAPVPKKLLMMAGIDDCYTSARGCTATLGNFAK
ATFDAISKTYSYLTPDLWKETVFTKSPYQEFTDHLVKTHTRV

Sequence of entity 4 (SE), FASTA

>9P7Y_4 Small ribosomal subunit protein eS4, X isoform (chains SE)
ARGPKKHLKRVAAPKHWMLDKLTGVFAPRPSTGPHKLRECLPLIIFLRNRLKYALTGDEV
KKICMQRFIKIDGKVRTDITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRITPEEAKY
KLCKVRKIFVGTKGIPHLVTHDARTIRYPDPLIKVNDTIQIDLETGKITDFIKFDTGNLC
MVTGGANLGRIGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGKGNKPWISLPRG
KGIRLTIAEERDKRLAAKQSSG

Sequence of entity 5 (SG), FASTA

>9P7Y_5 40S ribosomal protein S6 (chains SG)
MKLNISFPATGCQKLIEVDDERKLRTFYEKRMATEVAADALGEEWKGYVVRISGGNDKQG
FPMKQGVLTHGRVRLLLSKGHSCYRPRRTGERKRKSVRGCIVDANLSVLNLVIVKKGEKD
IPGLTDTTVPRRLGPKRASRIRKLFNLSKEDDVRQYVVRKPLNKEGKKPRTKAPKIQRLV
TPRVLQHKRRRIALKKQRTKKNKEEAAEYAKLLAKRMKEAKEKRQEQIAKRRRLSSL

Sequence of entity 6 (SH), FASTA

>9P7Y_6 Small ribosomal subunit protein eS7 (chains SH)
SAKIVKPNGEKPDEFESGISQALLELEMNSDLKAQLRELNITAAKEIEVGGGRKAIIIFV
PVPQLKSFQKIQVRLVRELEKKFSGKHVVFIAQRRILPKPTRKKNKQKRPRSRTLTAVHD
AILEDLVFPSEIVGKRIRVKLDGSRLIKVHLDKAQQNNVEHKVETFSGVYKKLTGKDVNF
EFPEFQ

Sequence of entity 7 (SI), FASTA

>9P7Y_7 40S ribosomal protein S8 (chains SI)
GISRDNWHKRRKTGGKRKPYHKKRKYELGRPAANTKIGPRRIHTVRVRGGNKKYRALRLD
VGNFSWGSECCTRKTRIIDVVYNASNNELVRTKTLVKNCIVLIDSTPYRQWYESHYALPL
GRKKGAKLTPEEEEILNKKRSKKIQKKYDERKKNAKISSLLEEQFQQGKLLACIASRPGQ
CGRADGYVLEGKELEFYLRKIKARKG

Sequence of entity 8 (SJ), FASTA

>9P7Y_8 40S ribosomal protein S9 (chains SJ)
PVARSWVCRKTYVTPRRPFEKSRLDQELKLIGEYGLRNKREVWRVKFTLAKIRKAARELL
TLDEKDPRRLFEGNALLRRLVRIGVLDEGKMKLDYILGLKIEDFLERRLQTQVFKLGLAK
SIHHARVLIRQRHIRVRKQVVNIPSFIVRLDSQKHIDFSLRSPYGGGRPGRVKRKNAKKG
QGGAG

Sequence of entity 9 (SL), FASTA

>9P7Y_9 40S ribosomal protein S11 (chains SL)
ADIQTERAYQKQPTIFQNKKRVLLGETGKEKLPRYYKNIGLGFKTPKEAIEGTYIDKKCP
FTGNVSIRGRILSGVVTKMKMQRTIVIRRDYLHYIRKYNRFEKRHKNMSVHLSPCFRDVQ
IGDIVTVGECRPLSKTVRFNVLKVTKAAGTKKQ

Sequence of entity 10 (SN), FASTA

>9P7Y_10 40S ribosomal protein S13 (chains SN)
GRMHAPGKGLSQSALPYRRSVPTWLKLTSDDVKEQIYKLAKKGLTPSQIGVILRDSHGVA
QVRFVTGNKILRILKSKGLAPDLPEDLYHLIKKAVAVRKHLERNRKDKDAKFRLILIESR
IHRLARYYKTKRVLPPNWKYESSTASALVA

Sequence of entity 11 (SO), FASTA

>9P7Y_11 Small ribosomal subunit protein uS11 (chains SO)
EQVISLGPQVAEGENVFGVCHIFASFNDTFVHVTDLSGKETICRVTGGMKVKADRDESSP
YAAMLAAQDVAQRCKELGITALHIKLRATGGNRTKTPGPGAQSALRALARSGMKIGRIED
VTPIPSDSTRRKGGRRGRRL

Sequence of entity 12 (SV), FASTA

>9P7Y_12 Small ribosomal subunit protein eS21 (chains SV)
MQNDAGEFVDLYVPRKCSASNRIIGAKDHASIQMNVAEVDKVTGRFNGQFKTYAICGAIR
RMGESDDSILRLAKADGIVSKNF

Ligands and cofactors

ID	Name	Formula	Copies
SPD	Spermidine	C7 H19 N3	10
SPM	Spermine	C10 H26 N4	7
ZN	Zinc ion	Zn	6
MG	Magnesium ion	Mg	219

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 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

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