9P73: In situ human eEF2-A/P-P/E state 80S ribosome

Name: PDB 9P73: In situ human eEF2-A/P-P/E state 80S ribosome
Published: 2025-12-24
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

In situ human eEF2-A/P-P/E state 80S ribosome. Determined by electron microscopy at 2.66 Å resolution. Released 24 Dec 2025.

Method: Electron microscopy
Resolution: 2.66 Å
Organism: Homo sapiens
Chains: 85
Atoms: 227,131
Mol. weight: 3359.9 kDa
Ligands: MG, ZN, SPM, SPD
Released: 24 Dec 2025

Explore 9P73 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9P73 contains 595 α-helices and 612 β-strands across 79 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 CB: 37 helices, 46 β-strands

Element	Residues	Length	Sheet
α-helix	7-13	7
β-strand	19-26	8	10
α-helix	32-42	11
β-strand	73-80	8	10
α-helix	81-82	2
α-helix	83-88	6
β-strand	97-104	8	10
α-helix	114-121	8
β-strand	124-130	7	10
β-strand	134	1	10
α-helix	137-148	12
β-strand	152-158	7	10
α-helix	160-161	2
α-helix	162-166	5
α-helix	171-192	22
β-strand	212-216	5	10
β-strand	221-223	3	10
α-helix	225-235	11
α-helix	248-259	12
β-strand	265-267	3	11
β-strand	272-274	3	11
β-strand	278	1	12
β-strand	284	1	12
β-strand	287	1	11
α-helix	288-289	2
α-helix	290-294	5
α-helix	295-305	11
α-helix	309-319	11
α-helix	333-343	11
β-strand	345	1	10
α-helix	346-357	12
α-helix	359-360	2
α-helix	361-372	12
β-strand	373	1	13
α-helix	380-387	8
β-strand	395-403	9	14
β-strand	410-418	9	14
β-strand	420-421	2	15
β-strand	426-430	5	14
β-strand	442-446	5	14
β-strand	449-454	6	14
β-strand	457-461	5	14
β-strand	464-465	2	15
β-strand	468-473	6	14
α-helix	476-478	3
β-strand	480	1	16
β-strand	482	1	16
β-strand	483-486	4	14
β-strand	494	1	13
α-helix	495-497	3
β-strand	505-511	7	17
α-helix	517-530	14
β-strand	535-538	4	17
β-strand	544-548	5	17
α-helix	551-560	10
α-helix	561-565	5
β-strand	570-573	4	17
α-helix	574-578	5
β-strand	581-583	3	18
β-strand	591-594	4	19
β-strand	601-608	8	19
α-helix	613-619	7
α-helix	628-638	11
α-helix	643-647	5
β-strand	649-651	3	19
α-helix	654-656	3
β-strand	660-664	5	19
α-helix	672-688	17
β-strand	697	1	18
β-strand	700-708	9	19
α-helix	718-720	3
α-helix	722-735	14
β-strand	738-740	3	18
β-strand	741-742	2	20
β-strand	744-751	8	21
α-helix	756-765	10
β-strand	769-775	7	21
β-strand	782-789	8	21
α-helix	796-804	9
β-strand	809-814	6	21
β-strand	818-819	2	20
α-helix	830-842	13
α-helix	848-849	2

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	63
β-strand	139	1	63

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

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	108
α-helix	29-32	4
α-helix	34-38	5
β-strand	40-50	11	109
α-helix	51	1
β-strand	57-64	8	109
β-strand	71-77	7	109
β-strand	79	1	110
β-strand	83	1	29
β-strand	87-91	5	109
β-strand	101-103	3	109
α-helix	104-106	3
β-strand	112-113	2	111
β-strand	116	1	112
β-strand	126	1	112
β-strand	134-140	7	111
α-helix	142-144	3
β-strand	145-149	5	111
β-strand	155-159	5	111
β-strand	163-165	3	109
β-strand	166	1	111
β-strand	169	1	110
α-helix	174-176	3
α-helix	182-190	9
β-strand	193	1	108
α-helix	201-203	3
β-strand	224-225	2	113
α-helix	229-230	2
β-strand	237-238	2	113

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	122
β-strand	45-59	15	123
β-strand	71-80	10	123
α-helix	82-83	2
β-strand	84-95	12	124
β-strand	98-106	9	124
α-helix	107	1
α-helix	112-115	4
α-helix	116-118	3
α-helix	140-156	17
β-strand	159-165	7	124
α-helix	168-170	3
β-strand	180-184	5	124
β-strand	185-186	2	122
α-helix	190-199	10
β-strand	204-205	2	124
α-helix	207-210	4
β-strand	216-222	7	123
α-helix	223-224	2
β-strand	225-229	5	125
α-helix	231-234	4
α-helix	237-241	5
β-strand	270-273	4	125
β-strand	276-287	12	123
β-strand	292-293	2	126
β-strand	297-298	2	126
α-helix	300-302	3
β-strand	320	1	127
β-strand	324	1	127
β-strand	330-334	5	123
β-strand	344-349	6	123
β-strand	365-368	4	123
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	105
α-helix	31-40	10
β-strand	45-49	5	105
α-helix	54-67	14
β-strand	70-74	5	105
α-helix	78-85	8
β-strand	93-98	6	105

71 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	71	Homo sapiens
Elongation factor 2	CB	protein	856	Homo sapiens	P13639 (AlphaFold model)
P/E site tRNA	PE	RNA	75	Homo sapiens
Small ribosomal subunit protein uS3	SD	protein	227	Homo sapiens	P23396 (AlphaFold model)
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
40S ribosomal protein S15	SP	protein	127	Homo sapiens	P62841
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

73 more molecules are not listed.

Sequence of entity 1 (AP), FASTA

>9P73_1 A/P site tRNA (chains AP)
GUCUCCGUAGUGUAGGGUAUCACGUUCGCCUAACACGCGAAAGGUCCUCGGUUCGAAACC
GGGCGGAAACA

Sequence of entity 2 (CB), FASTA

>9P73_2 Elongation factor 2 (chains CB)
NFTVDQIRAIMDKKANIRNMSVIAHVDHGKSTLTDSLVCKAGIIASARAGETRFTDTRKD
EQERCITIKSTAISLFYELSENDLNFIKQSKDGAGFLINLIDSPGHVDFSSEVTAALRVT
DGALVVVDCVSGVCVQTETVLRQAIAERIKPVLMMNKMDRALLELQLEPEELYQTFQRIV
ENVNVIISTYGEGESGPMGNIMIDPVLGTVGFGSGLHGWAFTLKQFAEMYVAKFAAKGEG
QLGPAERAKKVEDMMKKLWGDRYFDPANGKFSKSATSPEGKKLPRTFCQLILDPIFKVFD
AIMNFKKEETAKLIEKLDIKLDSEDKDKEGKPLLKAVMRRWLPAGDALLQMITIHLPSPV
TAQKYRCELLYEGPPDDEAAMGIKSCDPKGPLMMYISKMVPTSDKGRFYAFGRVFSGLVS
TGLKVRIMGPNYTPGKKEDLYLKPIQRTILMMGRYVEPIEDVPCGNIVGLVGVDQFLVKT
GTITTFEHAHNMRVMKFSVSPVVRVAVEAKNPADLPKLVEGLKRLAKSDPMVQCIIEESG
EHIIAGAGELHLEICLKDLEEDHACIPIKKSDPVVSYRETVSEESNVLCLSKSPNKHNRL
YMKARPFPDGLAEDIDKGEVSARQELKQRARYLAEKYEWDVAEARKIWCFGPDGTGPNIL
TDITKGVQYLNEIKDSVVAGFQWATKEGALCEENMRGVRFDVHDVTLHADAIHRGGGQII
PTARRCLYASVLTAQPRLMEPIYLVEIQCPEQVVGGIYGVLNRKRGHVFEESQVAGTPMF
VVKAYLPVNESFGFTADLRSNTGGQAFPQCVFDHWQILPGDPFDNSSRPSQVVAETRKRK
GLKEGIPALDNFLDKL

Sequence of entity 3 (PE), FASTA

>9P73_3 P/E site tRNA (chains PE)
GCCCGGAUAGCUCAGCUGUAGAGCAUCAGACUUUUAAUCUGAGGGUCCAGGGUUCAAGUC
CCUGUUCGGGCGCCA

Sequence of entity 4 (SD), FASTA

>9P73_4 Small ribosomal subunit protein uS3 (chains SD)
MAVQISKKRKFVADGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLG
EKGRRIRELTAVVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRRACY
GVLRFIMESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPVNYYVDTAVRHVLLRQG
VLGIKVKIMLPWDPTGKIGPKKPLPDHVSIVEPKDEILPTTPISEQK

Sequence of entity 5 (SF), FASTA

>9P73_5 40S ribosomal protein S5 (chains SF)
DIKLFGKWSTDDVQINDISLQDYIAVKEKYAKYLPHSAGRYAAKRFRKAQCPIVERLTNS
MMMHGRNNGKKLMTVRIVKHAFEIIHLLTGENPLQVLVNAIINSGPREDSTRIGRAGTVR
RQAVDVSPLRRVNQAIWLLCTGAREAAFRNIKTIAECLADELINAAKGSSNSYAIKKKDE
LERVAKSNR

Sequence of entity 6 (SK), FASTA

>9P73_6 40S ribosomal protein S10 (chains SK)
MLMPKKNRIAIYELLFKEGVMVAKKDVHMPKHPELADKNVPNLHVMKAMQSLKSRGYVKE
QFAWRHFYWYLTNEGIQYLRDYLHLPPEIVPATLRRSR

Sequence of entity 7 (SM), FASTA

>9P73_7 Small ribosomal subunit protein eS12 (chains SM)
VMDVNTALQEVLKTALIHDGLARGIREAAKALDKRQAHLCVLASNCDEPMYVKLVEALCA
EHQINLIKVDDNKKLGEWVGLCKIDREGKPRKVVGCSCVVVKDYGKESQAKDVIEEYFKC
KK

Sequence of entity 8 (SP), FASTA

>9P73_8 40S ribosomal protein S15 (chains SP)
RTFRKFTYRGVDLDQLLDMSYEQLMQLYSARQRRRLNRGLRRKQHSLLKRLRKAKKEAPP
MEKPEVVKTHLRDMIILPEMVGSMVGVYNGKTFNQVEIKPEMIGHYLGEFSITYKPVKHG
RPGIGAT

Sequence of entity 9 (SQ), FASTA

>9P73_9 Small ribosomal subunit protein uS9 (chains SQ)
SKGPLQSVQVFGRKKTATAVAHCKRGNGLIKVNGRPLEMIEPRTLQYKLLEPVLLLGKER
FAGVDIRVRVKGGGHVAQIYAIRQSISKALVAYYQKYVDEASKKEIKDILIQYDRTLLVA
DPRRCESKKFGGPGARARYQKSYR

Sequence of entity 10 (SR), FASTA

>9P73_10 Small ribosomal subunit protein eS17 (chains SR)
MGRVRTKTVKKAARVIIEKYYTRLGNDFHTNKRVCEEIAIIPSKKLRNKIAGYVTHLMKR
IQRGPVRGISIKLQEEERERRDNYVPEVSALDQEIIEVDPDTKEMLKLLDFGSLSNLQVT
QPTVGMNFKTPRGPV

Sequence of entity 11 (SS), FASTA

>9P73_11 40S ribosomal protein S18 (chains SS)
MSLVIPEKFQHILRVLNTNIDGRRKIAFAITAIKGVGRRYAHVVLRKADIDLTKRAGELT
EDEVERVITIMQNPRQYKIPDWFLNRQKDVKDGKYSQVLANGLDNKLREDLERLKKIRAH
RGLRHFWGLRVRGQHTKTTGRRGRT

Sequence of entity 12 (ST), FASTA

>9P73_12 40S ribosomal protein S19 (chains ST)
PGVTVKDVNQQEFVRALAAFLKKSGKLKVPEWVDTVKLAKHKELAPYDENWFYTRAASTA
RHLYLRGGAGVGSMTKIYGGRQRNGVMPSHFSRGSKSVARRVLQALEGLKMVEKDQDGGR
KLTPQGQRDLDRIAGQVAAANKK

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 P13639 (AlphaFold model), which also has an AlphaFold model), best resolution first:

29IZ 2.08 Å, Dormant 80S:eEF2:SERBP1:tRNA complex from human cells treated with toxin NT-2
11IQ 2.4 Å, Rabbit 80S with eEF2,eIF5A and SERBP1
8XSX 2.4 Å, Cryo-EM structure of the human 80S ribosome with Tigecycline, E-tRNA, SERBP1 and eEF2
9P7D 2.57 Å, In situ human Hibernating class4 80S ribosome
9P7E 2.59 Å, In situ human Hibernating class5 80S ribosome
9T6D 2.67 Å, NAA40-NAC bound human 80S (combined translation states)
9P9I 2.77 Å, In situ human unrotated hibernating without CCDC124 state 80S ribosome
9M0P 2.78 Å, Cryo-EM structure of human 80S ribosome in complex with montanine
9P7C 2.78 Å, In situ human Hibernating class3 80S ribosome
9P7A 2.81 Å, In situ human hibernating class2 80S ribosome
9B0P 2.82 Å, In situ human Hibernating class1 80S ribosome
9P9H 2.84 Å, In situ human unrotated hibernating with CCDC124 state 80S ribosome

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