9B0P: In situ human Hibernating class1 80S ribosome

Name: PDB 9B0P: In situ human Hibernating class1 80S ribosome
Published: 2025-03-19
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

In situ human Hibernating class1 80S ribosome. Determined by electron microscopy at 2.82 Å resolution. Released 19 Mar 2025.

Method: Electron microscopy
Resolution: 2.82 Å
Organism: Homo sapiens
Chains: 85
Atoms: 229,857
Mol. weight: 3871.49 kDa
Ligands: MG, ZN
Released: 19 Mar 2025

Explore 9B0P in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9B0P contains 595 α-helices and 637 β-strands across 80 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: 11 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	15-38	24
β-strand	44	1	14
α-helix	45-62	18
β-strand	72-82	11	15
β-strand	85	1	16
α-helix	96-97	2
β-strand	99	1	14
β-strand	105-114	10	15
β-strand	117-126	10	15
β-strand	135	1	17
α-helix	139-156	18
β-strand	162	1	18
α-helix	163-176	14
β-strand	180-181	2	15
α-helix	182	1
β-strand	185-190	6	15
β-strand	200-203	4	15
α-helix	207-212	6
α-helix	213-215	3
β-strand	217	1	18
β-strand	223-231	9	15
β-strand	238	1	16
β-strand	246-249	4	19
α-helix	260-272	13
β-strand	278	1	19
α-helix	287-298	12
β-strand	302-305	4	19
β-strand	309	1	16
β-strand	316-324	9	15
β-strand	331-332	2	15
β-strand	343	1	17
α-helix	352-359	8

Chain CB: 42 helices, 44 β-strands

Element	Residues	Length	Sheet
α-helix	6-14	9
β-strand	19-26	8	46
α-helix	32-42	11
β-strand	74-80	7	46
α-helix	83-88	6
β-strand	97-104	8	46
α-helix	114-121	8
β-strand	124-130	7	46
β-strand	134	1	46
α-helix	137-148	12
α-helix	151	1
β-strand	152-158	7	46
α-helix	160-161	2
α-helix	162-166	5
α-helix	171-192	22
β-strand	212-216	5	46
β-strand	221-223	3	46
α-helix	225-235	11
α-helix	248-260	13
β-strand	265-267	3	47
β-strand	272-274	3	47
β-strand	278	1	48
β-strand	284	1	48
β-strand	287	1	47
α-helix	288-289	2
α-helix	290-294	5
α-helix	295-305	11
α-helix	309-319	11
α-helix	332-343	12
β-strand	345	1	46
α-helix	346-356	11
α-helix	359-360	2
α-helix	361-368	8
α-helix	369-371	3
β-strand	373	1	49
α-helix	380-387	8
β-strand	395-403	9	50
β-strand	410-418	9	50
β-strand	420-422	3	51
β-strand	428-429	2	50
β-strand	443-444	2	50
β-strand	449-454	6	50
β-strand	457-461	5	50
β-strand	463-465	3	51
β-strand	468-473	6	50
β-strand	483	1	50
β-strand	485-486	2	50
β-strand	494	1	49
α-helix	495-497	3
β-strand	505-511	7	52
α-helix	514-516	3
α-helix	517-530	14
β-strand	535-538	4	52
β-strand	544-548	5	52
α-helix	551-560	10
α-helix	561-565	5
β-strand	570-573	4	52
α-helix	574-576	3
β-strand	580-583	4	53
β-strand	591-594	4	54
β-strand	601-608	8	54
α-helix	613-619	7
α-helix	628-638	11
α-helix	643-646	4
β-strand	649-651	3	54
α-helix	654-656	3
β-strand	660-664	5	54
α-helix	672-686	15
α-helix	695-696	2
β-strand	697	1	53
β-strand	700-708	9	54
α-helix	713-715	3
α-helix	718-734	17
β-strand	738-742	5	53
β-strand	744-752	9	55
α-helix	753-755	3
α-helix	757-765	9
β-strand	769-775	7	55
β-strand	781-789	9	55
α-helix	790-792	3
α-helix	796-804	9
β-strand	809-813	5	55
β-strand	818-819	2	53
α-helix	830-841	12
α-helix	848-850	3
α-helix	851-853	3

Chain CD: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	209-211	3
α-helix	221-224	4
α-helix	283-290	8

Chain La: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
α-helix	7-9	3
α-helix	42-48	7
β-strand	53	1	5
β-strand	72-74	3	86
α-helix	75-81	7
α-helix	84-91	8
β-strand	97-98	2	179
α-helix	99	1
β-strand	100-102	3	87
α-helix	103-106	4
β-strand	110-112	3	86
β-strand	123-126	4	87
β-strand	128-129	2	86
α-helix	131-139	9
β-strand	143-146	4	87

Chain LA: 12 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	4-5	2
α-helix	10-12	3
α-helix	14-16	3
β-strand	18	1	98
α-helix	29-32	4
α-helix	34-38	5
β-strand	40-49	10	99
α-helix	50-51	2
β-strand	58-64	7	99
β-strand	71-77	7	99
β-strand	79	1	100
β-strand	83	1	101
β-strand	87-91	5	99
β-strand	101-103	3	99
α-helix	104-106	3
β-strand	112-113	2	102
β-strand	116	1	103
β-strand	126	1	103
β-strand	134-140	7	102
α-helix	142-144	3
β-strand	145-149	5	102
β-strand	155-159	5	102
β-strand	163-165	3	99
β-strand	166	1	102
β-strand	169	1	100
α-helix	174-176	3
α-helix	182-190	9
β-strand	193	1	98
α-helix	201-203	3
β-strand	224-225	2	104
α-helix	229-230	2
β-strand	237-238	2	104

Chain Lb: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	12-16	5
α-helix	22-24	3
α-helix	37-48	12
α-helix	49-51	3
α-helix	54-72	19
α-helix	92-100	9
α-helix	106-115	10

Chain LB: 17 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	9-10	2
α-helix	14-16	3
α-helix	21-22	2
α-helix	32-35	4
α-helix	40-41	2
β-strand	42-43	2	107
β-strand	45-59	15	108
β-strand	71-80	10	108
α-helix	82-83	2
β-strand	84-95	12	109
β-strand	98-106	9	109
α-helix	112-117	6
α-helix	131-134	4
α-helix	135-137	3
α-helix	140-156	17
β-strand	159-165	7	109
α-helix	168-170	3
β-strand	180-184	5	109
β-strand	185-186	2	107
α-helix	190-199	10
β-strand	204-205	2	109
β-strand	216-222	7	108
α-helix	223-224	2
β-strand	225-229	5	110
α-helix	231-235	5
α-helix	237-241	5
β-strand	270-273	4	110
β-strand	276-287	12	108
β-strand	292	1	111
β-strand	298	1	111
β-strand	320	1	112
β-strand	324	1	112
β-strand	330-335	6	108
β-strand	344-349	6	108
β-strand	365-368	4	108
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	31-39	9
β-strand	45-48	4	105
α-helix	54-67	14
β-strand	70-72	3	105
α-helix	78-84	7
β-strand	93-98	6	105

72 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
18S rRNA	S2	RNA	1869	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 uS19	SP	protein	121	Homo sapiens	P62841 (AlphaFold model)
Small ribosomal subunit protein uS9	SQ	protein	144	Homo sapiens	P62249
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
40S ribosomal protein S28	Sc	protein	64	Homo sapiens	P62857
40S ribosomal protein S29	Sd	protein	55	Homo sapiens	P62273
Receptor of activated protein C kinase 1	Sg	protein	313	Homo sapiens	P63244

73 more molecules are not listed.

Sequence of entity 1 (S2), FASTA

>9B0P_1 18S rRNA (chains S2)
UACCUGGUUGAUCCUGCCAGUAGCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUA
AGUACGCACGGCCGGUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUGGUUCCUU
UGGUCGCUCGCUCCUCUCCCACUUGGAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCCG
ACGGGCGCUGACCCCCUUCGCGGGGGGGAUGCGUGCAUUUAUCAGAUCAAAACCAACCCG
GUCAGCCCCUCUCCGGCCCCGGCCGGGGGGCGGGCGCCGGCGGCUUUGGUGACUCUAGAU
AACCUCGGGCCGAUCGCACGCCCCCCGUGGCGGCGACGACCCAUUCGAACGUCUGCCCUA
UCAACUUUCGAUGGUAGUCGCCGUGCCUACCAUGGUGACCACGGGUGACGGGGAAUCAGG
GUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCG
CGCAAAUUACCCACUCCCGACCCGGGGAGGUAGUGACGAAAAAUAACAAUACAGGACUCU
UUCGAGGCCCUGUAAUUGGAAUGAGUCCACUUUAAAUCCUUUAACGAGGAUCCAUUGGAG
GGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGC
UGCAGUUAAAAAGCUCGUAGUUGGAUCUUGGGAGCGGGCGGGCGGUCCGCCGCGAGGCGA
GCCACCGCCCGUCCCCGCCCCUUGCCUCUCGGCGCCCCCUCGAUGCUCUUAGCUGAGUGU
CCCGCGGGGCCCGAAGCGUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCCCGAGCC
GCCUGGAUACCGCAGCUAGGAAUAAUGGAAUAGGACCGCGGUUCUAUUUUGUUGGUUUUC
GGAACUGAGGCCAUGAUUAAGAGGGACGGCCGGGGGCAUUCGUAUUGCGCCGCUAGAGGU
GAAAUUCUUGGACCGGCGCAAGACGGACCAGAGCGAAAGCAUUUGCCAAGAAUGUUUUCA
UUAAUCAAGAACGAAAGUCGGAGGUUCGAAGACGAUCAGAUACCGUCGUAGUUCCGACCA
UAAACGAUGCCGACCGGCGAUGCGGCGGCGUUAUUCCCAUGACCCGCCGGGCAGCUUCCG
GGAAACCAAAGUCUUUGGGUUCCGGGGGGAGUAUGGUUGCAAAGCUGAAACUUAAAGGAA
UUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAA
CCUCACCCGGCCCGGACACGGACAGGAUUGACAGAUUGAUAGCUCUUUCUCGAUUCCGUG
GGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGAUAAC
GAACGAGACUCUGGCAUGCUAACUAGUUACGCGACCCCCGAGCGGUCGGCGUCCCCCAAC
UUCUUAGAGGGACAAGUGGCGUUCAGCCACCCGAGAUUGAGCAAUAACAGGUCUGUGAUG
CCCUUAGAUGUCCGGGGCUGCACGCGCGCUACACUGACUGGCUCAGCGUGUGCCUACCCU
ACGCCGGCAGGCGCGGGUAACCCGUUGAACCCCAUUCGUGAUGGGGAUCGGGGAUUGCAA
UUAUUCCCCAUGAACGAGGAAUUCCCAGUAAGUGCGGGUCAUAAGCUUGCGUUGAUUAAG
UCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGGAUGGUUUAGUGAGGCCC
UCGGAUCGGCCCCGCCGGGGUCGGCCCACGGCCCUGGCGGAGCGCUGAGAAGACGGUCGA
ACUUGACUAUCUAGAGGAAGUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAA
GGAUCAUUA

Sequence of entity 2 (SD), FASTA

>9B0P_2 Small ribosomal subunit protein uS3 (chains SD)
MAVQISKKRKFVADGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLG
EKGRRIRELTAVVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRRACY
GVLRFIMESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPVNYYVDTAVRHVLLRQG
VLGIKVKIMLPWDPTGKIGPKKPLPDHVSIVEPKDEILPTTPISEQK

Sequence of entity 3 (SF), FASTA

>9B0P_3 40S ribosomal protein S5 (chains SF)
DIKLFGKWSTDDVQINDISLQDYIAVKEKYAKYLPHSAGRYAAKRFRKAQCPIVERLTNS
MMMHGRNNGKKLMTVRIVKHAFEIIHLLTGENPLQVLVNAIINSGPREDSTRIGRAGTVR
RQAVDVSPLRRVNQAIWLLCTGAREAAFRNIKTIAECLADELINAAKGSSNSYAIKKKDE
LERVAKSNR

Sequence of entity 4 (SK), FASTA

>9B0P_4 40S ribosomal protein S10 (chains SK)
MLMPKKNRIAIYELLFKEGVMVAKKDVHMPKHPELADKNVPNLHVMKAMQSLKSRGYVKE
QFAWRHFYWYLTNEGIQYLRDYLHLPPEIVPATLRRSR

Sequence of entity 5 (SP), FASTA

>9B0P_5 Small ribosomal subunit protein uS19 (chains SP)
TYRGVDLDQLLDMSYEQLMQLYSARQRRRLNRGLRRKQHSLLKRLRKAKKEAPPMEKPEV
VKTHLRDMIILPEMVGSMVGVYNGKTFNQVEIKPEMIGHYLGEFSITYKPVKHGRPGIGA
T

Sequence of entity 6 (SQ), FASTA

>9B0P_6 Small ribosomal subunit protein uS9 (chains SQ)
SKGPLQSVQVFGRKKTATAVAHCKRGNGLIKVNGRPLEMIEPRTLQYKLLEPVLLLGKER
FAGVDIRVRVKGGGHVAQIYAIRQSISKALVAYYQKYVDEASKKEIKDILIQYDRTLLVA
DPRRCESKKFGGPGARARYQKSYR

Sequence of entity 7 (SS), FASTA

>9B0P_7 40S ribosomal protein S18 (chains SS)
MSLVIPEKFQHILRVLNTNIDGRRKIAFAITAIKGVGRRYAHVVLRKADIDLTKRAGELT
EDEVERVITIMQNPRQYKIPDWFLNRQKDVKDGKYSQVLANGLDNKLREDLERLKKIRAH
RGLRHFWGLRVRGQHTKTTGRRGRT

Sequence of entity 8 (ST), FASTA

>9B0P_8 40S ribosomal protein S19 (chains ST)
PGVTVKDVNQQEFVRALAAFLKKSGKLKVPEWVDTVKLAKHKELAPYDENWFYTRAASTA
RHLYLRGGAGVGSMTKIYGGRQRNGVMPSHFSRGSKSVARRVLQALEGLKMVEKDQDGGR
KLTPQGQRDLDRIAGQVAAANKK

Sequence of entity 9 (SU), FASTA

>9B0P_9 40S ribosomal protein S20 (chains SU)
AIHRIRITLTSRNVKSLEKVCADLIRGAKEKNLKVKGPVRMPTKTLRITTRKTPCGEGSK
TWDRFQMRIHKRLIDLHSPSEIVKQITSISIEPGVEVEVTIADA

Sequence of entity 10 (Sc), FASTA

>9B0P_10 40S ribosomal protein S28 (chains Sc)
RVQPIKLARVTKVLGRTGSQGQCTQVRVEFMDDTSRSIIRNVKGPVREGDVLTLLESERE
ARRL

Sequence of entity 11 (Sd), FASTA

>9B0P_11 40S ribosomal protein S29 (chains Sd)
GHQQLYWSHPRKFGQGSRSCRVCSNRHGLIRKYGLNMCRQCFRQYAKDIGFIKLD

Sequence of entity 12 (Sg), FASTA

>9B0P_12 Receptor of activated protein C kinase 1 (chains Sg)
TEQMTLRGTLKGHNGWVTQIATTPQFPDMILSASRDKTIIMWKLTRDETNYGIPQRALRG
HSHFVSDVVISSDGQFALSGSWDGTLRLWDLTTGTTTRRFVGHTKDVLSVAFSSDNRQIV
SGSRDKTIKLWNTLGVCKYTVQDESHSEWVSCVRFSPNSSNPIIVSCGWDKLVKVWNLAN
CKLKTNHIGHTGYLNTVTVSPDGSLCASGGKDGQAMLWDLNEGKHLYTLDGGDIINALCF
SPNRYWLCAATGPSIKIWDLEGKIIVDELKQEVISTSSKAEPPQCTSLAWSADGQTLFAG
YTDNLVRVWQVTI

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	255
ZN	Zinc ion	Zn	6

Primary citation

In situ human Hibernating class1 80S ribosome. Wei, Z., Yong, X. To be published.

Other PDB entries of the same protein (UniProt P23396 (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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