8XXN: Human 43S ribosome with PDCD4

Name: PDB 8XXN: Cryo-EM structure of the human 43S ribosome with PDCD4
Published: 2024-05-01
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Cryo-EM structure of the human 43S ribosome with PDCD4. Determined by electron microscopy at 3.6 Å resolution. Released 1 May 2024.

Method: Electron microscopy
Resolution: 3.6 Å
Organism: Homo sapiens
Chains: 50
Atoms: 114,565
Mol. weight: 2102.54 kDa
Ligands: MG, ZN
Released: 1 May 2024

Explore 8XXN in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8XXN contains 427 α-helices and 404 β-strands across 49 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 3A: 38 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	8-21	14
α-helix	24-36	13
α-helix	38-40	3
α-helix	47-61	15
α-helix	64-77	14
α-helix	84-115	32
α-helix	126-132	7
α-helix	137-144	8
α-helix	146-163	18
α-helix	171-188	18
α-helix	191-210	20
α-helix	217-219	3
α-helix	223-242	20
α-helix	246-262	17
α-helix	269-286	18
α-helix	289-306	18
α-helix	313-327	15
α-helix	333-335	3
α-helix	337-342	6
α-helix	352-359	8
α-helix	364-365	2
α-helix	368-377	10
α-helix	379-382	4
α-helix	385-388	4
α-helix	390-395	6
α-helix	403-416	14
α-helix	422-425	4
α-helix	428-446	19
β-strand	449-451	3	47
α-helix	452-458	7
α-helix	464-476	13
β-strand	482-485	4	47
β-strand	490-493	4	47
α-helix	500-502	3
α-helix	516-519	4
α-helix	522-537	16
α-helix	540-559	20
α-helix	564-599	36
α-helix	603-638	36
α-helix	643-684	42
α-helix	708-724	17

Chain 3B: 7 helices, 45 β-strands

Element	Residues	Length	Sheet
β-strand	188-190	3	49
α-helix	200-212	13
β-strand	219-221	3	50
β-strand	224-225	2	51
β-strand	228-229	2	51
β-strand	233	1	49
β-strand	234-236	3	50
α-helix	240-250	11
β-strand	254	1	52
β-strand	260	1	52
β-strand	262-264	3	49
α-helix	290-293	4
β-strand	306-310	5	53
β-strand	317-319	3	53
β-strand	340-342	3	54
β-strand	349-353	5	54
β-strand	356-361	6	54
β-strand	366-372	7	54
β-strand	378-381	4	55
β-strand	387-391	5	55
β-strand	404-408	5	55
β-strand	414-418	5	55
β-strand	430-431	2	56
β-strand	437-439	3	56
β-strand	448-450	3	56
β-strand	455-456	2	56
β-strand	469-472	4	57
β-strand	478-483	6	57
α-helix	490	1
β-strand	491-497	7	57
β-strand	503-509	7	57
β-strand	516-519	4	58
β-strand	525-530	6	58
β-strand	542-548	7	58
β-strand	556-561	6	58
β-strand	565-570	6	59
α-helix	571	1
β-strand	576-581	6	59
β-strand	587-594	8	59
β-strand	600-610	11	59
β-strand	613-616	4	60
β-strand	622-626	5	60
β-strand	633	1	61
β-strand	635-639	5	60
β-strand	645	1	60
β-strand	651	1	61
β-strand	656-659	4	62
β-strand	666-669	4	62
β-strand	681-684	4	62
β-strand	699-704	6	53
α-helix	714-721	8
α-helix	734-743	10

Chain 3C: 33 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	52-72	21
α-helix	76-92	17
α-helix	97-99	3
α-helix	104-121	18
α-helix	132-148	17
α-helix	326-338	13
α-helix	347-361	15
α-helix	368-385	18
α-helix	392-394	3
α-helix	395-414	20
β-strand	419-421	3	66
β-strand	439-441	3	66
α-helix	444-461	18
α-helix	467-473	7
α-helix	476-489	14
β-strand	490	1	67
β-strand	493	1	67
α-helix	496-510	15
α-helix	545-557	13
α-helix	563-578	16
α-helix	582-592	11
α-helix	594-596	3
α-helix	598-601	4
α-helix	603-623	21
α-helix	626-638	13
α-helix	642-645	4
α-helix	661-668	8
α-helix	679-701	23
α-helix	712-723	12
α-helix	733-745	13
α-helix	749-756	8
α-helix	760-764	5
α-helix	766-768	3
α-helix	772-795	24
β-strand	799	1	47
β-strand	801-803	3	68
α-helix	804-811	8
α-helix	815-827	13
β-strand	833-836	4	68
β-strand	841-844	4	68
α-helix	851-877	27

Chain 3E: 23 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	7-11	5
α-helix	19-29	11
α-helix	35-47	13
α-helix	51-61	11
α-helix	68-94	27
α-helix	111-120	10
α-helix	125-141	17
α-helix	144-157	14
α-helix	165-179	15
α-helix	183-198	16
α-helix	204-224	21
α-helix	229-236	8
α-helix	240-248	9
α-helix	254-262	9
α-helix	267-283	17
α-helix	291-297	7
α-helix	298-302	5
α-helix	306-319	14
α-helix	329-347	19
β-strand	348	1	68
β-strand	350-352	3	71
α-helix	353-359	7
α-helix	364-378	15
β-strand	382-385	4	71
β-strand	390-393	4	71
α-helix	394	1
α-helix	400-425	26

Chain 3F: 7 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	91-94	4	75
α-helix	96-107	12
β-strand	117-123	7	75
β-strand	128-137	10	75
β-strand	142	1	76
β-strand	145	1	76
α-helix	150-163	14
β-strand	168-175	8	75
α-helix	183-193	11
β-strand	198-202	5	75
β-strand	214-217	4	75
β-strand	233-234	2	75
β-strand	236-239	4	75
α-helix	243-253	11
β-strand	263-264	2	77
α-helix	268-294	27
α-helix	303-313	11
α-helix	320-356	37

Chain 3G: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	240-244	5	44
α-helix	252-259	8
β-strand	265-273	9	44
β-strand	279-287	9	44
α-helix	290-300	11
β-strand	304-305	2	11
β-strand	308-309	2	11
β-strand	311-314	4	44
α-helix	315-318	4

Chain 3H: 13 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	39-42	4	77
α-helix	43-55	13
β-strand	63-72	10	77
β-strand	75-81	7	77
α-helix	97-109	13
β-strand	116-122	7	77
α-helix	131-143	13
β-strand	149-152	4	77
α-helix	154-159	6
β-strand	164-169	6	77
α-helix	171-179	9
α-helix	184-189	6
α-helix	195-197	3
β-strand	198-200	3	77
α-helix	201-202	2
β-strand	203-206	4	77
α-helix	209-221	13
α-helix	229-231	3
α-helix	237-288	52
α-helix	307-312	6
α-helix	315-348	34

Chain 3I: 4 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	84
β-strand	13-18	6	85
β-strand	24-29	6	85
β-strand	34-38	5	85
β-strand	43-48	6	85
β-strand	55-60	6	86
β-strand	66-71	6	86
β-strand	75-80	6	86
β-strand	86-91	6	86
β-strand	96-101	6	87
β-strand	107-112	6	87
α-helix	113	1
β-strand	122-128	7	87
β-strand	135-140	6	87
α-helix	148	1
β-strand	149-154	6	88
α-helix	156-158	3
β-strand	160-165	6	88
β-strand	169-174	6	88
β-strand	180-185	6	88
β-strand	191-196	6	89
β-strand	202-207	6	89
β-strand	211-216	6	89
β-strand	221-227	7	89
α-helix	231	1
β-strand	232-238	7	90
β-strand	243-248	6	90
β-strand	265-271	7	90
β-strand	276-284	9	90
β-strand	288-293	6	84
β-strand	299-304	6	84
β-strand	309-313	5	84

41 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
60S ribosomal protein L41	Ln	protein	25	Homo sapiens	P62945 (AlphaFold model)
18S rRNA	S2	RNA	1869	Homo sapiens
40S ribosomal protein SA	SA	protein	295	Homo sapiens	P08865 (AlphaFold model)
40S ribosomal protein S3a	SB	protein	264	Homo sapiens	P61247 (AlphaFold model)
40S ribosomal protein S3	SD	protein	243	Homo sapiens	P23396 (AlphaFold model)
40S ribosomal protein S4, X isoform	SE	protein	263	Homo sapiens	P62701
40S ribosomal protein S5	SF	protein	204	Homo sapiens	P46782
40S ribosomal protein S7	SH	protein	194	Homo sapiens	P62081
40S ribosomal protein S8	SI	protein	208	Homo sapiens	P62241
40S ribosomal protein S10	SK	protein	165	Homo sapiens	P46783
40S ribosomal protein S11	SL	protein	158	Homo sapiens	P62280
40S ribosomal protein S15	SP	protein	145	Homo sapiens	P62841

38 more molecules are not listed.

Sequence of entity 1 (Ln), FASTA

>8XXN_1 60S ribosomal protein L41 (chains Ln)
MRAKWRKKRMRRLKRKRRKMRQRSK

Sequence of entity 2 (S2), FASTA

>8XXN_2 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 3 (SA), FASTA

>8XXN_3 40S ribosomal protein SA (chains SA)
MSGALDVLQMKEEDVLKFLAAGTHLGGTNLDFQMEQYIYKRKSDGIYIINLKRTWEKLLL
AARAIVAIENPADVSVISSRNTGQRAVLKFAAATGATPIAGRFTPGTFTNQIQAAFREPR
LLVVTDPRADHQPLTEASYVNLPTIALCNTDSPLRYVDIAIPCNNKGAHSVGLMWWMLAR
EVLRMRGTISREHPWEVMPDLYFYRDPEEIEKEEQAAAEKAVTKEEFQGEWTAPAPEFTA
TQPEVADWSEGVQVPSVPIQQFPTEDWSAQPATEDWSAAPTAQATEWVGATTDWS

Sequence of entity 4 (SB), FASTA

>8XXN_4 40S ribosomal protein S3a (chains SB)
MAVGKNKRLTKGGKKGAKKKVVDPFSKKDWYDVKAPAMFNIRNIGKTLVTRTQGTKIASD
GLKGRVFEVSLADLQNDEVAFRKFKLITEDVQGKNCLTNFHGMDLTRDKMCSMVKKWQTM
IEAHVDVKTTDGYLLRLFCVGFTKKRNNQIRKTSYAQHQQVRQIRKKMMEIMTREVQTND
LKEVVNKLIPDSIGKDIEKACQSIYPLHDVFVRKVKMLKKPKFELGKLMELHGEGSSSGK
ATGDETGAKVERADGYEPPVQESV

Sequence of entity 5 (SD), FASTA

>8XXN_5 40S ribosomal protein S3 (chains SD)
MAVQISKKRKFVADGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLG
EKGRRIRELTAVVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRRACY
GVLRFIMESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPVNYYVDTAVRHVLLRQG
VLGIKVKIMLPWDPTGKIGPKKPLPDHVSIVEPKDEILPTTPISEQKGGKPEPPAMPQPV
PTA

Sequence of entity 6 (SE), FASTA

>8XXN_6 40S ribosomal protein S4, X isoform (chains SE)
MARGPKKHLKRVAAPKHWMLDKLTGVFAPRPSTGPHKLRECLPLIIFLRNRLKYALTGDE
VKKICMQRFIKIDGKVRTDITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRITPEEAK
YKLCKVRKIFVGTKGIPHLVTHDARTIRYPDPLIKVNDTIQIDLETGKITDFIKFDTGNL
CMVTGGANLGRIGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGKGNKPWISLPR
GKGIRLTIAEERDKRLAAKQSSG

Sequence of entity 7 (SF), FASTA

>8XXN_7 40S ribosomal protein S5 (chains SF)
MTEWETAAPAVAETPDIKLFGKWSTDDVQINDISLQDYIAVKEKYAKYLPHSAGRYAAKR
FRKAQCPIVERLTNSMMMHGRNNGKKLMTVRIVKHAFEIIHLLTGENPLQVLVNAIINSG
PREDSTRIGRAGTVRRQAVDVSPLRRVNQAIWLLCTGAREAAFRNIKTIAECLADELINA
AKGSSNSYAIKKKDELERVAKSNR

Sequence of entity 8 (SH), FASTA

>8XXN_8 40S ribosomal protein S7 (chains SH)
MFSSSAKIVKPNGEKPDEFESGISQALLELEMNSDLKAQLRELNITAAKEIEVGGGRKAI
IIFVPVPQLKSFQKIQVRLVRELEKKFSGKHVVFIAQRRILPKPTRKSRTKNKQKRPRSR
TLTAVHDAILEDLVFPSEIVGKRIRVKLDGSRLIKVHLDKAQQNNVEHKVETFSGVYKKL
TGKDVNFEFPEFQL

Sequence of entity 9 (SI), FASTA

>8XXN_9 40S ribosomal protein S8 (chains SI)
MGISRDNWHKRRKTGGKRKPYHKKRKYELGRPAANTKIGPRRIHTVRVRGGNKKYRALRL
DVGNFSWGSECCTRKTRIIDVVYNASNNELVRTKTLVKNCIVLIDSTPYRQWYESHYALP
LGRKKGAKLTPEEEEILNKKRSKKIQKKYDERKKNAKISSLLEEQFQQGKLLACIASRPG
QCGRADGYVLEGKELEFYLRKIKARKGK

Sequence of entity 10 (SK), FASTA

>8XXN_10 40S ribosomal protein S10 (chains SK)
MLMPKKNRIAIYELLFKEGVMVAKKDVHMPKHPELADKNVPNLHVMKAMQSLKSRGYVKE
QFAWRHFYWYLTNEGIQYLRDYLHLPPEIVPATLRRSRPETGRPRPKGLEGERPARLTRG
EADRDTYRRSAVPPGADKKAEAGAGSATEFQFRGGFGRGRGQPPQ

Sequence of entity 11 (SL), FASTA

>8XXN_11 40S ribosomal protein S11 (chains SL)
MADIQTERAYQKQPTIFQNKKRVLLGETGKEKLPRYYKNIGLGFKTPKEAIEGTYIDKKC
PFTGNVSIRGRILSGVVTKMKMQRTIVIRRDYLHYIRKYNRFEKRHKNMSVHLSPCFRDV
QIGDIVTVGECRPLSKTVRFNVLKVTKAAGTKKQFQKF

Sequence of entity 12 (SP), FASTA

>8XXN_12 40S ribosomal protein S15 (chains SP)
MAEVEQKKKRTFRKFTYRGVDLDQLLDMSYEQLMQLYSARQRRRLNRGLRRKQHSLLKRL
RKAKKEAPPMEKPEVVKTHLRDMIILPEMVGSMVGVYNGKTFNQVEIKPEMIGHYLGEFS
ITYKPVKHGRPGIGATHSSRFIPLK

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	23
ZN	Zinc ion	Zn	3

Primary citation

Human tumor suppressor PDCD4 directly interacts with ribosomes to repress translation. Ye, X., Huang, Z., Li, Y. et al. Cell Res (2024) 34:522-525. DOI 10.1038/s41422-024-00962-z · PubMed

Other PDB entries of the same protein (UniProt P62945 (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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