8XXL: Human 40S ribosome with PDCD4

Name: PDB 8XXL: Cryo-EM structure of the human 40S ribosome with PDCD4
Published: 2024-05-01
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Cryo-EM structure of the human 40S ribosome with PDCD4. Determined by electron microscopy at 2.9 Å resolution. Released 1 May 2024.

Method: Electron microscopy
Resolution: 2.9 Å
Organism: Homo sapiens
Chains: 36
Atoms: 76,240
Mol. weight: 1277.99 kDa
Ligands: MG, ZN
Released: 1 May 2024

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

Secondary structure: helices and β-sheets

8XXL contains 202 α-helices and 244 β-strands across 35 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 CD: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	112-113	2
α-helix	114-117	4

Chain Ln: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	3-23	21

Chain Sa: 6 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	20-22	3	56
β-strand	29-31	3	56
β-strand	36-43	8	57
α-helix	47-49	3
α-helix	51-56	6
β-strand	57	1	5
α-helix	63-65	3
β-strand	66-73	8	57
α-helix	75-80	6
α-helix	91-93	3
α-helix	97-99	3

Chain SA: 10 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	12-21	10
β-strand	25	1	2
α-helix	35-37	3
β-strand	38-41	4	3
β-strand	47-49	3	3
α-helix	53-66	14
α-helix	71-73	3
β-strand	74-78	5	4
α-helix	84-94	11
β-strand	97-100	4	4
α-helix	102-104	3
β-strand	121-124	4	4
α-helix	131-136	6
β-strand	144-148	5	4
β-strand	159-162	4	4
α-helix	168-186	19
α-helix	199-202	4
α-helix	207-222	16

Chain Sb: 2 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	12-17	6
β-strand	32	1	28
β-strand	33-34	2	29
β-strand	47	1	28
β-strand	54-55	2	30
β-strand	62-65	4	30
α-helix	71	1
β-strand	72-73	2	30
β-strand	80-81	2	29

Chain SB: 7 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	28-34	7	6
β-strand	43-50	8	6
β-strand	65-66	2	6
β-strand	69-70	2	7
α-helix	72-75	4
β-strand	82-84	3	7
β-strand	87-92	6	6
β-strand	95-99	5	6
β-strand	102-105	4	7
α-helix	107-113	7
β-strand	118	1	8
β-strand	120-128	9	7
β-strand	134-142	9	7
β-strand	143	1	9
β-strand	154	1	8
α-helix	158-177	20
α-helix	181-185	5
α-helix	192-200	9
α-helix	201-203	3
β-strand	207	1	9
β-strand	211-219	9	7
α-helix	226-232	7

Chain Sc: 0 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	10-13	4	58
β-strand	14	1	59
β-strand	18-21	4	27
β-strand	27-29	3	27
β-strand	32	1	59
β-strand	45-47	3	27
β-strand	55-58	4	58

Chain SC: 11 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	65-71	7
α-helix	79-83	5
α-helix	91-97	7
β-strand	103-115	13	70
β-strand	120-131	12	70
β-strand	136-137	2	71
β-strand	138-144	7	70
α-helix	147-160	14
β-strand	163-164	2	71
β-strand	168	1	72
β-strand	179	1	72
β-strand	184-188	5	73
β-strand	191-196	6	73
β-strand	204-205	2	73
α-helix	208-215	8
β-strand	222-227	6	73
α-helix	233-245	13
α-helix	253-255	3
α-helix	258-260	3
α-helix	262-264	3
α-helix	265-268	4
α-helix	270-276	7

27 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

24 more molecules are not listed.

Sequence of entity 1 (Ln), FASTA

>8XXL_1 60S ribosomal protein L41 (chains Ln)
MRAKWRKKRMRRLKRKRRKMRQRSK

Sequence of entity 2 (S2), FASTA

>8XXL_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

>8XXL_3 40S ribosomal protein SA (chains SA)
MSGALDVLQMKEEDVLKFLAAGTHLGGTNLDFQMEQYIYKRKSDGIYIINLKRTWEKLLL
AARAIVAIENPADVSVISSRNTGQRAVLKFAAATGATPIAGRFTPGTFTNQIQAAFREPR
LLVVTDPRADHQPLTEASYVNLPTIALCNTDSPLRYVDIAIPCNNKGAHSVGLMWWMLAR
EVLRMRGTISREHPWEVMPDLYFYRDPEEIEKEEQAAAEKAVTKEEFQGEWTAPAPEFTA
TQPEVADWSEGVQVPSVPIQQFPTEDWSAQPATEDWSAAPTAQATEWVGATTDWS

Sequence of entity 4 (SB), FASTA

>8XXL_4 40S ribosomal protein S3a (chains SB)
MAVGKNKRLTKGGKKGAKKKVVDPFSKKDWYDVKAPAMFNIRNIGKTLVTRTQGTKIASD
GLKGRVFEVSLADLQNDEVAFRKFKLITEDVQGKNCLTNFHGMDLTRDKMCSMVKKWQTM
IEAHVDVKTTDGYLLRLFCVGFTKKRNNQIRKTSYAQHQQVRQIRKKMMEIMTREVQTND
LKEVVNKLIPDSIGKDIEKACQSIYPLHDVFVRKVKMLKKPKFELGKLMELHGEGSSSGK
ATGDETGAKVERADGYEPPVQESV

Sequence of entity 5 (SD), FASTA

>8XXL_5 40S ribosomal protein S3 (chains SD)
MAVQISKKRKFVADGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLG
EKGRRIRELTAVVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRRACY
GVLRFIMESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPVNYYVDTAVRHVLLRQG
VLGIKVKIMLPWDPTGKIGPKKPLPDHVSIVEPKDEILPTTPISEQKGGKPEPPAMPQPV
PTA

Sequence of entity 6 (SE), FASTA

>8XXL_6 40S ribosomal protein S4, X isoform (chains SE)
MARGPKKHLKRVAAPKHWMLDKLTGVFAPRPSTGPHKLRECLPLIIFLRNRLKYALTGDE
VKKICMQRFIKIDGKVRTDITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRITPEEAK
YKLCKVRKIFVGTKGIPHLVTHDARTIRYPDPLIKVNDTIQIDLETGKITDFIKFDTGNL
CMVTGGANLGRIGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGKGNKPWISLPR
GKGIRLTIAEERDKRLAAKQSSG

Sequence of entity 7 (SF), FASTA

>8XXL_7 40S ribosomal protein S5 (chains SF)
MTEWETAAPAVAETPDIKLFGKWSTDDVQINDISLQDYIAVKEKYAKYLPHSAGRYAAKR
FRKAQCPIVERLTNSMMMHGRNNGKKLMTVRIVKHAFEIIHLLTGENPLQVLVNAIINSG
PREDSTRIGRAGTVRRQAVDVSPLRRVNQAIWLLCTGAREAAFRNIKTIAECLADELINA
AKGSSNSYAIKKKDELERVAKSNR

Sequence of entity 8 (SH), FASTA

>8XXL_8 40S ribosomal protein S7 (chains SH)
MFSSSAKIVKPNGEKPDEFESGISQALLELEMNSDLKAQLRELNITAAKEIEVGGGRKAI
IIFVPVPQLKSFQKIQVRLVRELEKKFSGKHVVFIAQRRILPKPTRKSRTKNKQKRPRSR
TLTAVHDAILEDLVFPSEIVGKRIRVKLDGSRLIKVHLDKAQQNNVEHKVETFSGVYKKL
TGKDVNFEFPEFQL

Sequence of entity 9 (SI), FASTA

>8XXL_9 40S ribosomal protein S8 (chains SI)
MGISRDNWHKRRKTGGKRKPYHKKRKYELGRPAANTKIGPRRIHTVRVRGGNKKYRALRL
DVGNFSWGSECCTRKTRIIDVVYNASNNELVRTKTLVKNCIVLIDSTPYRQWYESHYALP
LGRKKGAKLTPEEEEILNKKRSKKIQKKYDERKKNAKISSLLEEQFQQGKLLACIASRPG
QCGRADGYVLEGKELEFYLRKIKARKGK

Sequence of entity 10 (SK), FASTA

>8XXL_10 40S ribosomal protein S10 (chains SK)
MLMPKKNRIAIYELLFKEGVMVAKKDVHMPKHPELADKNVPNLHVMKAMQSLKSRGYVKE
QFAWRHFYWYLTNEGIQYLRDYLHLPPEIVPATLRRSRPETGRPRPKGLEGERPARLTRG
EADRDTYRRSAVPPGADKKAEAGAGSATEFQFRGGFGRGRGQPPQ

Sequence of entity 11 (SL), FASTA

>8XXL_11 40S ribosomal protein S11 (chains SL)
MADIQTERAYQKQPTIFQNKKRVLLGETGKEKLPRYYKNIGLGFKTPKEAIEGTYIDKKC
PFTGNVSIRGRILSGVVTKMKMQRTIVIRRDYLHYIRKYNRFEKRHKNMSVHLSPCFRDV
QIGDIVTVGECRPLSKTVRFNVLKVTKAAGTKKQFQKF

Sequence of entity 12 (SP), FASTA

>8XXL_12 40S ribosomal protein S15 (chains SP)
MAEVEQKKKRTFRKFTYRGVDLDQLLDMSYEQLMQLYSARQRRRLNRGLRRKQHSLLKRL
RKAKKEAPPMEKPEVVKTHLRDMIILPEMVGSMVGVYNGKTFNQVEIKPEMIGHYLGEFS
ITYKPVKHGRPGIGATHSSRFIPLK

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	22
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

Browse structure collections

About this viewer

MolViewer shows 8XXL directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.