9BLN: Human Pdcd4

The structure of human Pdcd4 bound to the 40S-eIF4A-eIF3-eIF1 complex. Determined by electron microscopy at 3.9 Å resolution. Released 4 Sept 2024.

Method: Electron microscopy
Resolution: 3.9 Å
Organism: Homo sapiens
Chains: 50
Atoms: 104,352
Mol. weight: 2040.67 kDa
Ligands: MG, SPD, ZN
Released: 4 Sept 2024

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

Secondary structure: helices and β-sheets

9BLN contains 474 α-helices and 398 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 3: 18 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	3-16	14
α-helix	19-21	3
α-helix	23-25	3
α-helix	26-38	13
α-helix	45-56	12
α-helix	63-73	11
α-helix	81-88	8
α-helix	93-95	3
α-helix	97-110	14
α-helix	114-120	7
α-helix	126-130	5
α-helix	135-137	3
α-helix	138-149	12
β-strand	153	1	30
α-helix	155-162	8
α-helix	167-177	11
β-strand	180	1	31
β-strand	187	1	30
β-strand	188	1	31
α-helix	192-195	4
α-helix	197-198	2
α-helix	207-215	9

Chain 4: 9 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	91-93	3	34
α-helix	96-108	13
β-strand	117-122	6	35
β-strand	128-130	3	34
β-strand	131-135	5	35
α-helix	150-163	14
β-strand	168-174	7	35
α-helix	181-192	12
β-strand	199-201	3	35
β-strand	214-216	3	35
β-strand	217	1	36
β-strand	231	1	36
α-helix	245-255	11
α-helix	266-288	23
α-helix	289-291	3
α-helix	298-300	3
α-helix	302-314	13
α-helix	320-355	36

Chain 5: 21 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	184-207	24
α-helix	209-217	9
α-helix	224-246	23
α-helix	252-256	5
α-helix	257-262	6
α-helix	263-267	5
α-helix	269-270	2
α-helix	275-289	15
α-helix	298-302	5
α-helix	312-325	14
α-helix	329-334	6
α-helix	336-341	6
α-helix	358-374	17
α-helix	388-401	14
α-helix	406-416	11
α-helix	438-461	24
β-strand	469-470	2	39
α-helix	472-480	9
α-helix	491-496	6
α-helix	497-499	3
β-strand	504-506	3	39
β-strand	513-515	3	39
α-helix	527-548	22
α-helix	549-551	3

Chain 6: 20 helices, 0 β-strands

Element	Residues	Length
α-helix	18-25	8
α-helix	28-30	3
α-helix	31-34	4
α-helix	46-53	8
α-helix	63-70	8
α-helix	89-92	4
α-helix	97-105	9
α-helix	117-130	14
α-helix	155-164	10
α-helix	165-169	5
α-helix	175-192	18
α-helix	199-213	15
α-helix	252-256	5
α-helix	263-266	4
α-helix	269-277	9
α-helix	281-285	5
α-helix	297-301	5
α-helix	308-317	10
α-helix	342-346	5
α-helix	348-354	7

Chain 8: 14 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	38-39	2	44
α-helix	43-53	11
β-strand	65-72	8	44
β-strand	75-80	6	44
β-strand	83	1	44
α-helix	98-106	9
β-strand	116-122	7	44
α-helix	131-143	13
β-strand	149-152	4	44
β-strand	165-166	2	44
β-strand	167-169	3	45
α-helix	171-177	7
β-strand	198-200	3	45
α-helix	212-223	12
α-helix	225-229	5
α-helix	230-235	6
α-helix	236-240	5
α-helix	248-273	26
α-helix	274-278	5
α-helix	281-282	2
α-helix	283-287	5
α-helix	306-308	3
α-helix	316-350	35

Chain 9: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	3-23	21

Chain a: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	5-18	14
β-strand	20-24	5	46
α-helix	33-35	3
α-helix	42-55	14
β-strand	58-62	5	46
β-strand	66-71	6	46
α-helix	73-83	11

Chain b: 10 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	22-27	6
α-helix	30-36	7
α-helix	39-47	9
α-helix	51-66	16
α-helix	68	1
α-helix	72-75	4
β-strand	76-78	3	47
β-strand	84	1	48
α-helix	87-89	3
β-strand	93-97	5	47
β-strand	102-106	5	47
α-helix	109-111	3
β-strand	115	1	48
α-helix	116-119	4
α-helix	124-126	3

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
Eukaryotic translation initiation factor 3 subunit I	X	protein	325	Homo sapiens	Q13347 (AlphaFold model)
Eukaryotic translation initiation factor 3 subunit B	U	protein	661	Homo sapiens	P55884 (AlphaFold model)
Eukaryotic translation initiation factor 3 subunit K	3	protein	218	Homo sapiens	Q9UBQ5 (AlphaFold model)
Eukaryotic translation initiation factor 3 subunit F	4	protein	357	Homo sapiens	O00303 (AlphaFold model)
Eukaryotic translation initiation factor 3 subunit L	5	protein	564	Homo sapiens	Q9Y262
Eukaryotic translation initiation factor 3 subunit M	6	protein	374	Homo sapiens	Q7L2H7
Eukaryotic translation initiation factor 3 subunit H	8	protein	352	Homo sapiens	O15372
Small ribosomal subunit protein eS32	9	protein	25	Homo sapiens	P62945
rRNA	A	RNA	1719	Homo sapiens
Small ribosomal subunit protein uS17	B	protein	158	Homo sapiens	P62280
Small ribosomal subunit protein eS4, X isoform	C	protein	263	Homo sapiens	P62701
Small ribosomal subunit protein uS4	D	protein	194	Homo sapiens	P46781

38 more molecules are not listed.

Sequence of entity 1 (X), FASTA

>9BLN_1 Eukaryotic translation initiation factor 3 subunit I (chains X)
MKPILLQGHERSITQIKYNREGDLLFTVAKDPIVNVWYSVNGERLGTYMGHTGAVWCVDA
DWDTKHVLTGSADNSCRLWDCETGKQLALLKTNSAVRTCGFDFGGNIIMFSTDKQMGYQC
FVSFFDLRDPSQIDNNEPYMKIPCNDSKITSAVWGPLGECIIAGHESGELNQYSAKSGEV
LVNVKEHSRQINDIQLSRDMTMFVTASKDNTAKLFDSTTLEHQKTFRTERPVNSAALSPN
YDHVVLGGGQEAMDVTTTSTRIGKFEARFFHLAFEEEFGRVKGHFGPINSVAFHPDGKSY
SSGGEDGYVRIHYFDPQYFEFEFEA

Sequence of entity 2 (U), FASTA

>9BLN_2 Eukaryotic translation initiation factor 3 subunit B (chains U)
MQDADFVDDVSEEELLGDVLKDRPQEADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSK
FGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRVNLFTDFDKYM
TISDEWDIPEKQPFKDLGNLRYWLEEAECRDQYSVIFESGDRTSIFWNDVKDPVSIEERA
RWTETYVRWSPKGTYLATFHQRGIALWGGEKFKQIQRFSHQGVQLIDFSPCERYLVTFSP
LMDTQDDPQAIIIWDILTGHKKRGFHCESSAHWPIFKWSHDGKFFARMTLDTLSIYETPS
MGLLDKKSLKISGIKDFSWSPGGNIIAFWVPEDKDIPARVTLMQLPTRQEIRVRNLFNVV
DCKLHWQKNGDYLCVKVDRTPKGTQGVVTNFEIFRMREKQVPVDVVEMKETIIAFAWEPN
GSKFAVLHGEAPRISVSFYHVKNNGKIELIKMFDKQQANIIFWSPQGQFVVLAGLRSMNG
ALAFVDTSDCTVMNIAEHYMASDVEWDPTGRYVVTSVSWWSHKVDNAYWLWTFQGRLLQK
NNKDRFCQLLWRPRPPTLLSQEQIKQIKKDLKKYSKIFEQKDRLSQSKASKELVERRRTM
MEDFRKYRKMAQELYMEQKNERLELRGGVDTDELDSNVDDWEEETIEFFVTEEIIPLGNQ
E

Sequence of entity 3 (3), FASTA

>9BLN_3 Eukaryotic translation initiation factor 3 subunit K (chains 3)
MAMFEQMRANVGKLLKGIDRYNPENLATLERYVETQAKENAYDLEANLAVLKLYQFNPAF
FQTTVTAQILLKALTNLPHTDFTLCKCMIDQAHQEERPIRQILYLGDLLETCHFQAFWQA
LDENMDLLEGITGFEDSVRKFICHVVGITYQHIDRWLLAEMLGDLSDSQLKVWMSKYGWS
ADESGQIFICSQEESIKPKNIVEKIDFDSVSSIMASSQ

Sequence of entity 4 (4), FASTA

>9BLN_4 Eukaryotic translation initiation factor 3 subunit F (chains 4)
MATPAVPVSAPPATPTPVPAAAPASVPAPTPAPAAAPVPAAAPASSSDPAAAAAATAAPG
QTPASAQAPAQTPAPALPGPALPGPFPGGRVVRLHPVILASIVDSYERRNEGAARVIGTL
LGTVDKHSVEVTNCFSVPHNESEDEVAVDMEFAKNMYELHKKVSPNELILGWYATGHDIT
EHSVLIHEYYSREAPNPIHLTVDTSLQNGRMSIKAYVSTLMGVPGRTMGVMFTPLTVKYA
YYDTERIGVDLIMKTCFSPNRVIGLSSDLQQVGGASARIQDALSTVLQYAEDVLSGKVSA
DNTVGRFLMSLVNQVPKIVPDDFETMLNSNINDLLMVTYLANLTQSQIALNEKLVNL

Sequence of entity 5 (5), FASTA

>9BLN_5 Eukaryotic translation initiation factor 3 subunit L (chains 5)
MSYPADDYESEAAYDPYAYPSDYDMHTGDPKQDLAYERQYEQQTYQVIPEVIKNFIQYFH
KTVSDLIDQKVYELQASRVSSDVIDQKVYEIQDIYENSWTKLTERFFKNTPWPEAEAIAP
QVGNDAVFLILYKELYYRHIYAKVSGGPSLEQRFESYYNYCNLFNYILNADGPAPLELPN
QWLWDIIDEFIYQFQSFSQYRCKTAKKSEEEIDFLRSNPKIWNVHSVLNVLHSLVDKSNI
NRQLEVYTSGGDPESVAGEYGRHSLYKMLGYFSLVGLLRLHSLLGDYYQAIKVLENIELN
KKSMYSRVPECQVTTYYYVGFAYLMMRRYQDAIRVFANILLYIQRTKSMFQRTTYKYEMI
NKQNEQMHALLAIALTMYPMRIDESIHLQLREKYGDKMLRMQKGDPQVYEELFSYSCPKF
LSPVVPNYDNVHPNYHKEPFLQQLKVFSDEVQQQAQLSTIRSFLKLYTTMPVAKLAGFLD
LTEQEFRIQLLVFKHKMKNLVWTSGISALDGEFQSASEVDFYIDKDMIHIADTKVARRYG
DFFIRQIHKFEELNRTLKKMGQRP

Sequence of entity 6 (6), FASTA

>9BLN_6 Eukaryotic translation initiation factor 3 subunit M (chains 6)
MSVPAFIDISEEDQAAELRAYLKSKGAEISEENSEGGLHVDLAQIIEACDVCLKEDDKDV
ESVMNSVVSLLLILEPDKQEALIESLCEKLVKFREGERPSLRLQLLSNLFHGMDKNTPVR
YTVYCSLIKVAASCGAIQYIPTELDQVRKWISDWNLTTEKKHTLLRLLYEALVDCKKSDA
ASKVMVELLGSYTEDNASQARVDAHRCIVRALKDPNAFLFDHLLTLKPVKFLEGELIHDL
LTIFVSAKLASYVKFYQNNKDFIDSLGLLHEQNMAKMRLLTFMGMAVENKEISFDTMQQE
LQIGADDVEAFVIDAVRTKMVYCKIDQTQRKVVVSHSTHRTFGKQQWQQLYDTLNAWKQN
LNKVKNSLLSLSDT

Sequence of entity 7 (8), FASTA

>9BLN_7 Eukaryotic translation initiation factor 3 subunit H (chains 8)
MASRKEGTGSTATSSSSTAGAAGKGKGKGGSGDSAVKQVQIDGLVVLKIIKHYQEEGQGT
EVVQGVLLGLVVEDRLEITNCFPFPQHTEDDADFDEVQYQMEMMRSLRHVNIDHLHVGWY
QSTYYGSFVTRALLDSQFSYQHAIEESVVLIYDPIKTAQGSLSLKAYRLTPKLMEVCKEK
DFSPEALKKANITFEYMFEEVPIVIKNSHLINVLMWELEKKSAVADKHELLSLASSNHLG
KNLQLLMDRVDEMSQDIVKYNTYMRNTSKQQQQKHQYQQRRQQENMQRQSRGEPPLPEED
LSKLFKPPQPPARMDSLLIAGQINTYCQNIKEFTAQNLGKLFMAQALQEYNN

Sequence of entity 8 (9), FASTA

>9BLN_8 Small ribosomal subunit protein eS32 (chains 9)
MRAKWRKKRMRRLKRKRRKMRQRSK

Sequence of entity 9 (A), FASTA

>9BLN_9 rRNA (chains A)
UACCUGGUUGAUCCUGCCAGUAGCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUG
AGUACGCACGGCCGGUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUGGUUCCUU
UGGUCGCUCGCUCCUACUUGGAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCCGACGGG
CGCUGACCCCCUUCGCGGGGGGGAUGCGUGCAUUUAUCAGUGGUGACUCUAGAUAACCUC
GGGCCGAUCGCACGCCCCCCGUGGCGGCGACGACCCAUUCGAACGUCUGCCCUAUCAACU
UUCGAUGGUAGUCGCCGUGCCUACCAUGGUGACCACGGGUGACGGGGAAUCAGGGUUCGA
UUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAA
UUACCCACUCCCGACCCGGGGAGGUAGUGACGAAAAAUAACAAUACAGGACUCUUUCGAG
GCCCUGUAAUUGGAAUGAGUCCACUUUAAAUCCUUUAACGAGGAUCCAUUGGAGGGCAAG
UCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGCUGCAGU
UAAAAAGCUCGUAGUUGGAUCUUGGGAGCGGCCCCGCCCCUCUCGGCGGCCCGAAGCGUU
UACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCCCGAGCCGCCUGGAUACCGCAGCUAGG
AAUAAUGGAAUAGGACCGCGGUUCUAUUUUGUUGGUUUUCGGAACUGAGGCCAUGAUUAA
GAGGGACGGCCGGGGGCAUUCGUAUUGCGCCGCUAGAGGUGAAAUUCUUGGACCGGCGCA
AGACGGACCAGAGCGAAAGCAUUUGCCAAGAAUGUUUUCAUUAAUCAAGAACGAAAGUCG
GAGGUUCGAAGACGAUCAGAUACCGUCGUAGUUCCGACCAUAAACGAUGCCGACCGGCGA
UGCGGCGGCGUUAUUCCCAUGACCCGCCGGGCAGCUUCCGGGAAACCAAAGUCUUUGGGU
UCCGGGGGGAGUAUGGUUGCAAAGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCA
GGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAACCUCACCCGGCCCGGACACG
GACAGGAUUGACAGAUUGAUAGCUCUUUCUCGAUUCCGUGGGUGGUGGUGCAUGGCNGUU
CUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGAUAACGAACGAGACUCUGGCAUGCU
AACUAGUUACGCGACCCCCGAGCGGUCGGCGUCCCCCAACUUCUUAGAGGGACAAGUGGC
GUUCAGCCACCCGAGAUUGAGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCGGGGCUG
CACGCGCGCUACACUGACUGGCUCAGCGUGUGCCUACCCUACGCCGGCAGGCGCGGGUAA
CCCGUUGAACCCCAUUCGUGAUGGGGAUCGGGGAUUGCAAUUAUUCCCCAUGAACGAGGA
AUUCCCAGUAAGUGCGGGUCAUAAGCUUGCGUUGAUUAAGUCCCUGCCCUUUGUACACAC
CGCCCGUCGCUACUACCGAUUGGAUGGUUUAGUGAGGCCCUCGGAUCGGCCCCGCCGGGG
GCCCUGGCGGAGCGCUGAGAAGACGGUCGAACUUGACUAUCUAGAGGAAGUAAAAGUCGU
AACAAGGUUUCNGUAGGUGAACCUGCGGAAGGAUCAUUA

Sequence of entity 10 (B), FASTA

>9BLN_10 Small ribosomal subunit protein uS17 (chains B)
MADIQTERAYQKQPTIFQNKKRVLLGETGKEKLPRYYKNIGLGFKTPKEAIEGTYIDKKC
PFTGNVSIRGRILSGVVTKMKMQRTIVIRRDYLHYIRKYNRFEKRHKNMSVHLSPCFRDV
QIGDIVTVGECRPLSKTVRFNVLKVTKAAGTKKQFQKF

Sequence of entity 11 (C), FASTA

>9BLN_11 Small ribosomal subunit protein eS4, X isoform (chains C)
MARGPKKHLKRVAAPKHWMLDKLTGVFAPRPSTGPHKLRECLPLIIFLRNRLKYALTGDE
VKKICMQRFIKIDGKVRTDITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRITPEEAK
YKLCKVRKIFVGTKGIPHLVTHDARTIRYPDPLIKVNDTIQIDLETGKITDFIKFDTGNL
CMVTGGANLGRIGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGKGNKPWISLPR
GKGIRLTIAEERDKRLAAKQSSG

Sequence of entity 12 (D), FASTA

>9BLN_12 Small ribosomal subunit protein uS4 (chains D)
MPVARSWVCRKTYVTPRRPFEKSRLDQELKLIGEYGLRNKREVWRVKFTLAKIRKAAREL
LTLDEKDPRRLFEGNALLRRLVRIGVLDEGKMKLDYILGLKIEDFLERRLQTQVFKLGLA
KSIHHARVLIRQRHIRVRKQVVNIPSFIVRLDSQKHIDFSLRSPYGGGRPGRVKRKNAKK
GQGGAGAGDDEEED

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	88
SPD	Spermidine	C7 H19 N3	1
ZN	Zinc ion	Zn	3

Water and common crystallization additives (K, ACY) are not listed.

Primary citation

Human tumor suppressor protein Pdcd4 binds at the mRNA entry channel in the 40S small ribosomal subunit. Brito Querido, J., Sokabe, M., Diaz-Lopez, I. et al. Nat Commun (2024) 15:6633-6633. DOI 10.1038/s41467-024-50672-8 · PubMed

Other PDB entries of the same protein (UniProt Q13347 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6ZP4 2.9 Å, SARS-CoV-2 Nsp1 bound to a human 43S preinitiation ribosome complex - state 2
8PJ5 2.9 Å, Structure of human 48S translation initiation complex after eIF2 release prior 60S…
8PJ6 2.9 Å, Structure of human 48S translation initiation complex with initiator tRNA, eIF1A and…
6ZON 3.0 Å, SARS-CoV-2 Nsp1 bound to a human 43S preinitiation ribosome complex - state 1
8PJ4 3.2 Å, Structure of human 48S translation initiation complex after eIF5 release (48S-4)
8PJ1 3.4 Å, Structure of human 48S translation initiation complex in open codon scanning state (48S-1)
8PJ2 3.4 Å, Structure of human 48S translation initiation complex in AUG recognition state after…
7A09 3.5 Å, Structure of a human ABCE1-bound 43S pre-initiation complex - State III
8OZ0 3.5 Å, Structure of a human 48S translation initiation complex with eIF4F and eIF4A
8XXN 3.6 Å, Cryo-EM structure of the human 43S ribosome with PDCD4
6ZMW 3.7 Å, Structure of a human 48S translational initiation complex
8PJ3 3.7 Å, Structure of human 48S translation initiation complex upon transfer of initiator tRNA to…

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