9BKD: Human Pdcd4

The structure of human Pdcd4 bound to the 40S small ribosomal subunit. Determined by electron microscopy at 2.6 Å resolution. Released 4 Sept 2024.

Method: Electron microscopy
Resolution: 2.6 Å
Organism: Homo sapiens
Chains: 36
Atoms: 74,436
Mol. weight: 1232.82 kDa
Ligands: SPD, MG, ZN
Released: 4 Sept 2024

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

Secondary structure: helices and β-sheets

9BKD contains 232 α-helices and 229 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 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	62
α-helix	33-35	3
α-helix	42-55	14
β-strand	58-62	5	62
β-strand	66-71	6	62
α-helix	73-83	11

Chain b: 9 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	63
β-strand	84	1	64
α-helix	87-89	3
β-strand	93-97	5	63
β-strand	102-106	5	63
β-strand	115	1	64
α-helix	116-119	4
α-helix	124-126	3

Chain B: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	32-34	3
α-helix	44-47	4
α-helix	48-52	5
β-strand	72-79	8	40
β-strand	85-96	12	40
β-strand	101-112	12	40
β-strand	125-130	6	40
β-strand	138-146	9	40
α-helix	147-148	2

Chain c: 1 helix, 28 β-strands

Element	Residues	Length	Sheet
β-strand	4-11	8	65
β-strand	18-23	6	66
β-strand	30-35	6	66
β-strand	40-45	6	66
β-strand	53-59	7	66
β-strand	66-71	6	67
β-strand	78-82	5	67
β-strand	86-90	5	67
β-strand	97-102	6	67
β-strand	110-113	4	68
β-strand	120-124	5	68
β-strand	128-132	5	68
β-strand	138-141	4	68
β-strand	154-156	3	61
β-strand	164-168	5	61
β-strand	174-178	5	61
β-strand	184-189	6	61
β-strand	195-200	6	69
β-strand	206-211	6	69
β-strand	215-220	6	69
β-strand	225-231	7	69
β-strand	236-241	6	70
β-strand	247-252	6	70
β-strand	255-260	6	70
β-strand	265-271	7	70
α-helix	282-285	4
β-strand	286-291	6	65
β-strand	297-302	6	65
β-strand	307-313	7	65

Chain C: 13 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	10	1	41
α-helix	11-13	3
α-helix	16-18	3
β-strand	27	1	41
α-helix	31-32	2
α-helix	38-40	3
β-strand	41-43	3	42
α-helix	44-45	2
α-helix	46-51	6
α-helix	58-65	8
β-strand	71-72	2	43
β-strand	75-76	2	43
β-strand	83-85	3	42
β-strand	89-92	4	43
β-strand	97-103	7	43
β-strand	109-113	5	43
α-helix	118-120	3
β-strand	121-125	5	44
β-strand	126-131	6	45
α-helix	133-135	3
β-strand	137-141	5	45
β-strand	146	1	45
β-strand	159-163	5	44
β-strand	169-173	5	44
β-strand	180-183	4	46
β-strand	192-199	8	46
β-strand	207-211	5	46
β-strand	217-221	5	46
α-helix	222-224	3
β-strand	225-229	5	46
α-helix	237-239	3
α-helix	244-247	4
α-helix	248-256	9

Chain d: 6 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	6-8	3
α-helix	11-24	14
α-helix	52-66	15
α-helix	72-78	7
β-strand	81-85	5	7
β-strand	88-93	6	7
α-helix	97-110	14
β-strand	113-115	3	8
β-strand	121-123	3	8
α-helix	125-142	18

Chain D: 13 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	22-35	14
α-helix	40-62	23
α-helix	64	1
α-helix	68-84	17
α-helix	89-91	3
α-helix	94-97	4
α-helix	102-106	5
β-strand	109	1	47
α-helix	110-116	7
α-helix	123-131	9
β-strand	135-137	3	48
β-strand	140-141	2	48
α-helix	147	1
β-strand	148	1	47
α-helix	149-150	2
β-strand	157-159	3	48
α-helix	169-171	3
α-helix	172-177	6

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
Small ribosomal subunit protein eS6	S	protein	249	Homo sapiens	P62753 (AlphaFold model)
Small ribosomal subunit protein eS7	G	protein	194	Homo sapiens	P62081 (AlphaFold model)
40S ribosomal protein S27	H	protein	84	Homo sapiens	P42677 (AlphaFold model)
40S ribosomal protein S21	K	protein	83	Homo sapiens	P63220 (AlphaFold model)
40S ribosomal protein S2	L	protein	293	Homo sapiens	P15880
40S ribosomal protein S3a	O	protein	264	Homo sapiens	P61247
Small ribosomal subunit protein uS2	N	protein	295	Homo sapiens	P08865
40S ribosomal protein S26	Q	protein	115	Homo sapiens	P62854
40S ribosomal protein S14	P	protein	151	Homo sapiens	P62263
40S ribosomal protein S13	I	protein	151	Homo sapiens	P62277
60S ribosomal protein L41	9	protein	25	Homo sapiens	P62945
18S rRNA	A	RNA	1719	Homo sapiens

24 more molecules are not listed.

Sequence of entity 1 (S), FASTA

>9BKD_1 Small ribosomal subunit protein eS6 (chains S)
MKLNISFPATGCQKLIEVDDERKLRTFYEKRMATEVAADALGEEWKGYVVRISGGNDKQG
FPMKQGVLTHGRVRLLLSKGHSCYRPRRTGERKRKSVRGCIVDANLSVLNLVIVKKGEKD
IPGLTDTTVPRRLGPKRASRIRKLFNLSKEDDVRQYVVRKPLNKEGKKPRTKAPKIQRLV
TPRVLQHKRRRIALKKQRTKKNKEEAAEYAKLLAKRMKEAKEKRQEQIAKRRRLSSLRAS
TSKSESSQK

Sequence of entity 2 (G), FASTA

>9BKD_2 Small ribosomal subunit protein eS7 (chains G)
MFSSSAKIVKPNGEKPDEFESGISQALLELEMNSDLKAQLRELNITAAKEIEVGGGRKAI
IIFVPVPQLKSFQKIQVRLVRELEKKFSGKHVVFIAQRRILPKPTRKSRTKNKQKRPRSR
TLTAVHDAILEDLVFPSEIVGKRIRVKLDGSRLIKVHLDKAQQNNVEHKVETFSGVYKKL
TGKDVNFEFPEFQL

Sequence of entity 3 (H), FASTA

>9BKD_3 40S ribosomal protein S27 (chains H)
MPLAKDLLHPSPEEEKRKHKKKRLVQSPNSYFMDVKCPGCYKITTVFSHAQTVVLCVGCS
TVLCQPTGGKARLTEGCSFRRKQH

Sequence of entity 4 (K), FASTA

>9BKD_4 40S ribosomal protein S21 (chains K)
MQNDAGEFVDLYVPRKCSASNRIIGAKDHASIQMNVAEVDKVTGRFNGQFKTYAICGAIR
RMGESDDSILRLAKADGIVSKNF

Sequence of entity 5 (L), FASTA

>9BKD_5 40S ribosomal protein S2 (chains L)
MADDAGAAGGPGGPGGPGMGNRGGFRGGFGSGIRGRGRGRGRGRGRGRGARGGKAEDKEW
MPVTKLGRLVKDMKIKSLEEIYLFSLPIKESEIIDFFLGASLKDEVLKIMPVQKQTRAGQ
RTRFKAFVAIGDYNGHVGLGVKCSKEVATAIRGAIILAKLSIVPVRRGYWGNKIGKPHTV
PCKVTGRCGSVLVRLIPAPRGTGIVSAPVPKKLLMMAGIDDCYTSARGCTATLGNFAKAT
FDAISKTYSYLTPDLWKETVFTKSPYQEFTDHLVKTHTRVSVQRTQAPAVATT

Sequence of entity 6 (O), FASTA

>9BKD_6 40S ribosomal protein S3a (chains O)
MAVGKNKRLTKGGKKGAKKKVVDPFSKKDWYDVKAPAMFNIRNIGKTLVTRTQGTKIASD
GLKGRVFEVSLADLQNDEVAFRKFKLITEDVQGKNCLTNFHGMDLTRDKMCSMVKKWQTM
IEAHVDVKTTDGYLLRLFCVGFTKKRNNQIRKTSYAQHQQVRQIRKKMMEIMTREVQTND
LKEVVNKLIPDSIGKDIEKACQSIYPLHDVFVRKVKMLKKPKFELGKLMELHGEGSSSGK
ATGDETGAKVERADGYEPPVQESV

Sequence of entity 7 (N), FASTA

>9BKD_7 Small ribosomal subunit protein uS2 (chains N)
MSGALDVLQMKEEDVLKFLAAGTHLGGTNLDFQMEQYIYKRKSDGIYIINLKRTWEKLLL
AARAIVAIENPADVSVISSRNTGQRAVLKFAAATGATPIAGRFTPGTFTNQIQAAFREPR
LLVVTDPRADHQPLTEASYVNLPTIALCNTDSPLRYVDIAIPCNNKGAHSVGLMWWMLAR
EVLRMRGTISREHPWEVMPDLYFYRDPEEIEKEEQAAAEKAVTKEEFQGEWTAPAPEFTA
TQPEVADWSEGVQVPSVPIQQFPTEDWSAQPATEDWSAAPTAQATEWVGATTDWS

Sequence of entity 8 (Q), FASTA

>9BKD_8 40S ribosomal protein S26 (chains Q)
MTKKRRNNGRAKKGRGHVQPIRCTNCARCVPKDKAIKKFVIRNIVEAAAVRDISEASVFD
AYVLPKLYVKLHYCVSCAIHSKVVRNRSREARKDRTPPPRFRPAGAAPRPPPKPM

Sequence of entity 9 (P), FASTA

>9BKD_9 40S ribosomal protein S14 (chains P)
MAPRKGKEKKEEQVISLGPQVAEGENVFGVCHIFASFNDTFVHVTDLSGKETICRVTGGM
KVKADRDESSPYAAMLAAQDVAQRCKELGITALHIKLRATGGNRTKTPGPGAQSALRALA
RSGMKIGRIEDVTPIPSDSTRRKGGRRGRRL

Sequence of entity 10 (I), FASTA

>9BKD_10 40S ribosomal protein S13 (chains I)
MGRMHAPGKGLSQSALPYRRSVPTWLKLTSDDVKEQIYKLAKKGLTPSQIGVILRDSHGV
AQVRFVTGNKILRILKSKGLAPDLPEDLYHLIKKAVAVRKHLERNRKDKDAKFRLILIES
RIHRLARYYKTKRVLPPNWKYESSTASALVA

Sequence of entity 11 (9), FASTA

>9BKD_11 60S ribosomal protein L41 (chains 9)
MRAKWRKKRMRRLKRKRRKMRQRSK

Sequence of entity 12 (A), FASTA

>9BKD_12 18S 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

Ligands and cofactors

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

Water and common crystallization additives (K) 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 P62753 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6F4Q 1.12 Å, Human JMJD5 (Q275C) in complex with Mn(II), NOG and RPS6-A138C (129-144) (complex-2)
6F4P 1.45 Å, Human JMJD5 in complex with MN, NOG and RPS6 (129-144) (complex-1)
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)

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