9CPA: Mammalian DHX29-bound 43S Pre-initiation Complex

Name: PDB 9CPA: Structure of a Mammalian DHX29-bound 43S Pre-initiation Complex
Published: 2025-07-23
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: translation

Structure of a Mammalian DHX29-bound 43S Pre-initiation Complex. Determined by electron microscopy at 6.0 Å resolution. Released 23 Jul 2025.

Method: Electron microscopy
Resolution: 6.0 Å
Organisms: Oryctolagus cuniculus, Homo sapiens
Chains: 51
Atoms: 129,228
Mol. weight: 2252.91 kDa
Released: 23 Jul 2025

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

Secondary structure: helices and β-sheets

9CPA contains 465 α-helices and 450 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 0: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	28-30	3	115
β-strand	41-45	5	115
β-strand	52-57	6	115
α-helix	58-61	4
α-helix	71-88	18
β-strand	92-94	3	115
α-helix	113-122	10
β-strand	126	1	116
β-strand	128	1	115
α-helix	141-142	2

Chain a: 6 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	6-8	3	71
β-strand	13-15	3	71
β-strand	20-28	9	71
α-helix	37-48	12
β-strand	55-62	8	71
α-helix	63	1
β-strand	69-76	8	71
α-helix	79-85	7
α-helix	88-91	4
α-helix	108-114	7
α-helix	122-126	5

Chain A: 8 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	19-24	6	74
β-strand	31-36	6	74
β-strand	43-47	5	74
β-strand	50	1	75
β-strand	52	1	75
β-strand	68-77	10	74
β-strand	82-86	5	74
α-helix	92-118	27
α-helix	126-130	5
α-helix	131-135	5
α-helix	136-143	8
α-helix	149-158	10
α-helix	172-183	12
α-helix	204-213	10
β-strand	226-229	4	76
β-strand	235-238	4	76
α-helix	248-263	16

Chain b: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	20-22	3	124
β-strand	29-31	3	124
β-strand	36-43	8	125
α-helix	47-49	3
α-helix	50-56	7
β-strand	57	1	116
β-strand	66-73	8	125
α-helix	75-80	6
α-helix	96-99	4

Chain B: 11 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	56-60	5	77
α-helix	68-74	7
β-strand	95-103	9	77
β-strand	117-118	2	78
β-strand	128-129	2	78
β-strand	138-147	10	77
α-helix	152-154	3
α-helix	155-162	8
β-strand	167-173	7	77
α-helix	181-193	13
β-strand	198-204	7	77
α-helix	210-223	14
β-strand	234-236	3	77
α-helix	245-254	10
α-helix	258-260	3
α-helix	266-267	2
β-strand	268-273	6	79
β-strand	291-298	8	79
β-strand	301-302	2	80
β-strand	306-314	9	79
α-helix	315	1
β-strand	324-336	13	79
β-strand	339-340	2	79
β-strand	343-344	2	80
β-strand	348-354	7	79
α-helix	358-360	3
β-strand	369-372	4	79
β-strand	379-390	12	81
α-helix	407-411	5
β-strand	416-421	6	81
β-strand	424-434	11	81
β-strand	437-448	12	81
β-strand	454-459	6	81
β-strand	464-472	9	81

Chain c: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	32-34	3	72
β-strand	45-47	3	72
α-helix	53-55	3
β-strand	66	1	73
β-strand	71	1	73

Chain C: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	10-11	2
α-helix	12-20	9
β-strand	25-26	2	2
β-strand	38-41	4	2
β-strand	47-49	3	2
α-helix	51-67	17
β-strand	74-78	5	3
α-helix	82-93	12
β-strand	97-100	4	3
β-strand	121-125	5	3
α-helix	131-137	7
β-strand	145-147	3	3
β-strand	159-160	2	3
α-helix	169-185	17
α-helix	208-225	18

Chain d: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
α-helix	7-9	3
β-strand	10-21	12	109
β-strand	27-33	7	109
β-strand	41-46	6	109
β-strand	55-58	4	109

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
eL41	l	protein	25	Oryctolagus cuniculus	A0A087WNH4 (AlphaFold model)
uS2 (SA)	C	protein	295	Oryctolagus cuniculus	G1TLT8 (AlphaFold model)
Small ribosomal subunit protein uS5	E	protein	226	Oryctolagus cuniculus	G1SWM1 (AlphaFold model)
40S ribosomal protein S4	G	protein	263	Oryctolagus cuniculus	G1TK17 (AlphaFold model)
40S ribosomal protein S6	I	protein	249	Oryctolagus cuniculus	G1TM55
40S ribosomal protein S7	J	protein	194	Oryctolagus cuniculus	G1SVB0
Small ribosomal subunit protein eS8	K	protein	208	Oryctolagus cuniculus	G1TJW1
Ribosomal protein S9 (Predicted)	L	protein	194	Oryctolagus cuniculus	B7NZS8
Ribosomal protein S11	N	protein	158	Oryctolagus cuniculus	G1TRM4
Ribosomal protein S13	P	protein	151	Oryctolagus cuniculus	G1SP51
40S ribosomal protein S21	X	protein	83	Oryctolagus cuniculus	G1TM82
Ribosomal protein S15a	Y	protein	130	Oryctolagus cuniculus	G1TG89

39 more molecules are not listed.

Sequence of entity 1 (l), FASTA

>9CPA_1 eL41 (chains l)
MRAKWRKKRMRRLKRKRRKMRQRSK

Sequence of entity 2 (C), FASTA

>9CPA_2 uS2 (SA) (chains C)
MSGALDVLQMKEEDVLKFLAAGTHLGGTNLDFQMEQYIYKRKSDGIYIINLKRTWEKLLL
AARAIVAIENPADVSVISSRNTGQRAVLKFAAATGATPIAGRFTPGTFTNQIQAAFREPR
LLVVTDPRADHQPLTEASYVNLPTIALCNTDSPLRYVDIAIPCNNKGAHSVGLMWWMLAR
EVLRMRGTISREHPWEVMPDLYFYRDPEEIEKEEQAAAEKAVTKEEFQGEWTAPAPEFTA
TQPEVADWSEGVQVPSVPIQQFPTEDWSAQPATEDWSAAPTAQATEWVGTTTEWS

Sequence of entity 3 (E), FASTA

>9CPA_3 Small ribosomal subunit protein uS5 (chains E)
GKAGDKEWLPVTKLGRLVKDMKIKSLEEIYLFSLPIKESEIIDFFLGAALKDKVLKIMPV
QKQTQAGQRTRFKAFVAIGDYNGHVGLGMKCSKEVATAIRGAIILAKLSIVPVRRGYWGN
KIGKPHTVRCKVTGRCGSVLVRLIPAPRGTGIISAPVPKKLLLMAGIDDCYTSAGGCTAT
LGNFAKATFDAISKTYSYLTPDLWKETVFTKSPYQEFTDHLVKTHT

Sequence of entity 4 (G), FASTA

>9CPA_4 40S ribosomal protein S4 (chains G)
MARGPKKHLKRVAAPKHWMLDKLTSVFAPRPSTGPHKLRECLPLIIFLRNKLKYALTGDE
VKKICMQRFIKIDGKVRADITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRITPEEAK
YKLCKVRKIFVGTKGIPHLVTHDARTIRYPDPLIKMNDTIQIDLETGKITDFIKFDTGNL
CMVTGGANLGRIGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGKGNKPWISLPR
GKGIRLTIAEERDKRLAAKQSSG

Sequence of entity 5 (I), FASTA

>9CPA_5 40S ribosomal protein S6 (chains I)
MKLNISFPATGCQKLIEVDDERKLRTFYEKRMATEVAADALGEEWKGYVVRISGGNDKQG
FPMKQGVLTHGRVRLLLSKGHSCYRPRRTGERKRKSVRGCIVDANLSVLNLVIVKKGEKD
IPGLTDTTVPRRLGPKRASRIRKLFNLSKEDDVRQYVVRKPLNKEGKKPRTKAPKIQRLV
TPRVLQHKRRRIALKKQRTKKNKEEAAEYAKLLAKRMKEAKEKRQEQIAKRRRLSSLRAS
TSKSESSQK

Sequence of entity 6 (J), FASTA

>9CPA_6 40S ribosomal protein S7 (chains J)
MFSSSAKIVKPNGEKPDEFESGISQALLELEMNSDLKAQLRELNITAAKEIEVGGGRKAI
IIFVPVPQLKSFQKIQVRLVRELEKKFSGKHVVFIAQRRILPKPTRKSRTKNKQKRPRSR
TLTAVHDAILEDLVFPSEIVGKRIRVKLDGSRLIKVHLDKAQQNNVEHKVETFSGVYKKL
TGKDVNFEFPEFQL

Sequence of entity 7 (K), FASTA

>9CPA_7 Small ribosomal subunit protein eS8 (chains K)
MGISRDNWHKRRKTGGKRKPYHKKRKYELGRPAANTKIGPRRIHTVGVRGGNKKYRALRL
DVGNFSWGSECCTRKTRIIDVVYNASNNELVRTKTLVKNCIVLIDSTPYRQWYESHYALP
LGRKKGAKLTPEEEEILNKKRSKKIQKKYDERKKNAKISSLLEEQFQQGKLLACIASRPG
QCGRADGYVLEGKELEFYLRKIKARKGK

Sequence of entity 8 (L), FASTA

>9CPA_8 Ribosomal protein S9 (Predicted) (chains L)
MPVARSWVCRKTYVTPRRPFEKSRLDQELKLIGEYGLRNKREVWRVKFTLAKIRKAAREL
LTLDEKDPRRLFEGNALLRRLVRIGVLDEGKMKLDYILGLKIEDFLERRLQTQVFKLGLA
KSIHHARVLIRQRHIRVRKQVVNIPSFIVRLDSQKHIDFSLRSPYGGGRPGRVKRKNAKK
GQGGAGAGDDEEED

Sequence of entity 9 (N), FASTA

>9CPA_9 Ribosomal protein S11 (chains N)
MADIQTERAYQKQPTIFQNKKRVLLGETGKEKLPRYYKNIGLGFKTPKEAIEGTYIDKKC
PFTGNVSIRGRILSGVVTKMKMQRTIVIRRDYLHYIRKYNRFEKRHKNMSVHLSPCFRDV
QIGDIVTVGECRPLSKTVRFNVLKVTKAAGTKKQFQKF

Sequence of entity 10 (P), FASTA

>9CPA_10 Ribosomal protein S13 (chains P)
MGRMHAPGKGLSQSALPYRRSVPTWLKLTSDDVKEQIYKLAKKGLTPSQIGVILRDSHGV
AQVRFVTGNKILRILKSKGLAPDLPEDLYHLIKKAVAVRKHLERNRKDKDAKFRLILIES
RIHRLARYYKTKRVLPPNWKYESSTASALVA

Sequence of entity 11 (X), FASTA

>9CPA_11 40S ribosomal protein S21 (chains X)
MQSNAGEFVDLYVPRKCSASNRIIGAKDHASIPMNVAEVDKVTGRFNGQSKTYAICGAIR
RMGESDDSILRLAKSHGIVSQNF

Sequence of entity 12 (Y), FASTA

>9CPA_12 Ribosomal protein S15a (chains Y)
MVRMNVLADALKSINNAEKRGKRQVLIRPCSKVIVRFLTVMMKHGYIGEFEIIDDHRAGK
IVVNLTGRLNKCGVISPRFDVQLKDLEKWQNNLLPSRQFGFIVLTTSAGIMDHEEARRKH
TGGKILGFFF

Primary citation

The translation initiation factor DHX29 appears to pull on mRNA in a direction opposite to scanning. Cui, D., Pestova, T., Hellen, C. et al. bioRxiv (2025). DOI 10.1101/2025.07.13.664561 · PubMed

Other PDB entries of the same protein (UniProt A0A087WNH4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7O7Y 2.2 Å, Rabbit 80S ribosome stalled close to the mutated SARS-CoV-2 slippery site by a…
7OYD 2.3 Å, Cryo-EM structure of a rabbit 80S ribosome with zebrafish Dap1b
11IQ 2.4 Å, Rabbit 80S with eEF2,eIF5A and SERBP1
7O7Z 2.4 Å, Rabbit 80S ribosome stalled close to the mutated SARS-CoV-2 slippery site by a…
8Q87 2.4 Å, Structure of the G. gallus 80S rotated ribosome in complex with eEF2 and SERBP1
8Q7Z 2.5 Å, Structure of the G. gallus 80S non-rotated ribosome
8SCB 2.5 Å, Terminating ribosome with SRI-41315
9MR4 2.65 Å, NAC: Ribosome nascent chain complex(Oxa1L)
9RHU 2.65 Å, Rabbit 80S ribosome in complex with eRF1-AAQ, stalled at the Stop codon in mutated F2A…
8RJB 2.69 Å, Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in…
8VVQ 2.7 Å, Codon sampling state of elongation inhibitor-treated mammalian ribosomes obtained from…
8RJD 2.79 Å, Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in…

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