7SYW: PDB entry 7SYW

Structure of the wt IRES eIF5B-containing 48S initiation complex, closed conformation. Structure 15(wt). Determined by electron microscopy at 3.7 Å resolution. Released 13 Jul 2022.

Method: Electron microscopy
Resolution: 3.7 Å
Organisms: Oryctolagus cuniculus, Homo sapiens, Hepatitis C virus (isolate 1)
Chains: 39
Atoms: 86,759
Mol. weight: 1501.8 kDa
Ligands: ZN, GTP, MG
Released: 13 Jul 2022

Explore 7SYW in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7SYW contains 224 α-helices and 303 β-strands across 36 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 a: 5 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	47	1	4
β-strand	50	1	82
α-helix	52-61	10
α-helix	62-64	3
β-strand	68	1	5
α-helix	70-77	8
β-strand	79	1	4
α-helix	81-94	14
β-strand	98-102	5	5
β-strand	107-110	4	5
α-helix	111-113	3

Chain A: 1 helix, 8 β-strands

Element	Residues	Length	Sheet
β-strand	30	1	2
β-strand	33	1	2
β-strand	34-41	8	3
β-strand	46-51	6	3
β-strand	56-60	5	3
β-strand	76-80	5	3
β-strand	88	1	3
β-strand	90-94	5	3
α-helix	97-106	10

Chain b: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	20-22	3	9
β-strand	28	1	75
β-strand	29-31	3	9
β-strand	36-43	8	10
α-helix	49-55	7
α-helix	62-65	4
β-strand	66-73	8	10
α-helix	75-80	6
α-helix	91-93	3
α-helix	96-99	4

Chain B: 10 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	13-21	9
β-strand	25	1	6
α-helix	32-34	3
β-strand	41	1	7
α-helix	43-45	3
β-strand	47	1	7
β-strand	48	1	6
α-helix	51-67	17
α-helix	71-73	3
β-strand	74-78	5	8
α-helix	84-94	11
β-strand	97-100	4	8
β-strand	121-124	4	8
α-helix	131-138	8
β-strand	144-148	5	8
β-strand	159-162	4	8
α-helix	168-186	19
α-helix	199-202	4
α-helix	207-216	10

Chain c: 2 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	12-17	6
β-strand	32-36	5	14
β-strand	43-47	5	14
β-strand	55	1	15
β-strand	62	1	15
β-strand	64-65	2	16
β-strand	72-73	2	16
α-helix	74	1
β-strand	78	1	14
β-strand	81	1	14

Chain C: 7 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	24-27	4
β-strand	28-30	3	11
β-strand	33-34	2	12
β-strand	43-45	3	12
β-strand	48-50	3	11
β-strand	53	1	13
β-strand	56	1	13
α-helix	58-61	4
β-strand	66-70	5	12
β-strand	82-91	10	12
β-strand	96-105	10	12
α-helix	107-113	7
β-strand	120-124	5	12
β-strand	127-128	2	12
β-strand	134-143	10	12
α-helix	158-176	19
α-helix	181-188	8
α-helix	192-200	9
β-strand	207-217	11	12
α-helix	225-230	6

Chain d: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
α-helix	6-8	3
β-strand	10-21	12	20
β-strand	27-34	8	20
β-strand	41-47	7	20
β-strand	55-58	4	20

Chain D: 10 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	65-71	7
α-helix	79-83	5
α-helix	92-97	6
β-strand	103-115	13	17
β-strand	120-131	12	17
β-strand	137-144	8	17
α-helix	148-160	13
β-strand	162-163	2	17
β-strand	168	1	18
β-strand	179	1	18
β-strand	184-188	5	19
β-strand	191-197	7	19
β-strand	204-205	2	19
α-helix	208-217	10
β-strand	221	1	18
β-strand	222-227	6	19
α-helix	233-245	13
α-helix	253-255	3
α-helix	258-259	2
α-helix	262-264	3
α-helix	265-276	12

28 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
18S rRNA	2	RNA	1870	Oryctolagus cuniculus
Eukaryotic translation initiation factor 1A, X-chromosomal	A	protein	144	Homo sapiens	P47813 (AlphaFold model)
40S ribosomal protein SA	B	protein	295	Oryctolagus cuniculus	G1TLT8 (AlphaFold model)
eS1	C	protein	264	Oryctolagus cuniculus	G1SS70 (AlphaFold model)
40S ribosomal protein S2	D	protein	221	Oryctolagus cuniculus	G1SV32 (AlphaFold model)
uS3	E	protein	281	Oryctolagus cuniculus	G1TNM3
40S ribosomal protein S4	F	protein	263	Oryctolagus cuniculus	G1TA47
uS7	G	protein	204	Oryctolagus cuniculus	G1TFM5
eS6	H	protein	249	Oryctolagus cuniculus	A0A5K1UJS7
40S ribosomal protein S7	I	protein	432	Oryctolagus cuniculus	G1SVB0
eS8	J	protein	208	Oryctolagus cuniculus	G1TJW1
uS4	K	protein	194	Oryctolagus cuniculus	B7NZS8

27 more molecules are not listed.

Sequence of entity 1 (2), FASTA

>7SYW_1 18S rRNA (chains 2)
UACCUGGUUGAUCCUGCCAGUAGCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUA
AGUACGCACGGCCGGUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUGGUUCCUU
UGGUCGCUCGCUCCUCUCCUACUUGGAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCCG
ACGGGCGCUGACCCCCUUCGCGGGGGGGAUGCGUGCAUUUAUCAGAUCAAAACCAACCCG
GUCAGCCUCCCCCCGGCCCCGGCCGGGGGGGUGGGCGCCGGCGGCUUUGGUGACUCUAGA
UAACCUCGGGCCGAUCGCACGCCCUCCGUGGCGGCGACGACCCAUUCGAACGUCUGCCCU
AUCAACUUUCGAUGGUAGUCGCCGUGCCUACCAUGGUGACCACGGGUGACGGGGAAUCAG
GGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGC
GCGCAAAUUACCCACUCCCGACCCGGGGAGGUAGUGACGAAAAAUAACAAUACAGGACUC
UUUCGAGGCCCUGUAAUUGGAAUGAGUCCACUUUAAAUCCUUUAACGAGGAUCCAUUGGA
GGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUG
CUGCAGUUAAAAAGCUCGUAGUUGGAUCUUGGGAGCGGGCGGGCGGUCCGCCGCGAGGCG
AGCCACCGCCCGUCCCCGCCCCUUGCCUCUCGGCGCCCCCUCGAUGCUCUUAGCUGAGUG
UCCCGCGGGGCCCGAAGCGUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCCCGAGC
CGCCUGGAUACCGCAGCUAGGAAUAAUGGAAUAGGACCGCGGUUCUAUUUUGUUGGUUUU
CGGAACUGAGGCCAUGAUUAAGAGGGACGGCCGGGGGCAUUCGUAUUGCGCCGCUAGAGG
UGAAAUUCUUGGACCGGCGCAAGACGGACCAGAGCGAAAGCAUUUGCCAAGAAUGUUUUC
AUUAAUCAAGAACGAAAGUCGGAGGUUCGAAGACGAUCAGAUACCGUCGUAGUUCCGACC
AUAAACGAUGCCGACCGGCGAUGCGGCGGCGUUAUUCCCAUGACCCGCCGGGCAGCUUCC
GGGAAACCAAAGUCUUUGGGUUCCGGGGGGAGUAUGGUUGCAAAGCUGAAACUUAAAGGA
AUUUGGCGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAA
ACCUCACCCGGCCCGGACACGGACAGGAUUGACAGAUUGAUAGCUCUUUCUCGAUUCCGU
GGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGAUAA
CGAACGAGACUCUGGCAUGCUAACUAGUUACGCGACCCCCGAGCGGUCGGCGUCCCCCAA
CUUCUUAGAGGGACAAGUGGCGUUCAGCCACCCGAGAUUGAGCAAUAACAGGUCUGUGAU
GCCCUUAGAUGUCCGGGGCUGCACGCGCGCUACACUGACUGGCUCAGCGUGUGCCUACCC
UACGCCGGCAGGCGCGGGUAACCCGUUGAACCCCAUUCGUGAUGGGGAUCGGGGAUUGCA
AUUAUUCCCCAUGAACGAGGAAUUCCCAGUAAGUGCGGGUCAUAAGCUUGCGUUGAUUAA
GUCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGGAUGGUUUAGUGAGGCC
CUCGGAUCGGCCCCGCCGGGGUCGGCCCACGGCCCUGGCGGAGCGCUGAGAAGACGGUCG
AACUUGACUAUCUAGAGGAAGUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGA
AGGAUCAUUA

Sequence of entity 2 (A), FASTA

>7SYW_2 Eukaryotic translation initiation factor 1A, X-chromosomal (chains A)
MPKNKGKGGKNRRRGKNENESEKRELVFKEDGQEYAQVIKMLGNGRLEAMCFDGVKRLCH
IRGKLRKKVWINTSDIILVGLRDYQDNKADVILKYNADEARSLKAYGELPEHAKINETDT
FGPGDDDEIQFDDIGDDDEDIDDI

Sequence of entity 3 (B), FASTA

>7SYW_3 40S ribosomal protein SA (chains B)
MSGALDVLQMKEEDVLKFLAAGTHLGGTNLDFQMEQYIYKRKSDGIYIINLKRTWEKLLL
AARAIVAIENPADVSVISSRNTGQRAVLKFAAATGATPIAGRFTPGTFTNQIQTAFREPR
LLVVTDPRADHQPLTEASYVNLPTIALCNTDSPLRYVDIAIPCNNKGAHSVGLMWWMLAR
EVLRMRGTISREHPWEVMPDLYFYRDPEEIEKEEQAAAEKAVTKEEFQGEWTAPAPEFTA
TQPEVADWSEGVQVPSVPIQQFPTEDWSAQPATEDWSAAPTAQATEWVGTTTEWS

Sequence of entity 4 (C), FASTA

>7SYW_4 eS1 (chains C)
MAVGKNKRLTKGGKKGAKKKVVDPFSKKDWYDVKAPAMFNIRNIGKTLVTRTQGTKIASD
GLKGRVFEVSLADLQNDEVAFRKFKLITEDVQGKNCLTNFHGMDLTRDKMCSMVKKWQTM
IEAHVDVKTTDGYLLRLFCVGFTKKRNNQIRKTSYAQHQQVRQIRKKMMEIMTREVQTND
LKEVVNKLIPDSIGKDIEKACQSIYPLHDVFVRKVKMLKKPKFELGKLMELHGEGSSSGK
ATGDETGAKVERADGYEPPVQESV

Sequence of entity 5 (D), FASTA

>7SYW_5 40S ribosomal protein S2 (chains D)
KEWLPVTKLGRLVKDMKIKSLEEIYLFSLPIKESEIIDFFLGASLKDEVLKIMPVQKQTR
AGQRTRFKAFVAIGDYNGHVGLGVKCSKEVATAIRGAIILAKLSIVPVRRGYWGNKIGKP
HTVPCKVTGRCGSVLVRLIPAPRGTGIVSAPVPKKLLMMAGIDDCYTSARGCTATLGNFA
KATFDAISKTYSYLTPDLWKETVFTKSPYQEFTDHLVKTHT

Sequence of entity 6 (E), FASTA

>7SYW_6 uS3 (chains E)
MSARRRRRRAAFRRRAEPFIPISVREPLPFLSAARGGKMAVQISKKRKFVADGIFKAELN
EFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLGEKGRRIRELTAVVQKRFGFPEG
SVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFIMESGAKGCEVVVSGKL
RGQRAKSMKFVDGLMIHSGDPVNYYVDTAVRHVLLRQGVLGIKVKIMLPWDPSGKIGPKK
PLPDHVSIVEPKDEILPTTPISEQKGGKPEPPAMPQPVPTA

Sequence of entity 7 (F), FASTA

>7SYW_7 40S ribosomal protein S4 (chains F)
MARGPKKHLKRVAAPKHWMLDKLTGVFAPRPSTGPHKLRECLPLIIFLRNRLKYALTGDE
VKKICMQRFIKIDGKVRTDITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRITPEEAK
YKLCKVRKIFVGTKGIPHLVTHDARTIRYPDPLIKVNDTIQIDLETGKITDFIKFDTGNL
CMVTGGANLGRIGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGKGNKPWISLPR
GKGIRLTIAEERDKRLAAKQSSG

Sequence of entity 8 (G), FASTA

>7SYW_8 uS7 (chains G)
MTEWETAAPAVAETPDIKLFGKWSTDDVQINDISLQDYIAVKEKYAKYLPHSAGRYAAKR
FRKAQCPIVERLTNSMMMHGRNNGKKLMTVRIVKHAFEIIHLLTGENPLQVLVNAIINSG
PREDSTRIGRAGTVRRQAVDVSPLRRVNQAIWLLCTGAREAAFRNIKTIAECLADELINA
AKGSSNSYAIKKKDELERVAKSNR

Sequence of entity 9 (H), FASTA

>7SYW_9 eS6 (chains H)
MKLNISFPATGCQKLIEVDDERKLRTFYEKRMATEVAADALGEEWKGYVVRISGGNDKQG
FPMKQGVLTHGRVRLLLSKGHSCYRPRRTGERKRKSVRGCIVDANLSVLNLVIVKKGEKD
IPGLTDTTVPRRLGPKRASRIRKLFNLSKEDDVRQYVVRKPLNKEGKKPRTKAPKIQRLV
TPRVLQHKRRRIALKKQRTKKNKEEAAEYAKLLAKRMKEAKEKRQEQIAKRRRLSSLRAS
TSKSESSQK

Sequence of entity 10 (I), FASTA

>7SYW_10 40S ribosomal protein S7 (chains I)
EPITNRVFQALTSSDFKQQDGGSFSLSRTHLSGFRSRPRRTTIASAATRPPPIPSRGGSA
PTGTPEGAGASRSSRTVPRLPPQPSGPPRAPRHPGFQRALPSLIRPEPGVRAPLLASAGT
RFKRPASQAVKALSARGLLQPQVQVGPRANRVPQRREPRQHLSGHAPGASEGGSASPTYW
SLGITSWDALGFPLRLGGSSGFRSSVALFRPLSFRRGDLPRSREIWASSSAGAQPGEAMF
SSSAKIVKPNGEKPDEFESGISQALLELEMNSDLKAQLRELNITAAKEIEVGGGRKAIII
FVPVPQLKSFQKIQVRLVRELEKKFSGKHVVFIAQRRILPKPTRKSRTKNKQKRPRSRTL
TAVHDAILEDLVFPSEIVGKRIRVKLDGSRLIKVHLDKAQQNNVEHKVETFSGVYKKLTG
KDVNFEFPEFQL

Sequence of entity 11 (J), FASTA

>7SYW_11 eS8 (chains J)
MGISRDNWHKRRKTGGKRKPYHKKRKYELGRPAANTKIGPRRIHTVRVRGGNKKYRALRL
DVGNFSWGSECCTRKTRIIDVVYNASNNELVRTKTLVKNCIVLIDSTPYRQWYESHYALP
LGRKKGAKLTPEEEEILNKKRSKKIQKKYDERKKNAKISSLLEEQFQQGKLLACIASRPG
QCGRADGYVLEGKELEFYLRKIKARKGK

Sequence of entity 12 (K), FASTA

>7SYW_12 uS4 (chains K)
MPVARSWVCRKTYVTPRRPFEKSRLDQELKLIGEYGLRNKREVWRVKFTLAKIRKAAREL
LTLDEKDPRRLFEGNALLRRLVRIGVLDEGKMKLDYILGLKIEDFLERRLQTQVFKLGLA
KSIHHARVLIRQRHIRVRKQVVNIPSFIVRLDSQKHIDFSLRSPYGGGRPGRVKRKNAKK
GQGGAGAGDDEEED

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	1
MG	Magnesium ion	Mg	1

Water and common crystallization additives (NA) are not listed.

Primary citation

Molecular architecture of 40S translation initiation complexes on the hepatitis C virus IRES. Brown, Z.P., Abaeva, I.S., De, S. et al. EMBO J (2022) 41:e110581-e110581. DOI 10.15252/embj.2022110581 · PubMed

Other PDB entries of the same protein (UniProt P47813 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8PPL 2.65 Å, MERS-CoV Nsp1 bound to the human 43S pre-initiation complex
28ZX 2.8 Å, human 48S PIC with mRNA (Kozak_1)
28ZV 2.9 Å, human 48S PIC with mRNA (non-Kozak)
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…
9H74 2.9 Å, Late-stage 48S Initiation Complex with eIF3 (LS48S-eIF3 IC) guided by the trans-RNA
28ZY 3.0 Å, human 48S PIC with mRNA (Kozak_2)
6YBW 3.1 Å, Structure of a human 48S translational initiation complex - 40S body
8SUP 3.1 Å, Structure of the 48S translation initiation complex assembled on the…
28ZU 3.2 Å, human 48S PIC with Kozak mRNA and eIF1A W70A mutant
7TQL 3.2 Å, CryoEM structure of the human 40S small ribosomal subunit in complex with translation…

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