5K0Y: PDB entry 5K0Y

m48S late-stage initiation complex, purified from rabbit reticulocytes lysates, displaying eIF2 ternary complex and eIF3 i and g subunits relocated to the intersubunit face. Determined by electron microscopy at 5.8 Å resolution. Released 13 Jul 2016.

Method: Electron microscopy
Resolution: 5.8 Å
Organisms: Oryctolagus cuniculus, Homo sapiens
Chains: 42
Atoms: 88,157
Mol. weight: 1291.32 kDa
Released: 13 Jul 2016

Explore 5K0Y in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5K0Y contains 201 α-helices and 299 β-strands across 39 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: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	7-20	14
β-strand	26-27	2	78
α-helix	32-44	13
β-strand	50-54	5	78
β-strand	60-63	4	78
β-strand	72-74	3	81
β-strand	80-81	2	81
α-helix	86-93	8
β-strand	101-106	6	81
β-strand	109-112	4	81
α-helix	113-119	7
β-strand	123-129	7	81

Chain b: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	82
β-strand	7-8	2	82
β-strand	32-33	2	83
β-strand	36	1	84
α-helix	37-38	2
β-strand	39	1	85
β-strand	46	1	85
β-strand	51	1	84
β-strand	54-55	2	83
α-helix	57-61	5
α-helix	65-76	12

Chain c: 7 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	50-56	7
α-helix	63-69	7
α-helix	76-82	7
β-strand	88-93	6	86
β-strand	96-97	2	86
β-strand	100	1	87
β-strand	105	1	87
β-strand	108-116	9	86
β-strand	121-129	9	86
α-helix	132-145	14
β-strand	148-149	2	86
β-strand	153	1	88
β-strand	164	1	88
β-strand	169-172	4	89
β-strand	177-182	6	89
β-strand	189-190	2	89
α-helix	193-202	10
β-strand	207-212	6	89
α-helix	219-234	16
α-helix	250-253	4

Chain d: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	5-14	10

Chain e: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	4-6	3
α-helix	7-19	13
α-helix	28-37	10
β-strand	39-40	2	1
α-helix	44-61	18
β-strand	62	1	2
β-strand	64	1	2
α-helix	72-81	10
α-helix	102-107	6

Chain f: 10 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	6-8	3
α-helix	12-21	10
α-helix	35-37	3
β-strand	38-41	4	3
α-helix	42	1
β-strand	47-49	3	3
α-helix	51-65	15
α-helix	71-73	3
β-strand	74-77	4	4
α-helix	81-83	3
α-helix	84-93	10
β-strand	97-99	3	4
β-strand	121-124	4	4
α-helix	131-137	7
β-strand	144-148	5	4
β-strand	160-162	3	4
α-helix	170-185	16

Chain g: 8 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	7-28	22
β-strand	34-42	9	5
β-strand	45-52	8	5
α-helix	55-59	5
α-helix	64-76	13
α-helix	79-80	2
β-strand	84-90	7	5
α-helix	99-112	14
α-helix	116-130	15
β-strand	133-142	10	6
β-strand	146-155	10	6
α-helix	163-167	5
β-strand	168-178	11	6
β-strand	180-189	10	6
β-strand	209-210	2	1
α-helix	221-222	2
β-strand	223-226	4	7

Chain G: 1 helix, 5 β-strands

Element	Residues	Length	Sheet
α-helix	48-52	5
β-strand	68-80	13	12
β-strand	85-94	10	12
β-strand	103-112	10	12
β-strand	125-131	7	12
β-strand	140-146	7	12

31 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
tRNA	N	RNA	75	Oryctolagus cuniculus
18S ribosomal RNA	A	RNA	1776	Oryctolagus cuniculus
mRNA	F	RNA	30	Oryctolagus cuniculus
Eukaryotic translation initiation factor 2 subunit 1	P	protein	266	Oryctolagus cuniculus	G1T2G4 (AlphaFold model)
ribosomal protein uS17	G	protein	158	Oryctolagus cuniculus	G1TRM4 (AlphaFold model)
ribosomal protein uS9	H	protein	141	Oryctolagus cuniculus	G1SGX4 (AlphaFold model)
40S ribosomal protein S4	I	protein	263	Oryctolagus cuniculus	G1TK17 (AlphaFold model)
ribosomal protein uS14	J	protein	53	Oryctolagus cuniculus	G1U7M4
Ribosomal protein S9 (Predicted)	K	protein	182	Oryctolagus cuniculus	B7NZS8
ribosomal protein uS13	L	protein	137	Oryctolagus cuniculus	G1TPG3
Eukaryotic translation initiation factor 3 subunit G	M	protein	38	Homo sapiens	O75821
Eukaryotic translation initiation factor 3 subunit G	O	protein	77	Homo sapiens	O75821

30 more molecules are not listed.

Sequence of entity 1 (N), FASTA

>5K0Y_1 tRNA (chains N)
AGCAGAGUGGCGCAGCGGAAGCGUGCUGGGCCCAUAACCCAGAGGUCGAUGGAUCGAAAC
CAUCCUCUGCUACCA

Sequence of entity 2 (A), FASTA

>5K0Y_2 18S ribosomal RNA (chains A)
UACCUGGUUGAUCCUGCCAGUAGCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUA
AGUACGCACGGCCGGUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUGGUUCCUU
UGGUCGCUCGCUCCUCUCCUACUUGGAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCCG
ACGGCGCUGACUCCCUUUGUGUGGGAUGCGUGCAUUUAUCAGAUCAAAACCAACCCGGUC
AGCGGCGGCGGCUUUGGUGACUCUAGAUAACCUCGGGCCGAUCGCAGCCCUCCGUGGCGG
CGACGACCCAUUCGAACGUCUGCCCUAUCAACUUUCGAUGGUAGUCGCCGUGCCUACCAU
GGUGACCACGGGUGACGGGGAAUCAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGC
UACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCACUCCCGACCCGGGGAGGUAG
UGACGAAAAAUAACAAUACAGGACUCUUUCGAGGCCCUGUAAUUGGAAUGAGUCCACUUU
AAAUCCUUUAACGAGGAUCCAUUGGAGGGCAAGUCUGGUCGCAGCAGCCGCGGUAAUUCC
AGCUCCAAUAGCGUAUAUUAAAGUUGCUGCAGUUAAAAAGCUCGUAGUUGGAUCUUGAGG
GCCCGCCCCUCGGCGCCCCCUCGAUGUGUCCCGCGGGGCCCGAAGCGUUUACUUUGAAAA
AAUUAGAGUGUUCAAAGCAGGCCCGAGCCGCCUGGAUACCGCAGCUAGGAAUAAUGGAAU
AGGACCGCGGUUCUAUUUUGUUGGUUUUCGGAACUGAGGCCAUGAUUAAGAGGGACGGCC
GGGGGCAUUCGUAUUGCGCCGCUAGAGGUGAAAUUCUUGGACCGGCGCAAGACGGACCAG
AGCGAAAGCAUUUGCCAAGAAUGUUUUCAUUAAUCAAGAACGAAAGUCGGAGGUUCGAAG
ACGAUCAGAUACCGUCGUAGUUCCGACCAUAAACGAUGCCGACUGGCGAUGCGGCGGCGU
UAUUCCCAUGACCCGCCGGGCAGCUUCCGGGAAACCAAAGUCUUUGGGUUCCGGGGGGAG
UAUGGUUGCAAAGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCC
UGCGGCUUAAUUUGACUCAACACGGGAAACCUCACCCGGCCCGGACACGGACAGGAUUGA
CAGAUUGAUAGCUCUUUCUCGAUUCUGUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUG
GAGCGAUUUGUCUGGUUAAUUCCGAUAACGAACGAGACUCUGGCAUGCUAACUAGUUACG
CGACCCCCGAGCGGUCGGCGUCCCCCAACUUCUUAGAGGGACAAGUGGCGUUCAGCCACC
CGAGAUUGAGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCGGGGCUGCACGCGCGCUAC
ACUGACUGGCUCAGCGUGUGCCUACCCUACGCCGGCAGGCGCGGGUAACCCGUUGAACCC
CAUUCGUGAUGGGGAUCGGGGAUUGCAAUUAUUCCCCAUGAACGAGGAAUUCCCAGUAAG
UGCGGGUCAUAAGCUUGCGUUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUA
CUACCGAUUGGAUGGUUUAGUGAGGCCCUCGGAUCGGCCCGCCGGGGUCGGCCCACGGCC
CUGGCGGAGCGCUGAGAAGACGGUCGAACUUGACUAUCUAGAGGAAGUAAAAGUCGUAAC
AAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA

Sequence of entity 3 (F), FASTA

>5K0Y_3 mRNA (chains F)
CAGACACCAUGGUGCACCUGACUCCUGAGG

Sequence of entity 4 (P), FASTA

>5K0Y_4 Eukaryotic translation initiation factor 2 subunit 1 (chains P)
CRFYQHKFPEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINKLIRI
GRNECVVVIRVDKEKGYIDLSKRRVSPEEAIKCEDKFTKSKTVYSILRHVAEVLEYTKDE
QLESLFQRTAWVFDDKYKRPGYGAYDAFKHAVSDPSILDSLDLNEDEREVLINNINRRLT
PQAVKIRADIEVACYGYEGIDAVKEALRAGLNCSTETMPIKINLIAPPRYVMTTTTLERT
EGLSVLNQAMAVIKEKIEEKRGVFNV

Sequence of entity 5 (G), FASTA

>5K0Y_5 ribosomal protein uS17 (chains G)
MADIQTERAYQKQPTIFQNKKRVLLGETGKEKLPRYYKNIGLGFKTPKEAIEGTYIDKKC
PFTGNVSIRGRILSGVVTKMKMQRTIVIRRDYLHYIRKYNRFEKRHKNMSVHLSPCFRDV
QIGDIVTVGECRPLSKTVRFNVLKVTKAAGTKKQFQKF

Sequence of entity 6 (H), FASTA

>5K0Y_6 ribosomal protein uS9 (chains H)
PLQSVQVFGRKKTATAVAHCKRGNGLIKVNGRPLEMIEPRTLQYKLLEPVLLLGKERFAG
VDIRVRVKGGGHVAQIYAIRQSISKALVAYYQKYVDEASKKEIKDILIQYDRTLLVADPR
RCESKKFGGPGARARYQKSYR

Sequence of entity 7 (I), FASTA

>5K0Y_7 40S ribosomal protein S4 (chains I)
MARGPKKHLKRVAAPKHWMLDKLTSVFAPRPSTGPHKLRECLPLIIFLRNKLKYALTGDE
VKKICMQRFIKIDGKVRADITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRITPEEAK
YKLCKVRKIFVGTKGIPHLVTHDARTIRYPDPLIKMNDTIQIDLETGKITDFIKFDTGNL
CMVTGGANLGRIGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGKGNKPWISLPR
GKGIRLTIAEERDKRLAAKQSSG

Sequence of entity 8 (J), FASTA

>5K0Y_8 ribosomal protein uS14 (chains J)
QQLYWSHPRKFGQGSRSCRVCSNRHGLIRKYGLNMCRQCFRQYAKDIGFIKLD

Sequence of entity 9 (K), FASTA

>5K0Y_9 Ribosomal protein S9 (Predicted) (chains K)
WVCRKTYVTPRRPFEKSRLDQELKLIGEYGLRNKREVWRVKFTLAKIRKAARELLTLDEK
DPRRLFEGNALLRRLVRIGVLDEGKMKLDYILGLKIEDFLERRLQTQVFKLGLAKSIHHA
RVLIRQRHIRVRKQVVNIPSFIVRLDSQKHIDFSLRSPYGGGRPGRVKRKNAKKGQGGAG
AG

Sequence of entity 10 (L), FASTA

>5K0Y_10 ribosomal protein uS13 (chains L)
PEKFQHILRVLNTNIDGRRKIAFAITAIKGVGRRYAHVVLRKADIDLTKRAGELTEDEVE
RVITIMQNPRQYKIPDWFLNRQKDVKDGKYSQVLANGLDNKLREDLERLKKIRAHRGLRH
FWGLRVRGQHTKTTGRR

Sequence of entity 11 (M), FASTA

>5K0Y_11 Eukaryotic translation initiation factor 3 subunit G (chains M)
KKFGNSEFDPPGPNVATTTVSDDVSMTFITSKEDLNCQ

Sequence of entity 12 (O), FASTA

>5K0Y_12 Eukaryotic translation initiation factor 3 subunit G (chains O)
ATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIA
GVSGFGYDHLILNVEWA

Primary citation

eIF3 Peripheral Subunits Rearrangement after mRNA Binding and Start-Codon Recognition. Simonetti, A., Brito Querido, J., Myasnikov, A.G. et al. Mol Cell (2016) 63:206-217. DOI 10.1016/j.molcel.2016.05.033 · PubMed

Other PDB entries of the same protein (UniProt G1T2G4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9H6Y 2.9 Å, Late-stage 48S Initiation Complex (LS48S IC) guided by the trans-RNA
9H74 2.9 Å, Late-stage 48S Initiation Complex with eIF3 (LS48S-eIF3 IC) guided by the trans-RNA
6YAL 3.0 Å, Mammalian 48S late-stage initiation complex with beta-globin mRNA
8P03 3.04 Å, 48S late-stage initiation complex with m6A mRNA
8P09 3.3 Å, 48S late-stage initiation complex with non methylated mRNA
6YAN 3.48 Å, Mammalian 48S late-stage translation initiation complex with histone 4 mRNA
6YAM 3.6 Å, Mammalian 48S late-stage translation initiation complex (LS48S+eIF3 IC) with beta-globin…
9CPA 6.0 Å, Structure of a Mammalian DHX29-bound 43S Pre-initiation Complex

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