3JAP image
Deposition Date 2015-06-18
Release Date 2015-08-12
Last Version Date 2024-02-21
Entry Detail
PDB ID:
3JAP
Keywords:
TRANSLATION
Title:
Structure of a partial yeast 48S preinitiation complex in closed conformation
Biological Source:
Source Organism(s):
Saccharomyces cerevisiae (Taxon ID: 4932)
Kluyveromyces lactis (Taxon ID: 28985)
synthetic construct (Taxon ID: 32630)
Expression System(s):
Escherichia coli bl21, Saccharomyces cerevisiae
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
4.90 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
3JAP validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:Met-tRNAi (U31:A39 variant)
Chain IDs:A (auth: 1)
Chain Length:75
Number of Molecules:1
Biological Source:Kluyveromyces lactis
Polymer Type:polyribonucleotide
Molecule:18S rRNA
Chain IDs:B (auth: 2)
Chain Length:1781
Number of Molecules:1
Biological Source:Kluyveromyces lactis
Polymer Type:polyribonucleotide
Molecule:mRNA
Chain IDs:C (auth: 3)
Chain Length:25
Number of Molecules:1
Biological Source:synthetic construct
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:uS2
Gene (Uniprot):RPS0
Chain IDs:D (auth: A)
Chain Length:254
Number of Molecules:1
Biological Source:Kluyveromyces lactis
UniProt ID:Q6CN12 Pfam ID:PF00318
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:eS1
Gene (Uniprot):RPS1
Chain IDs:E (auth: B)
Chain Length:82
Number of Molecules:1
Biological Source:Kluyveromyces lactis
UniProt ID:Q6CWD0 Pfam ID:PF01015
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:uS5
Gene (Uniprot):KLLA0_F09812g
Chain IDs:F (auth: C)
Chain Length:259
Number of Molecules:1
Biological Source:Kluyveromyces lactis
UniProt ID:Q6CKL3 Pfam ID:PF00333, PF03719
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:uS3
Gene (Uniprot):KLLA0_D08305g
Chain IDs:G (auth: D)
Chain Length:237
Number of Molecules:1
Biological Source:Kluyveromyces lactis
UniProt ID:Q6CRK7 Pfam ID:PF00189, PF07650
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:eS4
Gene (Uniprot):KLLA0_B03652g
Chain IDs:H (auth: E)
Chain Length:261
Number of Molecules:1
Biological Source:Kluyveromyces lactis
UniProt ID:Q6CWJ2 Pfam ID:PF08071, PF01479, PF00900, PF00467, PF16121
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:uS7
Gene (Uniprot):KLLA0_D10659g
Chain IDs:I (auth: F)
Chain Length:227
Number of Molecules:1
Biological Source:Kluyveromyces lactis
UniProt ID:Q6CRA3 Pfam ID:PF00177
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:eS6
Gene (Uniprot):RPS6
Chain IDs:J (auth: G)
Chain Length:326
Number of Molecules:1
Biological Source:Kluyveromyces lactis
UniProt ID:Q6CM04 Pfam ID:PF01092
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:eS7
Gene (Uniprot):KLLA0_C13519g
Chain IDs:K (auth: H)
Chain Length:190
Number of Molecules:1
Biological Source:Kluyveromyces lactis
UniProt ID:Q6CTD6 Pfam ID:PF01251
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:eS8
Gene (Uniprot):KLLA0_E20461g
Chain IDs:L (auth: I)
Chain Length:201
Number of Molecules:1
Biological Source:Kluyveromyces lactis
UniProt ID:Q6CMG3 Pfam ID:PF01201
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:uS4
Gene (Uniprot):KLLA0_E23673g
Chain IDs:M (auth: J)
Chain Length:188
Number of Molecules:1
Biological Source:Kluyveromyces lactis
UniProt ID:Q6CM18 Pfam ID:PF00163, PF01479
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:eS10
Gene (Uniprot):KLLA0_B08173g
Chain IDs:N (auth: K)
Chain Length:527
Number of Molecules:1
Biological Source:Kluyveromyces lactis
UniProt ID:Q6CVZ5 Pfam ID:PF03501
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:uS17
Gene (Uniprot):KLLA0_A10483g
Chain IDs:O (auth: L)
Chain Length:285
Number of Molecules:1
Biological Source:Kluyveromyces lactis
UniProt ID:Q6CX80 Pfam ID:PF16205, PF00366
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:eS12
Gene (Uniprot):KLLA0_F00352g
Chain IDs:P (auth: M)
Chain Length:134
Number of Molecules:1
Biological Source:Kluyveromyces lactis
UniProt ID:Q6CLU4 Pfam ID:PF01248
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:uS15
Gene (Uniprot):KLLA0_F18040g
Chain IDs:Q (auth: N)
Chain Length:151
Number of Molecules:1
Biological Source:Kluyveromyces lactis
UniProt ID:Q6CJK0 Pfam ID:PF08069, PF00312
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:uS11
Gene (Uniprot):RPS14
Chain IDs:R (auth: O)
Chain Length:137
Number of Molecules:1
Biological Source:Kluyveromyces lactis
UniProt ID:P27069 Pfam ID:PF00411
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:uS19
Gene (Uniprot):KLLA0_F07843g
Chain IDs:S (auth: P)
Chain Length:652
Number of Molecules:1
Biological Source:Kluyveromyces lactis
UniProt ID:Q6CKV4 Pfam ID:PF00203
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:uS9
Gene (Uniprot):RPS16
Chain IDs:T (auth: Q)
Chain Length:347
Number of Molecules:1
Biological Source:Kluyveromyces lactis
UniProt ID:Q875N2 Pfam ID:PF00380
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:eS17
Gene (Uniprot):KLLA0_B01474g
Chain IDs:U (auth: R)
Chain Length:136
Number of Molecules:1
Biological Source:Kluyveromyces lactis
UniProt ID:Q6CWU3 Pfam ID:PF00833
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:uS13
Gene (Uniprot):KLLA0_B01562g
Chain IDs:V (auth: S)
Chain Length:146
Number of Molecules:1
Biological Source:Kluyveromyces lactis
UniProt ID:Q6CWT9 Pfam ID:PF00416
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:eS19
Gene (Uniprot):KLLA0_A07194g
Chain IDs:W (auth: T)
Chain Length:144
Number of Molecules:1
Biological Source:Kluyveromyces lactis
UniProt ID:Q6CXM0 Pfam ID:PF01090
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:uS10
Gene (Uniprot):KLLA0_F25542g
Chain IDs:X (auth: U)
Chain Length:117
Number of Molecules:1
Biological Source:Kluyveromyces lactis
UniProt ID:Q6CIM1 Pfam ID:PF00338
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:eS21
Gene (Uniprot):RPS21
Chain IDs:Y (auth: V)
Chain Length:87
Number of Molecules:1
Biological Source:Kluyveromyces lactis
UniProt ID:Q6CXT6 Pfam ID:PF01249
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:uS8
Gene (Uniprot):RPS22
Chain IDs:Z (auth: W)
Chain Length:130
Number of Molecules:1
Biological Source:Kluyveromyces lactis
UniProt ID:Q6CW21 Pfam ID:PF00410
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:uS12
Gene (Uniprot):KLLA0_B11231g
Chain IDs:AA (auth: X)
Chain Length:145
Number of Molecules:1
Biological Source:Kluyveromyces lactis
UniProt ID:F2Z602 Pfam ID:PF00164
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:eS24
Gene (Uniprot):KLLA0_C07755g
Chain IDs:BA (auth: Y)
Chain Length:135
Number of Molecules:1
Biological Source:Kluyveromyces lactis
UniProt ID:Q6CU44 Pfam ID:PF01282
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:eS25
Gene (Uniprot):KLLA0_B06182g
Chain IDs:CA (auth: Z)
Chain Length:108
Number of Molecules:1
Biological Source:Kluyveromyces lactis
UniProt ID:Q6CW78 Pfam ID:PF03297
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:eS26
Gene (Uniprot):KLLA0_D05115g
Chain IDs:DA (auth: a)
Chain Length:254
Number of Molecules:1
Biological Source:Kluyveromyces lactis
UniProt ID:Q6CS01 Pfam ID:PF01283
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:eS27
Gene (Uniprot):KLLA0_E11661g
Chain IDs:EA (auth: b)
Chain Length:82
Number of Molecules:1
Biological Source:Kluyveromyces lactis
UniProt ID:Q6CNL2 Pfam ID:PF01667
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:eS28
Gene (Uniprot):RPS28
Chain IDs:FA (auth: c)
Chain Length:259
Number of Molecules:1
Biological Source:Kluyveromyces lactis
UniProt ID:P33285 Pfam ID:PF01200
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:uS14
Gene (Uniprot):RPS29
Chain IDs:GA (auth: d)
Chain Length:237
Number of Molecules:1
Biological Source:Kluyveromyces lactis
UniProt ID:Q6CPG3 Pfam ID:PF00253
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:eS30
Gene (Uniprot):KLLA0_C04809g
Chain IDs:HA (auth: e)
Chain Length:261
Number of Molecules:1
Biological Source:Kluyveromyces lactis
UniProt ID:Q6CUH5 Pfam ID:PF04758
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:eS31
Gene (Uniprot):ubi3
Chain IDs:IA (auth: f)
Chain Length:227
Number of Molecules:1
Biological Source:Kluyveromyces lactis
UniProt ID:P69061 Pfam ID:PF00240, PF01599
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RACK1
Gene (Uniprot):KLLA0_E12277g
Chain IDs:JA (auth: g)
Chain Length:326
Number of Molecules:1
Biological Source:Kluyveromyces lactis
UniProt ID:Q6CNI7 Pfam ID:PF00400
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:eL41
Gene (Uniprot):RPL41A
Chain IDs:KA (auth: h)
Chain Length:190
Number of Molecules:1
Biological Source:Kluyveromyces lactis
UniProt ID:P0CX86 Pfam ID:PF05162
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:eIF1A
Gene (Uniprot):TIF11
Chain IDs:LA (auth: i)
Chain Length:201
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P38912 Pfam ID:PF01176
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:eIF2 alpha
Gene (Uniprot):SUI2
Chain IDs:MA (auth: j)
Chain Length:188
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P20459 Pfam ID:PF00575, PF07541
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:eIF2 gamma
Gene (Uniprot):GCD11
Chain IDs:NA (auth: k)
Chain Length:527
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P32481 Pfam ID:PF00009, PF03144, PF09173
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:eIF2 beta
Gene (Uniprot):SUI3
Chain IDs:OA (auth: l)
Chain Length:285
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P09064 Pfam ID:PF01873
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:eIF1
Gene (Uniprot):SUI1
Chain IDs:PA (auth: m)
Chain Length:134
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P32911 Pfam ID:PF01253
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:eIF3a
Gene (Uniprot):RPG1
Chain IDs:QA (auth: o)
Chain Length:137
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P38249 Pfam ID:PF22591
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:eIF3c
Gene (Uniprot):NIP1
Chain IDs:RA (auth: p)
Chain Length:652
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P32497 Pfam ID:PF05470, PF01399
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:eIF3i
Gene (Uniprot):TIF34
Chain IDs:SA (auth: q)
Chain Length:347
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P40217 Pfam ID:PF00400
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:eIF3b
Gene (Uniprot):PRT1
Chain IDs:TA (auth: r)
Chain Length:136
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P06103
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:eIF3g
Gene (Uniprot):TIF35
Chain IDs:UA (auth: s)
Chain Length:146
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:A6ZZ25 Pfam ID:PF12353
Ligand Molecules
GCP
MET
MG
ZN
Primary Citation
Conformational Differences between Open and Closed States of the Eukaryotic Translation Initiation Complex.
Mol.Cell 59 399 412 (2015)
PMID: 26212456 DOI: 10.1016/j.molcel.2015.06.033

Abstact

Translation initiation in eukaryotes begins with the formation of a pre-initiation complex (PIC) containing the 40S ribosomal subunit, eIF1, eIF1A, eIF3, ternary complex (eIF2-GTP-Met-tRNAi), and eIF5. The PIC, in an open conformation, attaches to the 5' end of the mRNA and scans to locate the start codon, whereupon it closes to arrest scanning. We present single particle cryo-electron microscopy (cryo-EM) reconstructions of 48S PICs from yeast in these open and closed states, at 6.0 Å and 4.9 Å, respectively. These reconstructions show eIF2β as well as a configuration of eIF3 that appears to encircle the 40S, occupying part of the subunit interface. Comparison of the complexes reveals a large conformational change in the 40S head from an open mRNA latch conformation to a closed one that constricts the mRNA entry channel and narrows the P site to enclose tRNAi, thus elucidating key events in start codon recognition.

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Protein

Chemical

Disease

Primary Citation of related structures
3J81
3JAM
3JAQ
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