PDBe 3jap

Electron Microscopy
4.9Å resolution

Structure of a partial yeast 48S preinitiation complex in closed conformation

Released:

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero 47-mer (preferred)
Entry contents:
44 distinct polypeptide molecules
3 distinct RNA molecules
Macromolecules (47 distinct):
40S ribosomal protein S1 Chain: B
Molecule details ›
Chain: B
Length: 255 amino acids
Theoretical weight: 28.97 KDa
Source organism: Kluyveromyces lactis
UniProt:
  • Canonical: Q6CWD0 (Residues: 1-255; Coverage: 100%)
Gene names: KLLA0B05060g, RPS1
Sequence domains: Ribosomal S3Ae family
40S ribosomal protein S4 Chain: E
Molecule details ›
Chain: E
Length: 261 amino acids
Theoretical weight: 29.62 KDa
Source organism: Kluyveromyces lactis
UniProt:
  • Canonical: Q6CWJ2 (Residues: 1-261; Coverage: 100%)
Gene name: KLLA0_B03652g
Sequence domains:
40S ribosomal protein S6 Chain: G
Molecule details ›
Chain: G
Length: 236 amino acids
Theoretical weight: 26.97 KDa
Source organism: Kluyveromyces lactis
UniProt:
  • Canonical: Q6CM04 (Residues: 1-236; Coverage: 100%)
Gene names: KLLA0E24090g, RPS6
Sequence domains: Ribosomal protein S6e
40S ribosomal protein S7 Chain: H
Molecule details ›
Chain: H
Length: 190 amino acids
Theoretical weight: 21.74 KDa
Source organism: Kluyveromyces lactis
UniProt:
  • Canonical: Q6CTD6 (Residues: 1-190; Coverage: 100%)
Gene name: KLLA0_C13519g
Sequence domains: Ribosomal protein S7e
40S ribosomal protein S8 Chain: I
Molecule details ›
Chain: I
Length: 201 amino acids
Theoretical weight: 22.64 KDa
Source organism: Kluyveromyces lactis
UniProt:
  • Canonical: Q6CMG3 (Residues: 1-201; Coverage: 100%)
Gene name: KLLA0_E20461g
Sequence domains: Ribosomal protein S8e
40S ribosomal protein S0 Chain: A
Molecule details ›
Chain: A
Length: 254 amino acids
Theoretical weight: 28.26 KDa
Source organism: Kluyveromyces lactis
UniProt:
  • Canonical: Q6CN12 (Residues: 1-254; Coverage: 100%)
Gene names: KLLA0E16171g, RPS0
Sequence domains: Ribosomal protein S2
KLLA0D08305p Chain: D
Molecule details ›
Chain: D
Length: 237 amino acids
Theoretical weight: 26.3 KDa
Source organism: Kluyveromyces lactis
UniProt:
  • Canonical: Q6CRK7 (Residues: 1-237; Coverage: 100%)
Gene name: KLLA0_D08305g
Sequence domains:
KLLA0E23673p Chain: J
Molecule details ›
Chain: J
Length: 188 amino acids
Theoretical weight: 21.59 KDa
Source organism: Kluyveromyces lactis
UniProt:
  • Canonical: Q6CM18 (Residues: 1-188; Coverage: 100%)
Gene name: KLLA0_E23673g
Sequence domains:
KLLA0F09812p Chain: C
Molecule details ›
Chain: C
Length: 259 amino acids
Theoretical weight: 27.65 KDa
Source organism: Kluyveromyces lactis
UniProt:
  • Canonical: Q6CKL3 (Residues: 1-259; Coverage: 100%)
Gene name: KLLA0_F09812g
Sequence domains:
KLLA0D10659p Chain: F
Molecule details ›
Chain: F
Length: 227 amino acids
Theoretical weight: 25.39 KDa
Source organism: Kluyveromyces lactis
UniProt:
  • Canonical: Q6CRA3 (Residues: 1-227; Coverage: 100%)
Gene name: KLLA0_D10659g
Sequence domains: Ribosomal protein S7p/S5e
40S ribosomal protein S22 Chain: W
Molecule details ›
Chain: W
Length: 130 amino acids
Theoretical weight: 14.65 KDa
Source organism: Kluyveromyces lactis
UniProt:
  • Canonical: Q6CW21 (Residues: 1-130; Coverage: 100%)
Gene names: KLLA0B07601g, RPS22
Sequence domains: Ribosomal protein S8
40S ribosomal protein S16 Chain: Q
Molecule details ›
Chain: Q
Length: 143 amino acids
Theoretical weight: 15.87 KDa
Source organism: Kluyveromyces lactis
UniProt:
  • Canonical: Q875N2 (Residues: 1-143; Coverage: 100%)
Gene names: KLLA0E22077g, RPS16
Sequence domains: Ribosomal protein S9/S16
Eukaryotic translation initiation factor eIF-1 Chain: m
Molecule details ›
Chain: m
Length: 108 amino acids
Theoretical weight: 12.33 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P32911 (Residues: 1-108; Coverage: 100%)
Gene names: N0905, RFR1, SUI1, YNL244C
Sequence domains: Translation initiation factor SUI1
60S ribosomal protein L41-A Chain: h
Molecule details ›
Chain: h
Length: 25 amino acids
Theoretical weight: 3.35 KDa
Source organism: Kluyveromyces lactis
UniProt:
  • Canonical: P0CX86 (Residues: 1-25; Coverage: 100%)
Gene names: D1290, RPL41A, RPL47A, YDL184C, YL41A
Sequence domains: Ribosomal protein L41
KLLA0B08173p Chain: K
Molecule details ›
Chain: K
Length: 106 amino acids
Theoretical weight: 12.58 KDa
Source organism: Kluyveromyces lactis
UniProt:
  • Canonical: Q6CVZ5 (Residues: 1-106; Coverage: 100%)
Gene name: KLLA0_B08173g
Sequence domains: Plectin/S10 domain
40S ribosomal protein S12 Chain: M
Molecule details ›
Chain: M
Length: 134 amino acids
Theoretical weight: 14.47 KDa
Source organism: Kluyveromyces lactis
UniProt:
  • Canonical: Q6CLU4 (Residues: 1-134; Coverage: 100%)
Gene name: KLLA0_F00352g
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
KLLA0B01474p Chain: R
Molecule details ›
Chain: R
Length: 136 amino acids
Theoretical weight: 15.72 KDa
Source organism: Kluyveromyces lactis
UniProt:
  • Canonical: Q6CWU3 (Residues: 1-136; Coverage: 100%)
Gene name: KLLA0_B01474g
Sequence domains: Ribosomal S17
KLLA0A07194p Chain: T
Molecule details ›
Chain: T
Length: 144 amino acids
Theoretical weight: 15.88 KDa
Source organism: Kluyveromyces lactis
UniProt:
  • Canonical: Q6CXM0 (Residues: 1-144; Coverage: 100%)
Gene name: KLLA0_A07194g
Sequence domains: Ribosomal protein S19e
40S ribosomal protein S21 Chain: V
Molecule details ›
Chain: V
Length: 87 amino acids
Theoretical weight: 9.8 KDa
Source organism: Kluyveromyces lactis
UniProt:
  • Canonical: Q6CXT6 (Residues: 1-87; Coverage: 100%)
Gene names: KLLA0A05700g, RPS21
Sequence domains: Ribosomal protein S21e
40S ribosomal protein S24 Chain: Y
Molecule details ›
Chain: Y
Length: 135 amino acids
Theoretical weight: 15.19 KDa
Source organism: Kluyveromyces lactis
UniProt:
  • Canonical: Q6CU44 (Residues: 1-135; Coverage: 100%)
Gene name: KLLA0_C07755g
Sequence domains: Ribosomal protein S24e
KLLA0B06182p Chain: Z
Molecule details ›
Chain: Z
Length: 108 amino acids
Theoretical weight: 12 KDa
Source organism: Kluyveromyces lactis
UniProt:
  • Canonical: Q6CW78 (Residues: 1-108; Coverage: 100%)
Gene name: KLLA0_B06182g
Sequence domains: S25 ribosomal protein
40S ribosomal protein S26 Chain: a
Molecule details ›
Chain: a
Length: 119 amino acids
Theoretical weight: 13.54 KDa
Source organism: Kluyveromyces lactis
UniProt:
  • Canonical: Q6CS01 (Residues: 1-119; Coverage: 100%)
Gene name: KLLA0_D05115g
Sequence domains: Ribosomal protein S26e
40S ribosomal protein S27 Chain: b
Molecule details ›
Chain: b
Length: 82 amino acids
Theoretical weight: 8.88 KDa
Source organism: Kluyveromyces lactis
UniProt:
  • Canonical: Q6CNL2 (Residues: 1-82; Coverage: 100%)
Gene name: KLLA0_E11661g
Sequence domains: Ribosomal protein S27
40S ribosomal protein S28 Chain: c
Molecule details ›
Chain: c
Length: 67 amino acids
Theoretical weight: 7.55 KDa
Source organism: Kluyveromyces lactis
UniProt:
  • Canonical: P33285 (Residues: 1-67; Coverage: 100%)
Gene names: KLLA0F20383g, RPS28
Sequence domains: Ribosomal protein S28e
40S ribosomal protein S30 Chain: e
Molecule details ›
Chain: e
Length: 63 amino acids
Theoretical weight: 7.14 KDa
Source organism: Kluyveromyces lactis
UniProt:
  • Canonical: Q6CUH5 (Residues: 1-63; Coverage: 100%)
Gene name: KLLA0_C04809g
Sequence domains: Ribosomal protein S30
Ubiquitin-40S ribosomal protein S27a Chain: f
Molecule details ›
Chain: f
Length: 150 amino acids
Theoretical weight: 17.11 KDa
Source organism: Kluyveromyces lactis
UniProt:
  • Canonical: P69061 (Residues: 1-150; Coverage: 100%)
Gene names: KLLA0D18304g, ubi3
Sequence domains:
KLLA0F25542p Chain: U
Molecule details ›
Chain: U
Length: 117 amino acids
Theoretical weight: 13.34 KDa
Source organism: Kluyveromyces lactis
UniProt:
  • Canonical: Q6CIM1 (Residues: 1-117; Coverage: 100%)
Gene name: KLLA0_F25542g
Sequence domains: Ribosomal protein S10p/S20e
40S ribosomal protein S14 Chain: O
Molecule details ›
Chain: O
Length: 137 amino acids
Theoretical weight: 14.53 KDa
Source organism: Kluyveromyces lactis
UniProt:
  • Canonical: P27069 (Residues: 1-137; Coverage: 100%)
Gene names: CRY1, KLLA0B07623g, RPS14
Sequence domains: Ribosomal protein S11
KLLA0B11231p Chain: X
Molecule details ›
Chain: X
Length: 145 amino acids
Theoretical weight: 16.05 KDa
Source organism: Kluyveromyces lactis
UniProt:
  • Canonical: F2Z602 (Residues: 1-145; Coverage: 100%)
Gene name: KLLA0_B11231g
Sequence domains: Ribosomal protein S12/S23
KLLA0B01562p Chain: S
Molecule details ›
Chain: S
Length: 146 amino acids
Theoretical weight: 17.08 KDa
Source organism: Kluyveromyces lactis
UniProt:
  • Canonical: Q6CWT9 (Residues: 1-146; Coverage: 100%)
Gene name: KLLA0_B01562g
Sequence domains: Ribosomal protein S13/S18
40S ribosomal protein S29 Chain: d
Molecule details ›
Chain: d
Length: 56 amino acids
Theoretical weight: 6.66 KDa
Source organism: Kluyveromyces lactis
UniProt:
  • Canonical: Q6CPG3 (Residues: 1-56; Coverage: 100%)
Gene names: KLLA0E05071g, RPS29
Sequence domains: Ribosomal protein S14p/S29e
KLLA0F18040p Chain: N
Molecule details ›
Chain: N
Length: 151 amino acids
Theoretical weight: 16.99 KDa
Source organism: Kluyveromyces lactis
UniProt:
  • Canonical: Q6CJK0 (Residues: 1-151; Coverage: 100%)
Gene name: KLLA0_F18040g
Sequence domains:
KLLA0A10483p Chain: L
Molecule details ›
Chain: L
Length: 156 amino acids
Theoretical weight: 17.84 KDa
Source organism: Kluyveromyces lactis
UniProt:
  • Canonical: Q6CX80 (Residues: 1-156; Coverage: 100%)
Gene name: KLLA0_A10483g
Sequence domains:
KLLA0F07843p Chain: P
Molecule details ›
Chain: P
Length: 142 amino acids
Theoretical weight: 15.99 KDa
Source organism: Kluyveromyces lactis
UniProt:
  • Canonical: Q6CKV4 (Residues: 1-142; Coverage: 100%)
Gene name: KLLA0_F07843g
Sequence domains: Ribosomal protein S19
KLLA0E12277p Chain: g
Molecule details ›
Chain: g
Length: 326 amino acids
Theoretical weight: 35.83 KDa
Source organism: Kluyveromyces lactis
UniProt:
  • Canonical: Q6CNI7 (Residues: 1-326; Coverage: 100%)
Gene name: KLLA0_E12277g
Sequence domains: WD domain, G-beta repeat
Eukaryotic translation initiation factor 1A Chain: i
Molecule details ›
Chain: i
Length: 153 amino acids
Theoretical weight: 17.46 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P38912 (Residues: 1-153; Coverage: 100%)
Gene names: TIF11, YM8156.02C, YMR260C
Sequence domains: Translation initiation factor 1A / IF-1
Eukaryotic translation initiation factor 3 subunit A Chain: o
Molecule details ›
Chain: o
Length: 588 amino acids
Theoretical weight: 64.75 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P38249 (Residues: 1-495; Coverage: 51%)
Gene names: RPG1, TIF32, YBR0734, YBR079C
Eukaryotic translation initiation factor 3 subunit B Chain: r
Molecule details ›
Chain: r
Length: 31 amino acids
Theoretical weight: 3.96 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P06103 (Residues: 704-734; Coverage: 4%)
Gene names: CDC63, PRT1, YOR361C
Eukaryotic translation initiation factor 3 subunit C Chain: p
Molecule details ›
Chain: p
Length: 652 amino acids
Theoretical weight: 73.4 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P32497 (Residues: 251-812; Coverage: 69%)
Gene names: NIP1, YM9924.01C, YM9952.11C, YMR309C
Sequence domains: PCI domain
Eukaryotic translation initiation factor 3 subunit G Chain: s
Molecule details ›
Chain: s
Length: 52 amino acids
Theoretical weight: 5.94 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: A6ZZ25 (Residues: 45-96; Coverage: 19%)
Gene names: SCY_1313, TIF35
Eukaryotic translation initiation factor 3 subunit I Chain: q
Molecule details ›
Chain: q
Length: 347 amino acids
Theoretical weight: 38.8 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P40217 (Residues: 1-347; Coverage: 100%)
Gene names: TIF34, YM9375.16C, YMR146C
Sequence domains: WD domain, G-beta repeat
Eukaryotic translation initiation factor 2 subunit beta Chain: l
Molecule details ›
Chain: l
Length: 285 amino acids
Theoretical weight: 31.63 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P09064 (Residues: 1-285; Coverage: 100%)
Gene names: SUI3, TIF212, YPL237W
Sequence domains: Domain found in IF2B/IF5
Eukaryotic translation initiation factor 2 subunit alpha Chain: j
Molecule details ›
Chain: j
Length: 304 amino acids
Theoretical weight: 34.76 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P20459 (Residues: 1-304; Coverage: 100%)
Gene names: J1429, SUI2, TIF211, YJR007W
Sequence domains:
Eukaryotic translation initiation factor 2 subunit gamma Chain: k
Molecule details ›
Chain: k
Length: 527 amino acids
Theoretical weight: 57.94 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P32481 (Residues: 1-527; Coverage: 100%)
Gene names: GCD11, TIF213, YER025W
Sequence domains:
Messenger RNA Chain: 3
Molecule details ›
Chain: 3
Length: 25 nucleotides
Theoretical weight: 7.79 KDa
18S Ribosomal RNA Chain: 2
Molecule details ›
Chain: 2
Length: 1781 nucleotides
Theoretical weight: 573.81 KDa
Met-tRNAi (U31:A39 variant) Chain: 1
Molecule details ›
Chain: 1
Length: 75 nucleotides
Theoretical weight: 24.22 KDa

Ligands and Environments


No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 4.9Å
Relevant EMDB volumes: EMD-3048
Expression systems:
  • Escherichia coli BL21
  • Saccharomyces cerevisiae