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Structure of bacterial 30S-IF1-IF3-mRNA-tRNA translation pre-initiation complex(state-2C)

Electron Microscopy
5.1Å resolution
PDB entry 5lms coloured by chain, front view.
PDB entry 5lms coloured by chain, side view.
PDB entry 5lms coloured by chain, top view.
Source organism: Thermus thermophilus HB8
Assembly composition:
hetero 25-mer (preferred)
Entry contents: 22 distinct polypeptide molecules
3 distinct RNA molecules

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Assemblies

Assembly 1 (preferred)
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Multimeric state: hetero 25-mer
Accessible surface area: 287093.99 Å2
Buried surface area: 116915.11 Å2
Dissociation area: 1,770.21 Å2
Dissociation energy (ΔGdiss): 20.05 kcal/mol
Dissociation entropy (TΔSdiss): 12.75 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-215868

Macromolecules

Small ribosomal subunit protein uS2
Chain: B
Length: 256 amino acids
Theoretical weight: 29.32 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80371 (Residues: 1-256; Coverage: 100%)
Gene names: TTHA0861, rps2, rpsB
Pfam: Ribosomal protein S2
InterPro:
Small ribosomal subunit protein uS2 in PDB entry 5lms, assembly 1, front view.
Small ribosomal subunit protein uS2 in PDB entry 5lms, assembly 1, side view.
Small ribosomal subunit protein uS2 in PDB entry 5lms, assembly 1, top view.
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Small ribosomal subunit protein uS3
Chain: C
Length: 239 amino acids
Theoretical weight: 26.75 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80372 (Residues: 1-239; Coverage: 100%)
Gene names: TTHA1686, rps3, rpsC
Pfam:
InterPro:
Small ribosomal subunit protein uS3 in PDB entry 5lms, assembly 1, front view.
Small ribosomal subunit protein uS3 in PDB entry 5lms, assembly 1, side view.
Small ribosomal subunit protein uS3 in PDB entry 5lms, assembly 1, top view.
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Small ribosomal subunit protein uS4
Chain: D
Length: 209 amino acids
Theoretical weight: 24.37 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80373 (Residues: 1-209; Coverage: 100%)
Gene names: TTHA1665, rps4, rpsD
Pfam:
InterPro:
Small ribosomal subunit protein uS4 in PDB entry 5lms, assembly 1, front view.
Small ribosomal subunit protein uS4 in PDB entry 5lms, assembly 1, side view.
Small ribosomal subunit protein uS4 in PDB entry 5lms, assembly 1, top view.
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Small ribosomal subunit protein uS5
Chain: E
Length: 162 amino acids
Theoretical weight: 17.58 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHQ5 (Residues: 1-162; Coverage: 100%)
Gene names: TTHA1675, rpsE
Pfam:
InterPro:
Small ribosomal subunit protein uS5 in PDB entry 5lms, assembly 1, front view.
Small ribosomal subunit protein uS5 in PDB entry 5lms, assembly 1, side view.
Small ribosomal subunit protein uS5 in PDB entry 5lms, assembly 1, top view.
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Small ribosomal subunit protein bS6
Chain: F
Length: 101 amino acids
Theoretical weight: 11.99 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SLP8 (Residues: 1-101; Coverage: 100%)
Gene names: TTHA0245, rpsF
Pfam: Ribosomal protein S6
InterPro:
Small ribosomal subunit protein bS6 in PDB entry 5lms, assembly 1, front view.
Small ribosomal subunit protein bS6 in PDB entry 5lms, assembly 1, side view.
Small ribosomal subunit protein bS6 in PDB entry 5lms, assembly 1, top view.
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Small ribosomal subunit protein uS7
Chain: G
Length: 156 amino acids
Theoretical weight: 18.05 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P17291 (Residues: 1-156; Coverage: 100%)
Gene names: TTHA1696, rps7, rpsG
Pfam: Ribosomal protein S7p/S5e
InterPro:
Small ribosomal subunit protein uS7 in PDB entry 5lms, assembly 1, front view.
Small ribosomal subunit protein uS7 in PDB entry 5lms, assembly 1, side view.
Small ribosomal subunit protein uS7 in PDB entry 5lms, assembly 1, top view.
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Small ribosomal subunit protein uS8
Chain: H
Length: 138 amino acids
Theoretical weight: 15.87 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P0DOY9 (Residues: 1-138; Coverage: 100%)
Gene names: TTHA1678, rpsH
Pfam: Ribosomal protein S8
InterPro:
Small ribosomal subunit protein uS8 in PDB entry 5lms, assembly 1, front view.
Small ribosomal subunit protein uS8 in PDB entry 5lms, assembly 1, side view.
Small ribosomal subunit protein uS8 in PDB entry 5lms, assembly 1, top view.
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Small ribosomal subunit protein uS9
Chain: I
Length: 128 amino acids
Theoretical weight: 14.41 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80374 (Residues: 1-128; Coverage: 100%)
Gene names: TTHA1464, rps9, rpsI
Pfam: Ribosomal protein S9/S16
InterPro:
Small ribosomal subunit protein uS9 in PDB entry 5lms, assembly 1, front view.
Small ribosomal subunit protein uS9 in PDB entry 5lms, assembly 1, side view.
Small ribosomal subunit protein uS9 in PDB entry 5lms, assembly 1, top view.
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Small ribosomal subunit protein uS10
Chain: J
Length: 105 amino acids
Theoretical weight: 11.95 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHN7 (Residues: 1-105; Coverage: 100%)
Gene names: TTHA1693, rpsJ
Pfam: Ribosomal protein S10p/S20e
InterPro:
Small ribosomal subunit protein uS10 in PDB entry 5lms, assembly 1, front view.
Small ribosomal subunit protein uS10 in PDB entry 5lms, assembly 1, side view.
Small ribosomal subunit protein uS10 in PDB entry 5lms, assembly 1, top view.
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Small ribosomal subunit protein uS11
Chain: K
Length: 129 amino acids
Theoretical weight: 13.74 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80376 (Residues: 1-129; Coverage: 100%)
Gene names: TTHA1666, rps11, rpsK
Pfam: Ribosomal protein S11
InterPro:
Small ribosomal subunit protein uS11 in PDB entry 5lms, assembly 1, front view.
Small ribosomal subunit protein uS11 in PDB entry 5lms, assembly 1, side view.
Small ribosomal subunit protein uS11 in PDB entry 5lms, assembly 1, top view.
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Small ribosomal subunit protein uS12
Chain: L
Length: 132 amino acids
Theoretical weight: 14.64 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHN3 (Residues: 1-132; Coverage: 100%)
Gene names: TTHA1697, rpsL
Pfam: Ribosomal protein S12/S23
InterPro:
Small ribosomal subunit protein uS12 in PDB entry 5lms, assembly 1, front view.
Small ribosomal subunit protein uS12 in PDB entry 5lms, assembly 1, side view.
Small ribosomal subunit protein uS12 in PDB entry 5lms, assembly 1, top view.
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Small ribosomal subunit protein uS13
Chain: M
Length: 126 amino acids
Theoretical weight: 14.34 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80377 (Residues: 1-126; Coverage: 100%)
Gene names: TTHA1667, rps13, rpsM
Pfam: Ribosomal protein S13/S18
InterPro:
Small ribosomal subunit protein uS13 in PDB entry 5lms, assembly 1, front view.
Small ribosomal subunit protein uS13 in PDB entry 5lms, assembly 1, side view.
Small ribosomal subunit protein uS13 in PDB entry 5lms, assembly 1, top view.
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Small ribosomal subunit protein uS14
Chain: N
Length: 61 amino acids
Theoretical weight: 7.16 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P0DOY6 (Residues: 1-61; Coverage: 100%)
Gene names: TTHA1679, rpsN, rpsZ
Pfam: Ribosomal protein S14p/S29e
InterPro:
Small ribosomal subunit protein uS14 in PDB entry 5lms, assembly 1, front view.
Small ribosomal subunit protein uS14 in PDB entry 5lms, assembly 1, side view.
Small ribosomal subunit protein uS14 in PDB entry 5lms, assembly 1, top view.
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Small ribosomal subunit protein uS15
Chain: O
Length: 89 amino acids
Theoretical weight: 10.58 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SJ76 (Residues: 1-89; Coverage: 100%)
Gene names: TTHA1138, rpsO
Pfam: Ribosomal protein S15
InterPro:
Small ribosomal subunit protein uS15 in PDB entry 5lms, assembly 1, front view.
Small ribosomal subunit protein uS15 in PDB entry 5lms, assembly 1, side view.
Small ribosomal subunit protein uS15 in PDB entry 5lms, assembly 1, top view.
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Small ribosomal subunit protein bS16
Chain: P
Length: 88 amino acids
Theoretical weight: 10.41 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SJH3 (Residues: 1-88; Coverage: 100%)
Gene names: TTHA1035, rpsP
Pfam: Ribosomal protein S16
InterPro:
Small ribosomal subunit protein bS16 in PDB entry 5lms, assembly 1, front view.
Small ribosomal subunit protein bS16 in PDB entry 5lms, assembly 1, side view.
Small ribosomal subunit protein bS16 in PDB entry 5lms, assembly 1, top view.
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Small ribosomal subunit protein uS17
Chain: Q
Length: 105 amino acids
Theoretical weight: 12.33 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P0DOY7 (Residues: 1-105; Coverage: 100%)
Gene names: TTHA1683, rpsQ
Pfam: Ribosomal protein S17
InterPro:
Small ribosomal subunit protein uS17 in PDB entry 5lms, assembly 1, front view.
Small ribosomal subunit protein uS17 in PDB entry 5lms, assembly 1, side view.
Small ribosomal subunit protein uS17 in PDB entry 5lms, assembly 1, top view.
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Small ribosomal subunit protein bS18
Chain: R
Length: 88 amino acids
Theoretical weight: 10.26 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SLQ0 (Residues: 1-88; Coverage: 100%)
Gene names: TTHA0243, rpsR
Pfam: Ribosomal protein S18
InterPro:
Small ribosomal subunit protein bS18 in PDB entry 5lms, assembly 1, front view.
Small ribosomal subunit protein bS18 in PDB entry 5lms, assembly 1, side view.
Small ribosomal subunit protein bS18 in PDB entry 5lms, assembly 1, top view.
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Small ribosomal subunit protein uS19
Chain: S
Length: 93 amino acids
Theoretical weight: 10.61 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHP2 (Residues: 1-93; Coverage: 100%)
Gene names: TTHA1688, rpsS
Pfam: Ribosomal protein S19
InterPro:
Small ribosomal subunit protein uS19 in PDB entry 5lms, assembly 1, front view.
Small ribosomal subunit protein uS19 in PDB entry 5lms, assembly 1, side view.
Small ribosomal subunit protein uS19 in PDB entry 5lms, assembly 1, top view.
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Small ribosomal subunit protein bS20
Chain: T
Length: 106 amino acids
Theoretical weight: 11.74 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80380 (Residues: 1-106; Coverage: 100%)
Gene names: TTHA1397, rps20, rpsT
Pfam: Ribosomal protein S20
InterPro:
Small ribosomal subunit protein bS20 in PDB entry 5lms, assembly 1, front view.
Small ribosomal subunit protein bS20 in PDB entry 5lms, assembly 1, side view.
Small ribosomal subunit protein bS20 in PDB entry 5lms, assembly 1, top view.
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Small ribosomal subunit protein bTHX
Chain: V
Length: 27 amino acids
Theoretical weight: 3.35 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SIH3 (Residues: 1-27; Coverage: 100%)
Gene names: TTHA1396, rpsU
Pfam: 30S ribosomal protein Thx
InterPro:
Small ribosomal subunit protein bTHX in PDB entry 5lms, assembly 1, front view.
Small ribosomal subunit protein bTHX in PDB entry 5lms, assembly 1, side view.
Small ribosomal subunit protein bTHX in PDB entry 5lms, assembly 1, top view.
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Translation initiation factor IF-1
Chain: W
Length: 72 amino acids
Theoretical weight: 8.25 KDa
Source organism: Thermus thermophilus HB8
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q5SHR1 (Residues: 1-72; Coverage: 100%)
Gene names: TTHA1669, infA
Pfam: Translation initiation factor 1A / IF-1
InterPro:
Translation initiation factor IF-1 in PDB entry 5lms, assembly 1, front view.
Translation initiation factor IF-1 in PDB entry 5lms, assembly 1, side view.
Translation initiation factor IF-1 in PDB entry 5lms, assembly 1, top view.
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Translation initiation factor IF-3
Chain: X
Length: 171 amino acids
Theoretical weight: 19.9 KDa
Source organism: Thermus thermophilus HB8
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q5SKU2 (Residues: 1-171; Coverage: 100%)
Gene names: TTHA0551, infC
Pfam:
InterPro:
Translation initiation factor IF-3 in PDB entry 5lms, assembly 1, front view.
Translation initiation factor IF-3 in PDB entry 5lms, assembly 1, side view.
Translation initiation factor IF-3 in PDB entry 5lms, assembly 1, top view.
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RNA chain A
Name: 16S ribosomal RNA
Representative chains: A
Length: 1522 nucleotides
Theoretical weight: 493.96 KDa
Rfam: Bacterial small subunit ribosomal RNA
16S ribosomal RNA in PDB entry 5lms, assembly 1, front view.
16S ribosomal RNA in PDB entry 5lms, assembly 1, side view.
16S ribosomal RNA in PDB entry 5lms, assembly 1, top view.
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RNA chain Y
Name: Messenger RNA
Representative chains: Y
Length: 42 nucleotides
Theoretical weight: 13.47 KDa
Messenger RNA in PDB entry 5lms, assembly 1, front view.
Messenger RNA in PDB entry 5lms, assembly 1, side view.
Messenger RNA in PDB entry 5lms, assembly 1, top view.
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RNA chain Z
Name: tRNAi
Representative chains: Z
Length: 77 nucleotides
Theoretical weight: 24.86 KDa
Rfam: tRNA
tRNAi in PDB entry 5lms, assembly 1, front view.
tRNAi in PDB entry 5lms, assembly 1, side view.
tRNAi in PDB entry 5lms, assembly 1, top view.
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