› 7unv

Electron Microscopy
2.7Å resolution

Pseudomonas aeruginosa 70S ribosome initiation complex bound to IF2-GDPCP (structure II-A)

Released:
DOI: 10.2210/pdb7unv/pdb
PDB entry 7unv coloured by chain, front view.
PDB entry 7unv coloured by chain, side view.
PDB entry 7unv coloured by chain, top view.
Source organism: Pseudomonas aeruginosa PAO1
Primary publication:
Compact IF2 allows initiator tRNA accommodation into the P site and gates the ribosome to elongation
Basu RS, Sherman MB, Gagnon MG
Nat Commun 13 3388- (2022)
Related structures: EMD-26634

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 57-mer (preferred)
PDBe Complex ID:
PDB-CPX-103749 (preferred)
Entry contents:
52 distinct polypeptide molecules
5 distinct RNA molecules
Macromolecules (57 distinct):
Small ribosomal subunit protein uS2 Chain: b
Molecule details ›
Chain: b
Length: 246 amino acids
Theoretical weight: 27.38 KDa
Source organism: Pseudomonas aeruginosa PAO1
UniProt:
  • Canonical: O82850 (Residues: 1-246; Coverage: 100%)
Gene names: PA3656, rpsB
Sequence domains: Ribosomal protein S2
Small ribosomal subunit protein uS3 Chain: c
Molecule details ›
Chain: c
Length: 228 amino acids
Theoretical weight: 25.89 KDa
Source organism: Pseudomonas aeruginosa PAO1
UniProt:
  • Canonical: Q9HWE1 (Residues: 1-228; Coverage: 100%)
Gene names: PA4257, rpsC
Sequence domains:
Small ribosomal subunit protein uS4 Chain: d
Molecule details ›
Chain: d
Length: 206 amino acids
Theoretical weight: 23.32 KDa
Source organism: Pseudomonas aeruginosa PAO1
UniProt:
  • Canonical: O52759 (Residues: 1-206; Coverage: 100%)
Gene names: PA4239, rpsD
Sequence domains:
Small ribosomal subunit protein uS5 Chain: e
Molecule details ›
Chain: e
Length: 166 amino acids
Theoretical weight: 17.65 KDa
Source organism: Pseudomonas aeruginosa PAO1
UniProt:
  • Canonical: Q9HWF2 (Residues: 1-166; Coverage: 100%)
Gene names: PA4246, rpsE
Sequence domains:
Small ribosomal subunit protein bS6 Chain: f
Molecule details ›
Chain: f
Length: 139 amino acids
Theoretical weight: 16.19 KDa
Source organism: Pseudomonas aeruginosa PAO1
UniProt:
  • Canonical: Q9HUM9 (Residues: 1-139; Coverage: 100%)
Gene names: PA4935, rpsF
Sequence domains: Ribosomal protein S6
Small ribosomal subunit protein uS7 Chain: g
Molecule details ›
Chain: g
Length: 156 amino acids
Theoretical weight: 17.54 KDa
Source organism: Pseudomonas aeruginosa PAO1
UniProt:
  • Canonical: Q9HWD1 (Residues: 1-156; Coverage: 100%)
Gene names: PA4267, rpsG
Sequence domains: Ribosomal protein S7p/S5e
Small ribosomal subunit protein uS8 Chain: h
Molecule details ›
Chain: h
Length: 130 amino acids
Theoretical weight: 14.19 KDa
Source organism: Pseudomonas aeruginosa PAO1
UniProt:
  • Canonical: Q9HWE9 (Residues: 1-130; Coverage: 100%)
Gene names: PA4249, rpsH
Sequence domains: Ribosomal protein S8
Small ribosomal subunit protein uS9 Chain: i
Molecule details ›
Chain: i
Length: 130 amino acids
Theoretical weight: 14.64 KDa
Source organism: Pseudomonas aeruginosa PAO1
UniProt:
  • Canonical: Q9HVY3 (Residues: 1-130; Coverage: 100%)
Gene names: PA4432, rpsI
Sequence domains: Ribosomal protein S9/S16
Small ribosomal subunit protein uS10 Chain: j
Molecule details ›
Chain: j
Length: 103 amino acids
Theoretical weight: 11.79 KDa
Source organism: Pseudomonas aeruginosa PAO1
UniProt:
  • Canonical: Q9HWD4 (Residues: 1-103; Coverage: 100%)
Gene names: PA4264, rpsJ
Sequence domains: Ribosomal protein S10p/S20e
Small ribosomal subunit protein uS11 Chain: k
Molecule details ›
Chain: k
Length: 129 amino acids
Theoretical weight: 13.65 KDa
Source organism: Pseudomonas aeruginosa PAO1
UniProt:
  • Canonical: Q9HWF8 (Residues: 1-129; Coverage: 100%)
Gene names: PA4240, rpsK
Sequence domains: Ribosomal protein S11
Small ribosomal subunit protein uS12 Chain: l
Molecule details ›
Chain: l
Length: 123 amino acids
Theoretical weight: 13.83 KDa
Source organism: Pseudomonas aeruginosa PAO1
UniProt:
  • Canonical: Q9HWD0 (Residues: 1-123; Coverage: 100%)
Gene names: PA4268, rpsL
Sequence domains: Ribosomal protein S12/S23
Small ribosomal subunit protein uS13 Chain: m
Molecule details ›
Chain: m
Length: 118 amino acids
Theoretical weight: 13.29 KDa
Source organism: Pseudomonas aeruginosa PAO1
UniProt:
  • Canonical: Q9HWF7 (Residues: 1-118; Coverage: 100%)
Gene names: PA4241, rpsM
Sequence domains: Ribosomal protein S13/S18
Small ribosomal subunit protein uS14 Chain: n
Molecule details ›
Chain: n
Length: 101 amino acids
Theoretical weight: 11.59 KDa
Source organism: Pseudomonas aeruginosa PAO1
UniProt:
  • Canonical: Q9HWE8 (Residues: 1-101; Coverage: 100%)
Gene names: PA4250, rpsN
Sequence domains: Ribosomal protein S14p/S29e
Small ribosomal subunit protein uS15 Chain: o
Molecule details ›
Chain: o
Length: 89 amino acids
Theoretical weight: 10.14 KDa
Source organism: Pseudomonas aeruginosa PAO1
UniProt:
  • Canonical: Q9HV58 (Residues: 1-89; Coverage: 100%)
Gene names: PA4741, rpsO
Sequence domains: Ribosomal protein S15
Small ribosomal subunit protein bS16 Chain: p
Molecule details ›
Chain: p
Length: 83 amino acids
Theoretical weight: 9.22 KDa
Source organism: Pseudomonas aeruginosa PAO1
UniProt:
  • Canonical: Q9HXP9 (Residues: 1-83; Coverage: 100%)
Gene names: PA3745, rpsP
Sequence domains: Ribosomal protein S16
Small ribosomal subunit protein uS17 Chain: q
Molecule details ›
Chain: q
Length: 88 amino acids
Theoretical weight: 10.11 KDa
Source organism: Pseudomonas aeruginosa PAO1
UniProt:
  • Canonical: Q9HWE4 (Residues: 1-88; Coverage: 100%)
Gene names: PA4254, rpsQ
Sequence domains: Ribosomal protein S17
Small ribosomal subunit protein bS18 Chain: r
Molecule details ›
Chain: r
Length: 76 amino acids
Theoretical weight: 8.89 KDa
Source organism: Pseudomonas aeruginosa PAO1
UniProt:
  • Canonical: Q9HUN0 (Residues: 1-76; Coverage: 100%)
Gene names: PA4934, rpsR
Sequence domains: Ribosomal protein S18
Small ribosomal subunit protein uS19 Chain: s
Molecule details ›
Chain: s
Length: 91 amino acids
Theoretical weight: 10.38 KDa
Source organism: Pseudomonas aeruginosa PAO1
UniProt:
  • Canonical: Q9HWD9 (Residues: 1-91; Coverage: 100%)
Gene names: PA4259, rpsS
Sequence domains: Ribosomal protein S19
Small ribosomal subunit protein bS20 Chain: t
Molecule details ›
Chain: t
Length: 91 amino acids
Theoretical weight: 9.94 KDa
Source organism: Pseudomonas aeruginosa PAO1
UniProt:
  • Canonical: Q9HVM1 (Residues: 1-91; Coverage: 100%)
Gene names: PA4563, rpsT
Sequence domains: Ribosomal protein S20
Small ribosomal subunit protein bS21 Chain: u
Molecule details ›
Chain: u
Length: 71 amino acids
Theoretical weight: 8.51 KDa
Source organism: Pseudomonas aeruginosa PAO1
UniProt:
  • Canonical: Q9I5V8 (Residues: 1-71; Coverage: 100%)
Gene names: PA0579, rpsU
Sequence domains: Ribosomal protein S21
Translation initiation factor IF-2 Chain: x
Molecule details ›
Chain: x
Length: 840 amino acids
Theoretical weight: 91.05 KDa
Source organism: Pseudomonas aeruginosa PAO1
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9HV55 (Residues: 1-840; Coverage: 100%)
Gene names: PA4744, infB
Sequence domains:
Large ribosomal subunit protein uL2 Chain: C
Molecule details ›
Chain: C
Length: 273 amino acids
Theoretical weight: 29.64 KDa
Source organism: Pseudomonas aeruginosa PAO1
UniProt:
  • Canonical: Q9HWD8 (Residues: 1-273; Coverage: 100%)
Gene names: PA4260, rplB
Sequence domains:
Large ribosomal subunit protein uL3 Chain: D
Molecule details ›
Chain: D
Length: 211 amino acids
Theoretical weight: 22.63 KDa
Source organism: Pseudomonas aeruginosa PAO1
UniProt:
  • Canonical: Q9HWD5 (Residues: 1-211; Coverage: 100%)
Gene names: PA4263, rplC
Sequence domains: Ribosomal protein L3
Large ribosomal subunit protein uL4 Chain: E
Molecule details ›
Chain: E
Length: 200 amino acids
Theoretical weight: 21.67 KDa
Source organism: Pseudomonas aeruginosa PAO1
UniProt:
  • Canonical: Q9HWD6 (Residues: 1-200; Coverage: 100%)
Gene names: PA4262, rplD
Sequence domains: Ribosomal protein L4/L1 family
Large ribosomal subunit protein uL5 Chain: F
Molecule details ›
Chain: F
Length: 179 amino acids
Theoretical weight: 20.42 KDa
Source organism: Pseudomonas aeruginosa PAO1
UniProt:
  • Canonical: Q9HWE7 (Residues: 1-179; Coverage: 100%)
Gene names: PA4251, rplE
Sequence domains:
Large ribosomal subunit protein uL6 Chain: G
Molecule details ›
Chain: G
Length: 177 amino acids
Theoretical weight: 19.13 KDa
Source organism: Pseudomonas aeruginosa PAO1
UniProt:
  • Canonical: Q9HWF0 (Residues: 1-177; Coverage: 100%)
Gene names: PA4248, rplF
Sequence domains: Ribosomal protein L6
Large ribosomal subunit protein bL9 Chain: H
Molecule details ›
Chain: H
Length: 148 amino acids
Theoretical weight: 15.55 KDa
Source organism: Pseudomonas aeruginosa PAO1
UniProt:
  • Canonical: Q9HUN2 (Residues: 1-148; Coverage: 100%)
Gene names: PA4932, rplI
Sequence domains:
Large ribosomal subunit protein uL10 Chain: I
Molecule details ›
Chain: I
Length: 166 amino acids
Theoretical weight: 17.66 KDa
Source organism: Pseudomonas aeruginosa PAO1
UniProt:
  • Canonical: Q9HWC7 (Residues: 1-166; Coverage: 100%)
Gene names: PA4272, rplJ
Sequence domains: Ribosomal protein L10
Large ribosomal subunit protein uL11 Chain: J
Molecule details ›
Chain: J
Length: 143 amino acids
Theoretical weight: 14.93 KDa
Source organism: Pseudomonas aeruginosa PAO1
UniProt:
  • Canonical: Q9HWC5 (Residues: 1-143; Coverage: 100%)
Gene names: PA4274, rplK
Sequence domains:
Large ribosomal subunit protein uL13 Chain: L
Molecule details ›
Chain: L
Length: 142 amino acids
Theoretical weight: 16.06 KDa
Source organism: Pseudomonas aeruginosa PAO1
UniProt:
  • Canonical: Q9HVY2 (Residues: 1-142; Coverage: 100%)
Gene names: PA4433, rplM
Sequence domains: Ribosomal protein L13
Large ribosomal subunit protein uL14 Chain: M
Molecule details ›
Chain: M
Length: 122 amino acids
Theoretical weight: 13.44 KDa
Source organism: Pseudomonas aeruginosa PAO1
UniProt:
  • Canonical: Q9HWE5 (Residues: 1-122; Coverage: 100%)
Gene names: PA4253, rplN
Sequence domains: Ribosomal protein L14p/L23e
Large ribosomal subunit protein uL15 Chain: N
Molecule details ›
Chain: N
Length: 144 amino acids
Theoretical weight: 15.2 KDa
Source organism: Pseudomonas aeruginosa PAO1
UniProt:
  • Canonical: Q9HWF4 (Residues: 1-144; Coverage: 100%)
Gene names: PA4244, rplO
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
Large ribosomal subunit protein uL16 Chain: O
Molecule details ›
Chain: O
Length: 137 amino acids
Theoretical weight: 15.43 KDa
Source organism: Pseudomonas aeruginosa PAO1
UniProt:
  • Canonical: Q9HWE2 (Residues: 1-137; Coverage: 100%)
Gene names: PA4256, rplP
Sequence domains: Ribosomal protein L16p/L10e
Large ribosomal subunit protein bL17 Chain: P
Molecule details ›
Chain: P
Length: 129 amino acids
Theoretical weight: 14.53 KDa
Source organism: Pseudomonas aeruginosa PAO1
UniProt:
  • Canonical: O52761 (Residues: 1-129; Coverage: 100%)
Gene names: PA4237, rplQ
Sequence domains: Ribosomal protein L17
Large ribosomal subunit protein uL18 Chain: Q
Molecule details ›
Chain: Q
Length: 116 amino acids
Theoretical weight: 12.69 KDa
Source organism: Pseudomonas aeruginosa PAO1
UniProt:
  • Canonical: Q9HWF1 (Residues: 1-116; Coverage: 100%)
Gene names: PA4247, rplR
Sequence domains: Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
Large ribosomal subunit protein bL19 Chain: R
Molecule details ›
Chain: R
Length: 116 amino acids
Theoretical weight: 13.06 KDa
Source organism: Pseudomonas aeruginosa PAO1
UniProt:
  • Canonical: Q9HXQ2 (Residues: 1-116; Coverage: 100%)
Gene names: PA3742, rplS
Sequence domains: Ribosomal protein L19
Large ribosomal subunit protein bL20 Chain: S
Molecule details ›
Chain: S
Length: 118 amino acids
Theoretical weight: 13.4 KDa
Source organism: Pseudomonas aeruginosa PAO1
UniProt:
  • Canonical: Q9I0A2 (Residues: 1-118; Coverage: 100%)
Gene names: PA2741, rplT
Sequence domains: Ribosomal protein L20
Large ribosomal subunit protein bL21 Chain: T
Molecule details ›
Chain: T
Length: 103 amino acids
Theoretical weight: 11.68 KDa
Source organism: Pseudomonas aeruginosa PAO1
UniProt:
  • Canonical: Q9HVL6 (Residues: 1-103; Coverage: 100%)
Gene names: PA4568, rplU
Sequence domains: Ribosomal prokaryotic L21 protein
Large ribosomal subunit protein uL22 Chain: U
Molecule details ›
Chain: U
Length: 110 amino acids
Theoretical weight: 11.94 KDa
Source organism: Pseudomonas aeruginosa PAO1
UniProt:
  • Canonical: A0A1T1HVZ5 (Residues: 1-110; Coverage: 100%)
Gene names: MF4836_18985, rplV
Sequence domains: Ribosomal protein L22p/L17e
Large ribosomal subunit protein uL23 Chain: V
Molecule details ›
Chain: V
Length: 99 amino acids
Theoretical weight: 10.97 KDa
Source organism: Pseudomonas aeruginosa PAO1
UniProt:
  • Canonical: Q9HWD7 (Residues: 1-99; Coverage: 100%)
Gene names: PA4261, rplW
Sequence domains: Ribosomal protein L23
Large ribosomal subunit protein uL24 Chain: W
Molecule details ›
Chain: W
Length: 104 amino acids
Theoretical weight: 11.49 KDa
Source organism: Pseudomonas aeruginosa PAO1
UniProt:
  • Canonical: Q9HWE6 (Residues: 1-104; Coverage: 100%)
Gene names: PA4252, rplX
Sequence domains:
Large ribosomal subunit protein bL25 Chain: X
Molecule details ›
Chain: X
Length: 204 amino acids
Theoretical weight: 21.99 KDa
Source organism: Pseudomonas aeruginosa PAO1
UniProt:
  • Canonical: Q9HVC4 (Residues: 1-204; Coverage: 100%)
Gene names: PA4671, ctc, rplY
Sequence domains:
Large ribosomal subunit protein bL27 Chain: Y
Molecule details ›
Chain: Y
Length: 85 amino acids
Theoretical weight: 9.01 KDa
Source organism: Pseudomonas aeruginosa PAO1
UniProt:
  • Canonical: Q9HVL7 (Residues: 1-85; Coverage: 100%)
Gene names: PA4567, rpmA
Sequence domains: Ribosomal L27 protein
Large ribosomal subunit protein bL28 Chain: Z
Molecule details ›
Chain: Z
Length: 78 amino acids
Theoretical weight: 9.09 KDa
Source organism: Pseudomonas aeruginosa PAO1
UniProt:
  • Canonical: Q9HTN8 (Residues: 1-78; Coverage: 100%)
Gene names: PA5316, rpmB
Sequence domains: Ribosomal L28 family
Large ribosomal subunit protein uL29 Chain: 1
Molecule details ›
Chain: 1
Length: 63 amino acids
Theoretical weight: 7.21 KDa
Source organism: Pseudomonas aeruginosa PAO1
UniProt:
  • Canonical: Q9HWE3 (Residues: 1-63; Coverage: 100%)
Gene names: PA4255, rpmC
Sequence domains: Ribosomal L29 protein
Large ribosomal subunit protein uL30 Chain: 2
Molecule details ›
Chain: 2
Length: 58 amino acids
Theoretical weight: 6.49 KDa
Source organism: Pseudomonas aeruginosa PAO1
UniProt:
  • Canonical: Q9HWF3 (Residues: 1-58; Coverage: 100%)
Gene names: PA4245, rpmD
Sequence domains: Ribosomal protein L30p/L7e
Large ribosomal subunit protein bL31 Chain: 3
Molecule details ›
Chain: 3
Length: 71 amino acids
Theoretical weight: 7.93 KDa
Source organism: Pseudomonas aeruginosa PAO1
UniProt:
  • Canonical: Q9HUD0 (Residues: 1-71; Coverage: 100%)
Gene names: PA5049, rpmE
Sequence domains: Ribosomal protein L31
Large ribosomal subunit protein bL32 Chain: 4
Molecule details ›
Chain: 4
Length: 60 amino acids
Theoretical weight: 6.81 KDa
Source organism: Pseudomonas aeruginosa PAO1
UniProt:
  • Canonical: Q9HZN4 (Residues: 1-60; Coverage: 100%)
Gene names: PA2970, rpmF
Sequence domains: Ribosomal L32p protein family
Large ribosomal subunit protein bL33 Chain: 5
Molecule details ›
Chain: 5
Length: 51 amino acids
Theoretical weight: 6.06 KDa
Source organism: Pseudomonas aeruginosa PAO1
UniProt:
  • Canonical: Q9HTN9 (Residues: 1-51; Coverage: 100%)
Gene names: PA5315, rpmG
Sequence domains: Ribosomal protein L33
Large ribosomal subunit protein bL34 Chain: 6
Molecule details ›
Chain: 6
Length: 44 amino acids
Theoretical weight: 5.23 KDa
Source organism: Pseudomonas aeruginosa PAO1
UniProt:
  • Canonical: P29436 (Residues: 1-44; Coverage: 100%)
Gene names: PA5570, rpmH
Sequence domains: Ribosomal protein L34
Large ribosomal subunit protein bL35 Chain: 7
Molecule details ›
Chain: 7
Length: 64 amino acids
Theoretical weight: 7.39 KDa
Source organism: Pseudomonas aeruginosa PAO1
UniProt:
  • Canonical: Q9I0A1 (Residues: 1-64; Coverage: 100%)
Gene names: PA2742, rpmI
Sequence domains: Ribosomal protein L35
Large ribosomal subunit protein bL36A Chain: 8
Molecule details ›
Chain: 8
Length: 38 amino acids
Theoretical weight: 4.45 KDa
Source organism: Pseudomonas aeruginosa PAO1
UniProt:
  • Canonical: Q9HWF6 (Residues: 1-38; Coverage: 100%)
Gene names: PA4242, rpmJ
Sequence domains: Ribosomal protein L36
16S ribosomal RNA Chain: a
Molecule details ›
Chain: a
Length: 1536 nucleotides
Theoretical weight: 497.97 KDa
Sequence domains: Bacterial small subunit ribosomal RNA
P-site initiator tRNA Chain: v
Molecule details ›
Chain: v
Length: 77 nucleotides
Theoretical weight: 24.85 KDa
Sequence domains: tRNA
Messenger RNA Chain: w
Molecule details ›
Chain: w
Length: 24 nucleotides
Theoretical weight: 7.8 KDa
23S ribosomal RNA Chain: A
Molecule details ›
Chain: A
Length: 2891 nucleotides
Theoretical weight: 937.13 KDa
Sequence domains: Bacterial large subunit ribosomal RNA
5S ribosomal RNA Chain: B
Molecule details ›
Chain: B
Length: 120 nucleotides
Theoretical weight: 38.6 KDa
Sequence domains: 5S ribosomal RNA

Ligands and Environments

4 bound ligands:
Ligand MG 595 x MG
Ligand FME 1 x FME
Ligand GCP 1 x GCP
Ligand ZN 2 x ZN
15 modified residues:
Ligand 7MG 2 x 7MG
Ligand 2MG 5 x 2MG
Ligand 5MC 3 x 5MC
Ligand 4OC 1 x 4OC
Ligand UR3 2 x UR3
Ligand MA6 2 x MA6
Ligand 4SU 1 x 4SU
Ligand 5MU 2 x 5MU
Ligand PSU 1 x PSU
Ligand 1MG 1 x 1MG
Ligand 6MZ 2 x 6MZ
Ligand OMG 1 x OMG
Ligand OMC 1 x OMC
Ligand 2MA 1 x 2MA
Ligand OMU 1 x OMU

Experiments and Validation Details

Entry percentile scores
Resolution: 2.7Å
Relevant EMDB volumes: EMD-26634
Expression system: Escherichia coli

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