› 5o2r

Electron Microscopy
3.4Å resolution

Cryo-EM structure of the proline-rich antimicrobial peptide Api137 bound to the terminating ribosome

Released:
DOI: 10.2210/pdb5o2r/pdb
PDB entry 5o2r coloured by chain, front view.
PDB entry 5o2r coloured by chain, side view.
PDB entry 5o2r coloured by chain, top view.
Source organisms:
Primary publication:
An antimicrobial peptide that inhibits translation by trapping release factors on the ribosome.
Florin T, Maracci C, Graf M, Karki P, Klepacki D, Berninghausen O, Beckmann R, Vázquez-Laslop N, Wilson DN, Rodnina MV, Mankin AS
OpenAccess logo Nat Struct Mol Biol 24 752-757 (2017)
PMID: 28741611
Related structures: EMD-3730

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 58-mer (preferred)
PDBe Complex ID:
PDB-CPX-526038 (preferred)
Entry contents:
53 distinct polypeptide molecules
5 distinct RNA molecules
Macromolecules (58 distinct):
Large ribosomal subunit protein uL2 Chain: C
Molecule details ›
Chain: C
Length: 271 amino acids
Theoretical weight: 29.66 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P60422 (Residues: 2-272; Coverage: 99%)
Gene names: JW3279, b3317, rplB
Sequence domains:
Large ribosomal subunit protein uL3 Chain: D
Molecule details ›
Chain: D
Length: 209 amino acids
Theoretical weight: 22.28 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P60438 (Residues: 1-209; Coverage: 100%)
Gene names: JW3282, b3320, rplC
Sequence domains: Ribosomal protein L3
Large ribosomal subunit protein uL4 Chain: E
Molecule details ›
Chain: E
Length: 201 amino acids
Theoretical weight: 22.12 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P60723 (Residues: 1-201; Coverage: 100%)
Gene names: JW3281, b3319, eryA, rplD
Sequence domains: Ribosomal protein L4/L1 family
Large ribosomal subunit protein uL5 Chain: F
Molecule details ›
Chain: F
Length: 177 amino acids
Theoretical weight: 20.07 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P62399 (Residues: 2-178; Coverage: 99%)
Gene names: JW3270, b3308, rplE
Sequence domains:
Large ribosomal subunit protein uL6 Chain: G
Molecule details ›
Chain: G
Length: 176 amino acids
Theoretical weight: 18.8 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0AG55 (Residues: 2-177; Coverage: 99%)
Gene names: JW3267, b3305, rplF
Sequence domains: Ribosomal protein L6
Large ribosomal subunit protein bL9 Chain: H
Molecule details ›
Chain: H
Length: 149 amino acids
Theoretical weight: 15.79 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7R1 (Residues: 1-149; Coverage: 100%)
Gene names: JW4161, b4203, rplI
Sequence domains:
Large ribosomal subunit protein uL11 Chain: I
Molecule details ›
Chain: I
Length: 141 amino acids
Theoretical weight: 14.76 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7J7 (Residues: 2-142; Coverage: 99%)
Gene names: JW3946, b3983, relC, rplK
Sequence domains:
Large ribosomal subunit protein uL13 Chain: J
Molecule details ›
Chain: J
Length: 142 amino acids
Theoretical weight: 16.05 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0AA10 (Residues: 1-142; Coverage: 100%)
Gene names: JW3200, b3231, rplM
Sequence domains: Ribosomal protein L13
Large ribosomal subunit protein uL14 Chain: K
Molecule details ›
Chain: K
Length: 122 amino acids
Theoretical weight: 13.45 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0ADY3 (Residues: 1-122; Coverage: 99%)
Gene names: JW3272, b3310, rplN
Sequence domains: Ribosomal protein L14p/L23e
Large ribosomal subunit protein uL15 Chain: L
Molecule details ›
Chain: L
Length: 143 amino acids
Theoretical weight: 14.88 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P02413 (Residues: 2-144; Coverage: 99%)
Gene names: JW3263, b3301, rplO
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
Large ribosomal subunit protein uL16 Chain: M
Molecule details ›
Chain: M
Length: 136 amino acids
Theoretical weight: 15.31 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0ADY7 (Residues: 1-136; Coverage: 100%)
Gene names: JW3275, b3313, rplP
Sequence domains: Ribosomal protein L16p/L10e
Large ribosomal subunit protein bL17 Chain: N
Molecule details ›
Chain: N
Length: 120 amino acids
Theoretical weight: 13.72 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0AG44 (Residues: 1-120; Coverage: 95%)
Gene names: JW3256, b3294, rplQ
Sequence domains: Ribosomal protein L17
Large ribosomal subunit protein uL18 Chain: O
Molecule details ›
Chain: O
Length: 116 amino acids
Theoretical weight: 12.66 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0C018 (Residues: 2-117; Coverage: 99%)
Gene names: JW3266, b3304, rplR
Sequence domains: Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
Large ribosomal subunit protein bL19 Chain: P
Molecule details ›
Chain: P
Length: 114 amino acids
Theoretical weight: 13.03 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7K6 (Residues: 2-115; Coverage: 99%)
Gene names: JW2587, b2606, rplS
Sequence domains: Ribosomal protein L19
Large ribosomal subunit protein bL20 Chain: Q
Molecule details ›
Chain: Q
Length: 117 amino acids
Theoretical weight: 13.4 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7L3 (Residues: 2-118; Coverage: 99%)
Gene names: JW1706, b1716, pdzA, rplT
Sequence domains: Ribosomal protein L20
Large ribosomal subunit protein bL21 Chain: R
Molecule details ›
Chain: R
Length: 103 amino acids
Theoretical weight: 11.59 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0AG48 (Residues: 1-103; Coverage: 100%)
Gene names: JW3153, b3186, rplU
Sequence domains: Ribosomal prokaryotic L21 protein
Large ribosomal subunit protein uL22 Chain: S
Molecule details ›
Chain: S
Length: 110 amino acids
Theoretical weight: 12.25 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P61175 (Residues: 1-110; Coverage: 100%)
Gene names: JW3277, b3315, eryB, rplV
Sequence domains: Ribosomal protein L22p/L17e
Large ribosomal subunit protein uL23 Chain: T
Molecule details ›
Chain: T
Length: 93 amino acids
Theoretical weight: 10.55 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0ADZ0 (Residues: 1-93; Coverage: 93%)
Gene names: JW3280, b3318, rplW
Sequence domains: Ribosomal protein L23
Large ribosomal subunit protein uL24 Chain: U
Molecule details ›
Chain: U
Length: 102 amino acids
Theoretical weight: 11.08 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P60624 (Residues: 2-103; Coverage: 98%)
Gene names: JW3271, b3309, rplX
Sequence domains:
Large ribosomal subunit protein bL25 Chain: V
Molecule details ›
Chain: V
Length: 94 amino acids
Theoretical weight: 10.71 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P68919 (Residues: 1-94; Coverage: 100%)
Gene names: JW2173, b2185, rplY
Sequence domains: Ribosomal L25p family
Large ribosomal subunit protein bL27 Chain: W
Molecule details ›
Chain: W
Length: 75 amino acids
Theoretical weight: 8.17 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7L8 (Residues: 11-85; Coverage: 88%)
Gene names: JW3152, b3185, rpmA
Sequence domains: Ribosomal L27 protein
Large ribosomal subunit protein bL28 Chain: X
Molecule details ›
Chain: X
Length: 77 amino acids
Theoretical weight: 8.9 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7M2 (Residues: 2-78; Coverage: 99%)
Gene names: JW3612, b3637, rpmB
Sequence domains: Ribosomal L28 family
Large ribosomal subunit protein uL29 Chain: Y
Molecule details ›
Chain: Y
Length: 63 amino acids
Theoretical weight: 7.29 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7M6 (Residues: 1-63; Coverage: 100%)
Gene names: JW3274, b3312, rpmC
Sequence domains: Ribosomal L29 protein
Large ribosomal subunit protein uL30 Chain: Z
Molecule details ›
Chain: Z
Length: 58 amino acids
Theoretical weight: 6.42 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0AG51 (Residues: 2-59; Coverage: 98%)
Gene names: JW3264, b3302, rpmD
Sequence domains: Ribosomal protein L30p/L7e
Large ribosomal subunit protein bL32 Chain: 0
Molecule details ›
Chain: 0
Length: 56 amino acids
Theoretical weight: 6.33 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7N4 (Residues: 2-57; Coverage: 98%)
Gene names: JW1075, b1089, rpmF
Sequence domains: Ribosomal L32p protein family
Large ribosomal subunit protein bL33 Chain: 1
Molecule details ›
Chain: 1
Length: 50 amino acids
Theoretical weight: 5.81 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7N9 (Residues: 4-53; Coverage: 91%)
Gene names: JW3611, b3636, rpmG
Sequence domains: Ribosomal protein L33
Large ribosomal subunit protein bL34 Chain: 2
Molecule details ›
Chain: 2
Length: 46 amino acids
Theoretical weight: 5.4 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7P5 (Residues: 1-46; Coverage: 100%)
Gene names: JW3680, b3703, rimA, rpmH, ssaF
Sequence domains: Ribosomal protein L34
Large ribosomal subunit protein bL35 Chain: 3
Molecule details ›
Chain: 3
Length: 64 amino acids
Theoretical weight: 7.18 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7Q1 (Residues: 2-65; Coverage: 99%)
Gene names: JW1707, b1717, rpmI
Sequence domains: Ribosomal protein L35
Large ribosomal subunit protein bL36A Chain: 4
Molecule details ›
Chain: 4
Length: 38 amino acids
Theoretical weight: 4.38 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7Q6 (Residues: 1-38; Coverage: 100%)
Gene names: JW3261, b3299, rpmJ
Sequence domains: Ribosomal protein L36
Large ribosomal subunit protein uL10 Chain: 5
Molecule details ›
Chain: 5
Length: 131 amino acids
Theoretical weight: 14.11 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7J3 (Residues: 1-131; Coverage: 79%)
Gene names: JW3948, b3985, rplJ
Sequence domains: Ribosomal protein L10
Large ribosomal subunit protein bL31 Chain: 6
Molecule details ›
Chain: 6
Length: 66 amino acids
Theoretical weight: 7.52 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7M9 (Residues: 1-66; Coverage: 94%)
Gene names: JW3907, b3936, rpmE
Sequence domains: Ribosomal protein L31
Small ribosomal subunit protein uS2 Chain: b
Molecule details ›
Chain: b
Length: 218 amino acids
Theoretical weight: 24.25 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7V0 (Residues: 9-226; Coverage: 91%)
Gene names: JW0164, b0169, rpsB
Sequence domains: Ribosomal protein S2
Small ribosomal subunit protein uS3 Chain: c
Molecule details ›
Chain: c
Length: 206 amino acids
Theoretical weight: 23.08 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7V3 (Residues: 2-207; Coverage: 88%)
Gene names: JW3276, b3314, rpsC
Sequence domains:
Small ribosomal subunit protein uS4 Chain: d
Molecule details ›
Chain: d
Length: 205 amino acids
Theoretical weight: 23.38 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7V8 (Residues: 2-206; Coverage: 100%)
Gene names: JW3258, b3296, ramA, rpsD
Sequence domains:
Small ribosomal subunit protein uS5 Chain: e
Molecule details ›
Chain: e
Length: 157 amino acids
Theoretical weight: 16.53 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7W1 (Residues: 10-166; Coverage: 94%)
Gene names: JW3265, b3303, rpsE, spc
Sequence domains:
Small ribosomal subunit protein bS6, non-modified isoform Chain: f
Molecule details ›
Chain: f
Length: 100 amino acids
Theoretical weight: 11.67 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P02358 (Residues: 1-100; Coverage: 74%)
Gene names: JW4158, b4200, rpsF
Sequence domains: Ribosomal protein S6
Small ribosomal subunit protein uS7 Chain: g
Molecule details ›
Chain: g
Length: 151 amino acids
Theoretical weight: 16.86 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P02359 (Residues: 2-152; Coverage: 84%)
Gene names: JW3303, b3341, rpsG
Sequence domains: Ribosomal protein S7p/S5e
Small ribosomal subunit protein uS8 Chain: h
Molecule details ›
Chain: h
Length: 129 amino acids
Theoretical weight: 14.02 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7W7 (Residues: 2-130; Coverage: 99%)
Gene names: JW3268, b3306, rpsH
Sequence domains: Ribosomal protein S8
Small ribosomal subunit protein uS9 Chain: i
Molecule details ›
Chain: i
Length: 127 amino acids
Theoretical weight: 14.55 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7X3 (Residues: 4-130; Coverage: 98%)
Gene names: JW3199, b3230, rpsI
Sequence domains: Ribosomal protein S9/S16
Small ribosomal subunit protein uS10 Chain: j
Molecule details ›
Chain: j
Length: 98 amino acids
Theoretical weight: 11.2 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7R5 (Residues: 5-102; Coverage: 95%)
Gene names: JW3283, b3321, nusE, rpsJ
Sequence domains: Ribosomal protein S10p/S20e
Small ribosomal subunit protein uS11 Chain: k
Molecule details ›
Chain: k
Length: 116 amino acids
Theoretical weight: 12.39 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7R9 (Residues: 13-128; Coverage: 90%)
Gene names: JW3259, b3297, rpsK
Sequence domains: Ribosomal protein S11
Small ribosomal subunit protein uS12 Chain: l
Molecule details ›
Chain: l
Length: 123 amino acids
Theoretical weight: 13.64 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7S3 (Residues: 2-124; Coverage: 99%)
Gene names: JW3304, b3342, rpsL, strA
Sequence domains: Ribosomal protein S12/S23
Small ribosomal subunit protein uS13 Chain: m
Molecule details ›
Chain: m
Length: 114 amino acids
Theoretical weight: 12.63 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7S9 (Residues: 2-115; Coverage: 97%)
Gene names: JW3260, b3298, rpsM
Sequence domains: Ribosomal protein S13/S18
Small ribosomal subunit protein uS14 Chain: n
Molecule details ›
Chain: n
Length: 101 amino acids
Theoretical weight: 11.55 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0AG59 (Residues: 2-35, 36-101; Coverage: 99%)
Gene names: JW3269, b3307, rpsN
Sequence domains: Ribosomal protein S14p/S29e
Small ribosomal subunit protein uS15 Chain: o
Molecule details ›
Chain: o
Length: 88 amino acids
Theoretical weight: 10.16 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0ADZ4 (Residues: 2-89; Coverage: 99%)
Gene names: JW3134, b3165, rpsO, secC
Sequence domains: Ribosomal protein S15
Small ribosomal subunit protein bS16 Chain: p
Molecule details ›
Chain: p
Length: 82 amino acids
Theoretical weight: 9.21 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7T3 (Residues: 1-82; Coverage: 100%)
Gene names: JW2590, b2609, rpsP
Sequence domains: Ribosomal protein S16
Small ribosomal subunit protein uS17 Chain: q
Molecule details ›
Chain: q
Length: 80 amino acids
Theoretical weight: 9.26 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0AG63 (Residues: 4-83; Coverage: 95%)
Gene names: JW3273, b3311, neaA, rpsQ
Sequence domains: Ribosomal protein S17
Small ribosomal subunit protein bS18 Chain: r
Molecule details ›
Chain: r
Length: 65 amino acids
Theoretical weight: 7.61 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7T7 (Residues: 10-74; Coverage: 87%)
Gene names: JW4160, b4202, rpsR
Sequence domains: Ribosomal protein S18
Small ribosomal subunit protein uS19 Chain: s
Molecule details ›
Chain: s
Length: 79 amino acids
Theoretical weight: 9.06 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7U3 (Residues: 3-81; Coverage: 86%)
Gene names: JW3278, b3316, rpsS
Sequence domains: Ribosomal protein S19
Small ribosomal subunit protein bS20 Chain: t
Molecule details ›
Chain: t
Length: 85 amino acids
Theoretical weight: 9.51 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7U7 (Residues: 3-87; Coverage: 98%)
Gene names: JW0022, b0023, rpsT
Sequence domains: Ribosomal protein S20
Small ribosomal subunit protein bS21 Chain: u
Molecule details ›
Chain: u
Length: 65 amino acids
Theoretical weight: 7.76 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P68679 (Residues: 4-68; Coverage: 92%)
Gene names: JW3037, b3065, rpsU
Sequence domains: Ribosomal protein S21
Peptide chain release factor RF1 Chain: v
Molecule details ›
Chain: v
Length: 242 amino acids
Theoretical weight: 26.82 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7I0 (Residues: 110-351; Coverage: 67%)
Gene names: JW1202, b1211, prfA, sueB, uar
Sequence domains:
Apidaecin Chain: z
Molecule details ›
Chain: z
Length: 14 amino acids
Theoretical weight: 1.7 KDa
Source organism: Apis mellifera
Expression system: Not provided
UniProt:
  • Canonical: Q8WSY8 (Residues: 158-171; Coverage: 7%)
Sequence domains: Apidaecin
23S ribosomal RNA Chain: A
Molecule details ›
Chain: A
Length: 2903 nucleotides
Theoretical weight: 941.32 KDa
Sequence domains: Bacterial large subunit ribosomal RNA
5S ribosomal RNA Chain: B
Molecule details ›
Chain: B
Length: 120 nucleotides
Theoretical weight: 38.81 KDa
Sequence domains: 5S ribosomal RNA
Messenger RNA Chain: 7
Molecule details ›
Chain: 7
Length: 7 nucleotides
Theoretical weight: 2.21 KDa
16S ribosomal RNA Chain: a
Molecule details ›
Chain: a
Length: 1539 nucleotides
Theoretical weight: 498.73 KDa
Sequence domains: Bacterial small subunit ribosomal RNA
P-site Ile-tRNA Chain: x
Molecule details ›
Chain: x
Length: 77 nucleotides
Theoretical weight: 24.86 KDa
Sequence domains: tRNA

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.4Å
Relevant EMDB volumes: EMD-3730
Expression system: Not provided

Quick links

Citations

21 review citations

Antimicrobial peptides: Application informed by evolution.
Lazzaro et al. (2020)
20 more

15 mentions without citation

Ribosome-Targeting Antibiotics: Modes of Action, Mechanisms of Resistance, and Implications for Drug Design.
Lin et al. (2018)
14 more