› 3j5l

Electron Microscopy
6.6Å resolution

Structure of the E. coli 50S subunit with ErmBL nascent chain

Released:
DOI: 10.2210/pdb3j5l/pdb
PDB entry 3j5l coloured by chain, front view.
PDB entry 3j5l coloured by chain, side view.
PDB entry 3j5l coloured by chain, top view.
Source organisms:
Primary publication:
Molecular basis for erythromycin-dependent ribosome stalling during translation of the ErmBL leader peptide.
Arenz S, Ramu H, Gupta P, Berninghausen O, Beckmann R, Vázquez-Laslop N, Mankin AS, Wilson DN
Nat Commun 5 3501 (2014)
PMID: 24662426
Related structures: EMD-5771

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 34-mer (preferred)
PDBe Complex ID:
PDB-CPX-526466 (preferred)
Entry contents:
30 distinct polypeptide molecules
4 distinct RNA molecules
Macromolecules (34 distinct):
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
Erythromycin resistance leader peptide Chain: 6
Molecule details ›
Chain: 6
Length: 10 amino acids
Theoretical weight: 1.25 KDa
Source organism: Streptococcus sanguinis
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: 56 amino acids
Theoretical weight: 6.14 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7R1 (Residues: 1-56; Coverage: 38%)
Gene names: JW4161, b4203, rplI
Sequence domains: Ribosomal protein L9, N-terminal domain
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: 79 amino acids
Theoretical weight: 8.48 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7L8 (Residues: 7-85; Coverage: 93%)
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
5'-R(*CP*(MA6))-3' Chain: 5
Molecule details ›
Chain: 5
Length: 2 nucleotides
Theoretical weight: 617 Da
5'-R(*CP*CP*A)-3' Chain: 7
Molecule details ›
Chain: 7
Length: 3 nucleotides
Theoretical weight: 895 Da
23S ribosomal RNA Chain: A
Molecule details ›
Chain: A
Length: 2904 nucleotides
Theoretical weight: 941.61 KDa
Sequence domains: Bacterial large subunit ribosomal RNA
5S ribosomal RNA Chain: B
Molecule details ›
Chain: B
Length: 118 nucleotides
Theoretical weight: 38.18 KDa
Sequence domains: 5S ribosomal RNA

Ligands and Environments

2 bound ligands:
Ligand UNL 1 x UNL
Ligand ERY 1 x ERY
1 modified residue:
Ligand MA6 1 x MA6

Experiments and Validation Details

Entry percentile scores
Resolution: 6.6Å
Relevant EMDB volumes: EMD-5771

Quick links

Citations

13 review citations

The macrolide antibiotic renaissance.
Dinos GP. (2017)
12 more

9 mentions without citation

The Impact of the Stringent Response on TRAFAC GTPases and Prokaryotic Ribosome Assembly.
Bennison et al. (2019)
8 more