› 6xza

Electron Microscopy
2.66Å resolution

E. coli 70S ribosome in complex with dirithromycin, and deacylated tRNA(iMet) (focused classification).

Released:
DOI: 10.2210/pdb6xza/pdb
PDB entry 6xza coloured by chain, front view.
PDB entry 6xza coloured by chain, side view.
PDB entry 6xza coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Insights into the improved macrolide inhibitory activity from the high-resolution cryo-EM structure of dirithromycin bound to the E. coli 70S ribosome.
Pichkur EB, Paleskava A, Tereshchenkov AG, Kasatsky P, Komarova ES, Shiriaev DI, Bogdanov AA, Dontsova OA, Osterman IA, Sergiev PV, Polikanov YS, Myasnikov AG, Konevega AL
OpenAccess logo RNA 26 715-723 (2020)
PMID: 32144191
Related structures: EMD-10656

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 53-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-135572 (preferred)
Entry contents:
49 distinct polypeptide molecules
4 distinct RNA molecules
Macromolecules (53 distinct):
Small ribosomal subunit protein uS2 Chain: B1
Molecule details ›
Chain: B1
Length: 224 amino acids
Theoretical weight: 24.97 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7V0 (Residues: 4-227; Coverage: 93%)
Gene names: JW0164, b0169, rpsB
Sequence domains: Ribosomal protein S2
Small ribosomal subunit protein uS3 Chain: C1
Molecule details ›
Chain: C1
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: D1
Molecule details ›
Chain: D1
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: E1
Molecule details ›
Chain: E1
Length: 155 amino acids
Theoretical weight: 16.36 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7W1 (Residues: 10-164; Coverage: 93%)
Gene names: JW3265, b3303, rpsE, spc
Sequence domains:
Small ribosomal subunit protein bS6, non-modified isoform Chain: F1
Molecule details ›
Chain: F1
Length: 106 amino acids
Theoretical weight: 12.33 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P02358 (Residues: 1-106; Coverage: 79%)
Gene names: JW4158, b4200, rpsF
Sequence domains: Ribosomal protein S6
Small ribosomal subunit protein uS7 Chain: G1
Molecule details ›
Chain: G1
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: H1
Molecule details ›
Chain: H1
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: I1
Molecule details ›
Chain: I1
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: J1
Molecule details ›
Chain: J1
Length: 99 amino acids
Theoretical weight: 11.33 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7R5 (Residues: 4-102; Coverage: 96%)
Gene names: JW3283, b3321, nusE, rpsJ
Sequence domains: Ribosomal protein S10p/S20e
Small ribosomal subunit protein uS11 Chain: K1
Molecule details ›
Chain: K1
Length: 117 amino acids
Theoretical weight: 12.49 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7R9 (Residues: 13-129; Coverage: 91%)
Gene names: JW3259, b3297, rpsK
Sequence domains: Ribosomal protein S11
Small ribosomal subunit protein uS12 Chain: L1
Molecule details ›
Chain: L1
Length: 123 amino acids
Theoretical weight: 13.68 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: M1
Molecule details ›
Chain: M1
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: N1
Molecule details ›
Chain: N1
Length: 100 amino acids
Theoretical weight: 11.48 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0AG59 (Residues: 2-101; Coverage: 99%)
Gene names: JW3269, b3307, rpsN
Sequence domains: Ribosomal protein S14p/S29e
Small ribosomal subunit protein uS15 Chain: O1
Molecule details ›
Chain: O1
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: P1
Molecule details ›
Chain: P1
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: Q1
Molecule details ›
Chain: Q1
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: R1
Molecule details ›
Chain: R1
Length: 55 amino acids
Theoretical weight: 6.47 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7T7 (Residues: 20-74; Coverage: 73%)
Gene names: JW4160, b4202, rpsR
Sequence domains: Ribosomal protein S18
Small ribosomal subunit protein uS19 Chain: S1
Molecule details ›
Chain: S1
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: T1
Molecule details ›
Chain: T1
Length: 86 amino acids
Theoretical weight: 9.58 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7U7 (Residues: 2-87; Coverage: 99%)
Gene names: JW0022, b0023, rpsT
Sequence domains: Ribosomal protein S20
Small ribosomal subunit protein bS21 Chain: U1
Molecule details ›
Chain: U1
Length: 56 amino acids
Theoretical weight: 6.63 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P68679 (Residues: 2-57; Coverage: 79%)
Gene names: JW3037, b3065, rpsU
Sequence domains: Ribosomal protein S21
Large ribosomal subunit protein uL2 Chain: C2
Molecule details ›
Chain: C2
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: D2
Molecule details ›
Chain: D2
Length: 209 amino acids
Theoretical weight: 22.29 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: E2
Molecule details ›
Chain: E2
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: F2
Molecule details ›
Chain: F2
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: G2
Molecule details ›
Chain: G2
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 uL10 Chain: H2
Molecule details ›
Chain: H2
Length: 135 amino acids
Theoretical weight: 14.57 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7J3 (Residues: 2-136; Coverage: 82%)
Gene names: JW3948, b3985, rplJ
Sequence domains: Ribosomal protein L10
Large ribosomal subunit protein uL11 Chain: I2
Molecule details ›
Chain: I2
Length: 134 amino acids
Theoretical weight: 14.02 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7J7 (Residues: 8-141; Coverage: 94%)
Gene names: JW3946, b3983, relC, rplK
Sequence domains:
Large ribosomal subunit protein uL13 Chain: J2
Molecule details ›
Chain: J2
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: K2
Molecule details ›
Chain: K2
Length: 123 amino acids
Theoretical weight: 13.57 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0ADY3 (Residues: 1-123; Coverage: 100%)
Gene names: JW3272, b3310, rplN
Sequence domains: Ribosomal protein L14p/L23e
Large ribosomal subunit protein uL15 Chain: L2
Molecule details ›
Chain: L2
Length: 144 amino acids
Theoretical weight: 15.01 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P02413 (Residues: 1-144; Coverage: 100%)
Gene names: JW3263, b3301, rplO
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
Large ribosomal subunit protein uL16 Chain: M2
Molecule details ›
Chain: M2
Length: 136 amino acids
Theoretical weight: 15.33 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: N2
Molecule details ›
Chain: N2
Length: 125 amino acids
Theoretical weight: 14.19 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0AG44 (Residues: 1-125; Coverage: 98%)
Gene names: JW3256, b3294, rplQ
Sequence domains: Ribosomal protein L17
Large ribosomal subunit protein uL18 Chain: O2
Molecule details ›
Chain: O2
Length: 117 amino acids
Theoretical weight: 12.79 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0C018 (Residues: 1-117; Coverage: 100%)
Gene names: JW3266, b3304, rplR
Sequence domains: Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
Large ribosomal subunit protein bL19 Chain: P2
Molecule details ›
Chain: P2
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: Q2
Molecule details ›
Chain: Q2
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: R2
Molecule details ›
Chain: R2
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: S2
Molecule details ›
Chain: S2
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: T2
Molecule details ›
Chain: T2
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: U2
Molecule details ›
Chain: U2
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: V2
Molecule details ›
Chain: V2
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: W2
Molecule details ›
Chain: W2
Length: 76 amino acids
Theoretical weight: 8.28 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7L8 (Residues: 10-85; Coverage: 89%)
Gene names: JW3152, b3185, rpmA
Sequence domains: Ribosomal L27 protein
Large ribosomal subunit protein bL28 Chain: X2
Molecule details ›
Chain: X2
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: Y2
Molecule details ›
Chain: Y2
Length: 62 amino acids
Theoretical weight: 7.16 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7M6 (Residues: 2-63; Coverage: 98%)
Gene names: JW3274, b3312, rpmC
Sequence domains: Ribosomal L29 protein
Large ribosomal subunit protein uL30 Chain: Z2
Molecule details ›
Chain: Z2
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: a2
Molecule details ›
Chain: a2
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: b2
Molecule details ›
Chain: b2
Length: 51 amino acids
Theoretical weight: 5.93 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7N9 (Residues: 4-54; Coverage: 93%)
Gene names: JW3611, b3636, rpmG
Sequence domains: Ribosomal protein L33
Large ribosomal subunit protein bL34 Chain: c2
Molecule details ›
Chain: c2
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: d2
Molecule details ›
Chain: d2
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: e2
Molecule details ›
Chain: e2
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
16S ribosomal RNA Chain: A1
Molecule details ›
Chain: A1
Length: 1534 nucleotides
Theoretical weight: 497.4 KDa
Sequence domains: Bacterial small subunit ribosomal RNA
23S ribosomal RNA Chain: A2
Molecule details ›
Chain: A2
Length: 2897 nucleotides
Theoretical weight: 939.61 KDa
Sequence domains: Bacterial large subunit ribosomal RNA
5S ribosomal RNA Chain: B2
Molecule details ›
Chain: B2
Length: 120 nucleotides
Theoretical weight: 38.79 KDa
Sequence domains: 5S ribosomal RNA
Deacylated tRNAi(Met) Chain: f2
Molecule details ›
Chain: f2
Length: 76 nucleotides
Theoretical weight: 24.54 KDa
Sequence domains: tRNA

Ligands and Environments

1 bound ligand:
Ligand DI0 1 x DI0
19 modified residues:
Ligand PSU 11 x PSU
Ligand G7M 2 x G7M
Ligand 2MG 5 x 2MG
Ligand 5MC 4 x 5MC
Ligand 4OC 1 x 4OC
Ligand UR3 1 x UR3
Ligand MA6 2 x MA6
Ligand D2T 1 x D2T
Ligand 1MG 1 x 1MG
Ligand 5MU 3 x 5MU
Ligand 6MZ 2 x 6MZ
Ligand 3TD 1 x 3TD
Ligand OMG 1 x OMG
Ligand H2U 1 x H2U
Ligand OMC 1 x OMC
Ligand 2MA 1 x 2MA
Ligand OMU 1 x OMU
Ligand 4D4 1 x 4D4
Ligand 4SU 1 x 4SU

Experiments and Validation Details

Entry percentile scores
Resolution: 2.66Å
Relevant EMDB volumes: EMD-10656

Quick links

Citations

3 review citations

Structural Heterogeneities of the Ribosome: New Frontiers and Opportunities for Cryo-EM.
Poitevin et al. (2020)
2 more

1 mention without citation

Insights into the improved macrolide inhibitory activity from the high-resolution cryo-EM structure of dirithromycin bound to the E. coli 70S ribosome.
Pichkur et al. (2020)