› 4v4h

X-ray diffraction
3.46Å resolution

Crystal structure of the bacterial ribosome from Escherichia coli in complex with the antibiotic kasugamyin at 3.5A resolution.

Released:
DOI: 10.2210/pdb4v4h/pdb
PDB entry 4v4h coloured by chain, front view.
PDB entry 4v4h coloured by chain, side view.
PDB entry 4v4h coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Structural analysis of kasugamycin inhibition of translation.
Schuwirth BS, Day JM, Hau CW, Janssen GR, Dahlberg AE, Cate JH, Vila-Sanjurjo A
Nat Struct Mol Biol 13 879-86 (2006)
PMID: 16998486

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 52-mer (preferred)
PDBe Complex ID:
PDB-CPX-135668 (preferred)
Entry contents:
49 distinct polypeptide molecules
3 distinct RNA molecules
Macromolecules (52 distinct):
Small ribosomal subunit protein uS3 Chains: AC, CC
Molecule details ›
Chains: AC, CC
Length: 233 amino acids
Theoretical weight: 26.03 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7V3 (Residues: 1-233; Coverage: 100%)
Gene names: JW3276, b3314, rpsC
Sequence domains:
Small ribosomal subunit protein uS4 Chains: AD, CD
Molecule details ›
Chains: AD, CD
Length: 206 amino acids
Theoretical weight: 23.51 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7V8 (Residues: 1-206; Coverage: 100%)
Gene names: JW3258, b3296, ramA, rpsD
Sequence domains:
Small ribosomal subunit protein uS5 Chains: AE, CE
Molecule details ›
Chains: AE, CE
Length: 167 amino acids
Theoretical weight: 17.63 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7W1 (Residues: 1-167; Coverage: 100%)
Gene names: JW3265, b3303, rpsE, spc
Sequence domains:
Small ribosomal subunit protein bS6 Chains: AF, CF
Molecule details ›
Chains: AF, CF
Length: 135 amino acids
Theoretical weight: 15.73 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P02358 (Residues: 1-135; Coverage: 100%)
Gene names: JW4158, b4200, rpsF
Sequence domains: Ribosomal protein S6
Small ribosomal subunit protein uS7 Chains: AG, CG
Molecule details ›
Chains: AG, CG
Length: 179 amino acids
Theoretical weight: 20.06 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P02359 (Residues: 1-179; Coverage: 100%)
Gene names: JW3303, b3341, rpsG
Sequence domains: Ribosomal protein S7p/S5e
Small ribosomal subunit protein uS8 Chains: AH, CH
Molecule details ›
Chains: AH, CH
Length: 130 amino acids
Theoretical weight: 14.15 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7W7 (Residues: 1-130; Coverage: 100%)
Gene names: JW3268, b3306, rpsH
Sequence domains: Ribosomal protein S8
Small ribosomal subunit protein uS9 Chains: AI, CI
Molecule details ›
Chains: AI, CI
Length: 130 amino acids
Theoretical weight: 14.89 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7X3 (Residues: 1-130; Coverage: 100%)
Gene names: JW3199, b3230, rpsI
Sequence domains: Ribosomal protein S9/S16
Small ribosomal subunit protein uS10 Chains: AJ, CJ
Molecule details ›
Chains: AJ, CJ
Length: 103 amino acids
Theoretical weight: 11.76 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7R5 (Residues: 1-103; Coverage: 100%)
Gene names: JW3283, b3321, nusE, rpsJ
Sequence domains: Ribosomal protein S10p/S20e
Small ribosomal subunit protein uS11 Chains: AK, CK
Molecule details ›
Chains: AK, CK
Length: 129 amino acids
Theoretical weight: 13.87 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7R9 (Residues: 1-129; Coverage: 100%)
Gene names: JW3259, b3297, rpsK
Sequence domains: Ribosomal protein S11
Small ribosomal subunit protein uS12 Chains: AL, CL
Molecule details ›
Chains: AL, CL
Length: 124 amino acids
Theoretical weight: 13.77 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7S3 (Residues: 1-124; Coverage: 100%)
Gene names: JW3304, b3342, rpsL, strA
Sequence domains: Ribosomal protein S12/S23
Small ribosomal subunit protein uS13 Chains: AM, CM
Molecule details ›
Chains: AM, CM
Length: 118 amino acids
Theoretical weight: 13.13 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7S9 (Residues: 1-118; Coverage: 100%)
Gene names: JW3260, b3298, rpsM
Sequence domains: Ribosomal protein S13/S18
Small ribosomal subunit protein uS14 Chains: AN, CN
Molecule details ›
Chains: AN, CN
Length: 101 amino acids
Theoretical weight: 11.61 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0AG59 (Residues: 1-101; Coverage: 100%)
Gene names: JW3269, b3307, rpsN
Sequence domains: Ribosomal protein S14p/S29e
Small ribosomal subunit protein uS15 Chains: AO, CO
Molecule details ›
Chains: AO, CO
Length: 89 amino acids
Theoretical weight: 10.32 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0ADZ4 (Residues: 1-89; Coverage: 100%)
Gene names: JW3134, b3165, rpsO, secC
Sequence domains: Ribosomal protein S15
Small ribosomal subunit protein bS16 Chains: AP, CP
Molecule details ›
Chains: AP, CP
Length: 82 amino acids
Theoretical weight: 9.21 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7T3 (Residues: 1-82; Coverage: 100%)
Gene names: JW2590, b2609, rpsP
Sequence domains: Ribosomal protein S16
Small ribosomal subunit protein uS17 Chains: AQ, CQ
Molecule details ›
Chains: AQ, CQ
Length: 84 amino acids
Theoretical weight: 9.72 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0AG63 (Residues: 1-84; Coverage: 100%)
Gene names: JW3273, b3311, neaA, rpsQ
Sequence domains: Ribosomal protein S17
Small ribosomal subunit protein bS18 Chains: AR, CR
Molecule details ›
Chains: AR, CR
Length: 75 amino acids
Theoretical weight: 9.01 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7T7 (Residues: 1-75; Coverage: 100%)
Gene names: JW4160, b4202, rpsR
Sequence domains: Ribosomal protein S18
Small ribosomal subunit protein uS19 Chains: AS, CS
Molecule details ›
Chains: AS, CS
Length: 92 amino acids
Theoretical weight: 10.46 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7U3 (Residues: 1-92; Coverage: 100%)
Gene names: JW3278, b3316, rpsS
Sequence domains: Ribosomal protein S19
Small ribosomal subunit protein bS20 Chains: AT, CT
Molecule details ›
Chains: AT, CT
Length: 87 amino acids
Theoretical weight: 9.71 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7U7 (Residues: 1-87; Coverage: 100%)
Gene names: JW0022, b0023, rpsT
Sequence domains: Ribosomal protein S20
Small ribosomal subunit protein uS2 Chains: AB, CB
Molecule details ›
Chains: AB, CB
Length: 241 amino acids
Theoretical weight: 26.78 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7V0 (Residues: 1-241; Coverage: 100%)
Gene names: JW0164, b0169, rpsB
Sequence domains: Ribosomal protein S2
Small ribosomal subunit protein bS21 Chains: AU, CU
Molecule details ›
Chains: AU, CU
Length: 71 amino acids
Theoretical weight: 8.52 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P68679 (Residues: 1-71; Coverage: 100%)
Gene names: JW3037, b3065, rpsU
Sequence domains: Ribosomal protein S21
Large ribosomal subunit protein bL25 Chains: BV, DV
Molecule details ›
Chains: BV, DV
Length: 94 amino acids
Theoretical weight: 10.71 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P68919 (Residues: 1-94; Coverage: 100%)
Gene names: JW2173, b2185, rplY
Sequence domains: Ribosomal L25p family
Large ribosomal subunit protein uL2 Chains: BC, DC
Molecule details ›
Chains: BC, DC
Length: 273 amino acids
Theoretical weight: 29.92 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P60422 (Residues: 1-273; Coverage: 100%)
Gene names: JW3279, b3317, rplB
Sequence domains:
Large ribosomal subunit protein uL3 Chains: BD, DD
Molecule details ›
Chains: BD, DD
Length: 209 amino acids
Theoretical weight: 22.28 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P60438 (Residues: 1-209; Coverage: 100%)
Gene names: JW3282, b3320, rplC
Sequence domains: Ribosomal protein L3
Large ribosomal subunit protein uL4 Chains: BE, DE
Molecule details ›
Chains: BE, DE
Length: 201 amino acids
Theoretical weight: 22.12 KDa
Source organism: Escherichia coli
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 Chains: BF, DF
Molecule details ›
Chains: BF, DF
Length: 179 amino acids
Theoretical weight: 20.33 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P62399 (Residues: 1-179; Coverage: 100%)
Gene names: JW3270, b3308, rplE
Sequence domains:
50S RIBOSOMAL PROTEIN L6 Chains: BG, DG
Molecule details ›
Chains: BG, DG
Length: 177 amino acids
Theoretical weight: 18.93 KDa
Source organism: Escherichia coli
Large ribosomal subunit protein bL9 Chains: BH, DH
Molecule details ›
Chains: BH, DH
Length: 149 amino acids
Theoretical weight: 15.79 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7R1 (Residues: 1-149; Coverage: 100%)
Gene names: JW4161, b4203, rplI
Sequence domains:
50S RIBOSOMAL PROTEIN L13 Chains: BJ, DJ
Molecule details ›
Chains: BJ, DJ
Length: 142 amino acids
Theoretical weight: 16.05 KDa
Source organism: Escherichia coli
Large ribosomal subunit protein uL14 Chains: BK, DK
Molecule details ›
Chains: BK, DK
Length: 123 amino acids
Theoretical weight: 13.57 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0ADY3 (Residues: 1-123; Coverage: 100%)
Gene names: JW3272, b3310, rplN
Sequence domains: Ribosomal protein L14p/L23e
Large ribosomal subunit protein uL15 Chains: BL, DL
Molecule details ›
Chains: BL, DL
Length: 144 amino acids
Theoretical weight: 15.01 KDa
Source organism: Escherichia coli
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 Chains: BM, DM
Molecule details ›
Chains: BM, DM
Length: 136 amino acids
Theoretical weight: 15.31 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0ADY7 (Residues: 1-136; Coverage: 100%)
Gene names: JW3275, b3313, rplP
Sequence domains: Ribosomal protein L16p/L10e
Large ribosomal subunit protein bL17 Chains: BN, DN
Molecule details ›
Chains: BN, DN
Length: 127 amino acids
Theoretical weight: 14.39 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0AG44 (Residues: 1-127; Coverage: 100%)
Gene names: JW3256, b3294, rplQ
Sequence domains: Ribosomal protein L17
Large ribosomal subunit protein uL18 Chains: BO, DO
Molecule details ›
Chains: BO, DO
Length: 117 amino acids
Theoretical weight: 12.79 KDa
Source organism: Escherichia coli
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 Chains: BP, DP
Molecule details ›
Chains: BP, DP
Length: 115 amino acids
Theoretical weight: 13.16 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7K6 (Residues: 1-115; Coverage: 100%)
Gene names: JW2587, b2606, rplS
Sequence domains: Ribosomal protein L19
Large ribosomal subunit protein bL20 Chains: BQ, DQ
Molecule details ›
Chains: BQ, DQ
Length: 118 amino acids
Theoretical weight: 13.53 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7L3 (Residues: 1-118; Coverage: 100%)
Gene names: JW1706, b1716, pdzA, rplT
Sequence domains: Ribosomal protein L20
Large ribosomal subunit protein bL21 Chains: BR, DR
Molecule details ›
Chains: BR, DR
Length: 103 amino acids
Theoretical weight: 11.59 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0AG48 (Residues: 1-103; Coverage: 100%)
Gene names: JW3153, b3186, rplU
Sequence domains: Ribosomal prokaryotic L21 protein
Large ribosomal subunit protein uL22 Chains: BS, DS
Molecule details ›
Chains: BS, DS
Length: 110 amino acids
Theoretical weight: 12.25 KDa
Source organism: Escherichia coli
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 Chains: BT, DT
Molecule details ›
Chains: BT, DT
Length: 100 amino acids
Theoretical weight: 11.22 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0ADZ0 (Residues: 1-100; Coverage: 100%)
Gene names: JW3280, b3318, rplW
Sequence domains: Ribosomal protein L23
Large ribosomal subunit protein uL24 Chains: BU, DU
Molecule details ›
Chains: BU, DU
Length: 104 amino acids
Theoretical weight: 11.34 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P60624 (Residues: 1-104; Coverage: 100%)
Gene names: JW3271, b3309, rplX
Sequence domains:
Large ribosomal subunit protein bL27 Chains: BW, DW
Molecule details ›
Chains: BW, DW
Length: 85 amino acids
Theoretical weight: 9.15 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7L8 (Residues: 1-85; Coverage: 100%)
Gene names: JW3152, b3185, rpmA
Sequence domains: Ribosomal L27 protein
Large ribosomal subunit protein uL29 Chains: BX, DX
Molecule details ›
Chains: BX, DX
Length: 63 amino acids
Theoretical weight: 7.29 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7M6 (Residues: 1-63; Coverage: 100%)
Gene names: JW3274, b3312, rpmC
Sequence domains: Ribosomal L29 protein
Large ribosomal subunit protein uL30 Chains: BY, DY
Molecule details ›
Chains: BY, DY
Length: 59 amino acids
Theoretical weight: 6.55 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0AG51 (Residues: 1-59; Coverage: 100%)
Gene names: JW3264, b3302, rpmD
Sequence domains: Ribosomal protein L30p/L7e
Large ribosomal subunit protein bL31 Chains: BZ, DZ
Molecule details ›
Chains: BZ, DZ
Length: 70 amino acids
Theoretical weight: 7.89 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7M9 (Residues: 1-70; Coverage: 100%)
Gene names: JW3907, b3936, rpmE
Sequence domains: Ribosomal protein L31
Large ribosomal subunit protein bL32 Chains: B0, D0
Molecule details ›
Chains: B0, D0
Length: 57 amino acids
Theoretical weight: 6.46 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7N4 (Residues: 1-57; Coverage: 100%)
Gene names: JW1075, b1089, rpmF
Sequence domains: Ribosomal L32p protein family
Large ribosomal subunit protein bL33 Chains: B1, D1
Molecule details ›
Chains: B1, D1
Length: 55 amino acids
Theoretical weight: 6.39 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7N9 (Residues: 1-55; Coverage: 100%)
Gene names: JW3611, b3636, rpmG
Sequence domains: Ribosomal protein L33
Large ribosomal subunit protein bL34 Chains: B2, D2
Molecule details ›
Chains: B2, D2
Length: 46 amino acids
Theoretical weight: 5.4 KDa
Source organism: Escherichia coli
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 Chains: B3, D3
Molecule details ›
Chains: B3, D3
Length: 65 amino acids
Theoretical weight: 7.31 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7Q1 (Residues: 1-65; Coverage: 100%)
Gene names: JW1707, b1717, rpmI
Sequence domains: Ribosomal protein L35
Large ribosomal subunit protein bL36A Chains: B4, D4
Molecule details ›
Chains: B4, D4
Length: 38 amino acids
Theoretical weight: 4.38 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7Q6 (Residues: 1-38; Coverage: 100%)
Gene names: JW3261, b3299, rpmJ
Sequence domains: Ribosomal protein L36
Large ribosomal subunit protein uL11 Chains: BI, DI
Molecule details ›
Chains: BI, DI
Length: 142 amino acids
Theoretical weight: 14.89 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7J7 (Residues: 1-142; Coverage: 100%)
Gene names: JW3946, b3983, relC, rplK
Sequence domains:
16S ribosomal RNA Chains: AA, CA
Molecule details ›
Chains: AA, CA
Length: 1542 nucleotides
Theoretical weight: 499.69 KDa
Sequence domains: Bacterial small subunit ribosomal RNA
5S ribosomal RNA Chains: BA, DA
Molecule details ›
Chains: BA, DA
Length: 120 nucleotides
Theoretical weight: 38.79 KDa
Sequence domains: 5S ribosomal RNA
23S ribosomal RNA Chains: BB, DB
Molecule details ›
Chains: BB, DB
Length: 2904 nucleotides
Theoretical weight: 941.61 KDa
Sequence domains: Bacterial large subunit ribosomal RNA

Ligands and Environments

2 bound ligands:
Ligand KSG 2 x KSG
Ligand MG 343 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 12.3.1
Spacegroup: P212121
Unit cell:
a: 208.848Å b: 379.202Å c: 739.283Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.279 0.279 0.331

Quick links

Citations

16 review citations

The A-Z of bacterial translation inhibitors.
Wilson DN. (2009)
15 more

2 mentions without citation

Structural analysis of 70S ribosomes by cross-linking/mass spectrometry reveals conformational plasticity.
Tüting et al. (2020)
1 more