PDBe 5j88

X-ray diffraction
3.32Å resolution

Structure of the E coli 70S ribosome with the U1060A mutation in 16S rRNA

Released:

Function and Biology Details

Structure analysis Details

Assemblies composition:
hetero 53-mer (preferred)
hetero 52-mer
Entry contents:
51 distinct polypeptide molecules
4 distinct RNA molecules
Macromolecules (55 distinct):
30S ribosomal protein S2 Chains: AB, BB
Molecule details ›
Chains: AB, BB
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
30S ribosomal protein S3 Chains: AC, BC
Molecule details ›
Chains: AC, BC
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:
30S ribosomal protein S4 Chains: AD, BD
Molecule details ›
Chains: AD, BD
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:
30S ribosomal protein S5 Chains: AE, BE
Molecule details ›
Chains: AE, BE
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:
30S ribosomal protein S6, non-modified isoform Chains: AF, BF
Molecule details ›
Chains: AF, BF
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
30S ribosomal protein S7 Chains: AG, BG
Molecule details ›
Chains: AG, BG
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
30S ribosomal protein S8 Chains: AH, BH
Molecule details ›
Chains: AH, BH
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
30S ribosomal protein S9 Chains: AI, BI
Molecule details ›
Chains: AI, BI
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
30S ribosomal protein S10 Chains: AJ, BJ
Molecule details ›
Chains: AJ, BJ
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
30S ribosomal protein S11 Chains: AK, BK
Molecule details ›
Chains: AK, BK
Length: 129 amino acids
Theoretical weight: 13.87 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7R9 (Residues: 1-129; Coverage: 100%)
Gene names: JW3259, b3297, rpsK
Sequence domains: Ribosomal protein S11
30S ribosomal protein S12 Chains: AL, BL
Molecule details ›
Chains: AL, BL
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
30S ribosomal protein S13 Chains: AM, BM
Molecule details ›
Chains: AM, BM
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
30S ribosomal protein S14 Chains: AN, BN
Molecule details ›
Chains: AN, BN
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
30S ribosomal protein S15 Chains: AO, BO
Molecule details ›
Chains: AO, BO
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
30S ribosomal protein S16 Chains: AP, BP
Molecule details ›
Chains: AP, BP
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
30S ribosomal protein S17 Chains: AQ, BQ
Molecule details ›
Chains: AQ, BQ
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
30S ribosomal protein S18 Chains: AR, BR
Molecule details ›
Chains: AR, BR
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
30S ribosomal protein S19 Chains: AS, BS
Molecule details ›
Chains: AS, BS
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
30S ribosomal protein S20 Chains: AT, BT
Molecule details ›
Chains: AT, BT
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
30S ribosomal protein S21 Chains: AU, BU
Molecule details ›
Chains: AU, BU
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
50S ribosomal protein L32 Chains: C1, D1
Molecule details ›
Chains: C1, D1
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
50S ribosomal protein L33 Chains: C2, D2
Molecule details ›
Chains: C2, D2
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
50S ribosomal protein L34 Chains: C3, D3
Molecule details ›
Chains: C3, D3
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
50S ribosomal protein L35 Chains: C4, D4
Molecule details ›
Chains: C4, D4
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
50S ribosomal protein L36 Chains: C5, D5
Molecule details ›
Chains: C5, D5
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
50S ribosomal protein L30 Chains: C0, D0
Molecule details ›
Chains: C0, D0
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
50S ribosomal protein L2 Chains: CC, DC
Molecule details ›
Chains: CC, DC
Length: 272 amino acids
Theoretical weight: 29.79 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P60422 (Residues: 2-273; Coverage: 100%)
Gene names: JW3279, b3317, rplB
Sequence domains:
50S ribosomal protein L3 Chain: CD
Molecule details ›
Chain: CD
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
50S ribosomal protein L3 Chain: DD
Molecule details ›
Chain: DD
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
50S ribosomal protein L4 Chains: CE, DE
Molecule details ›
Chains: CE, DE
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
50S ribosomal protein L5 Chains: CF, DF
Molecule details ›
Chains: CF, DF
Length: 178 amino acids
Theoretical weight: 20.2 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P62399 (Residues: 2-179; Coverage: 99%)
Gene names: JW3270, b3308, rplE
Sequence domains:
50S ribosomal protein L6 Chains: CG, DG
Molecule details ›
Chains: CG, DG
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
50S ribosomal protein L9 Chains: CH, DH
Molecule details ›
Chains: CH, DH
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:
50S ribosomal protein L11 Chains: CJ, DJ
Molecule details ›
Chains: CJ, DJ
Length: 135 amino acids
Theoretical weight: 14.14 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7J7 (Residues: 8-142; Coverage: 95%)
Gene names: JW3946, b3983, relC, rplK
Sequence domains: Ribosomal protein L11, RNA binding domain
50S ribosomal protein L13 Chains: CK, DK
Molecule details ›
Chains: CK, DK
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
50S ribosomal protein L14 Chains: CL, DL
Molecule details ›
Chains: CL, DL
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
50S ribosomal protein L15 Chains: CM, DM
Molecule details ›
Chains: CM, DM
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
50S ribosomal protein L16 Chains: CN, DN
Molecule details ›
Chains: CN, DN
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
50S ribosomal protein L17 Chains: CO, DO
Molecule details ›
Chains: CO, DO
Length: 127 amino acids
Theoretical weight: 14.39 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0AG44 (Residues: 1-127; Coverage: 100%)
Gene names: JW3256, b3294, rplQ
Sequence domains: Ribosomal protein L17
50S ribosomal protein L18 Chains: CP, DP
Molecule details ›
Chains: CP, DP
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
50S ribosomal protein L19 Chains: CQ, DQ
Molecule details ›
Chains: CQ, DQ
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
50S ribosomal protein L20 Chains: CR, DR
Molecule details ›
Chains: CR, DR
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
50S ribosomal protein L21 Chains: CS, DS
Molecule details ›
Chains: CS, DS
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
50S ribosomal protein L22 Chains: CT, DT
Molecule details ›
Chains: CT, DT
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
50S ribosomal protein L23 Chains: CU, DU
Molecule details ›
Chains: CU, DU
Length: 100 amino acids
Theoretical weight: 11.22 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0ADZ0 (Residues: 1-100; Coverage: 100%)
Gene names: JW3280, b3318, rplW
Sequence domains: Ribosomal protein L23
50S ribosomal protein L24 Chains: CV, DV
Molecule details ›
Chains: CV, DV
Length: 103 amino acids
Theoretical weight: 11.21 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P60624 (Residues: 2-104; Coverage: 99%)
Gene names: JW3271, b3309, rplX
Sequence domains:
50S ribosomal protein L25 Chains: CW, DW
Molecule details ›
Chains: CW, DW
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
50S ribosomal protein L27 Chains: CX, DX
Molecule details ›
Chains: CX, DX
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
50S ribosomal protein L28 Chains: CY, DY
Molecule details ›
Chains: CY, DY
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
50S ribosomal protein L29 Chains: CZ, DZ
Molecule details ›
Chains: CZ, DZ
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
50S ribosomal protein L10 Chain: DI
Molecule details ›
Chain: DI
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
16S ribosomal RNA Chains: AA, BA
Molecule details ›
Chains: AA, BA
Length: 1534 nucleotides
Theoretical weight: 497.43 KDa
Sequence domains: Bacterial small subunit ribosomal RNA
5S ribosomal RNA Chains: CB, DB
Molecule details ›
Chains: CB, DB
Length: 120 nucleotides
Theoretical weight: 38.79 KDa
Sequence domains: 5S ribosomal RNA
23S ribosomal RNA Chain: CA
Molecule details ›
Chain: CA
Length: 2904 nucleotides
Theoretical weight: 941.81 KDa
Sequence domains: Bacterial large subunit ribosomal RNA
23S ribosomal RNA Chain: DA
Molecule details ›
Chain: DA
Length: 2904 nucleotides
Theoretical weight: 941.81 KDa
Sequence domains: Bacterial large subunit ribosomal RNA

Ligands and Environments

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 17-ID
Spacegroup: P212121
Unit cell:
a: 211.55Å b: 433.65Å c: 622.03Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.176 0.176 0.219