› 6boh

X-ray diffraction
3.4Å resolution

Antibiotic blasticidin S and E. coli release factor 1 (containing deletion 302-304) bound to the 70S ribosome

Released:
DOI: 10.2210/pdb6boh/pdb
PDB entry 6boh coloured by chain, front view.
PDB entry 6boh coloured by chain, side view.
PDB entry 6boh coloured by chain, top view.
Source organisms:
Primary publication:
Conformational Control of Translation Termination on the 70S Ribosome.
Svidritskiy E, Korostelev AA
Structure 26 821-828.e3 (2018)
PMID: 29731232

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 57-mer (preferred)
PDBe Complex ID:
PDB-CPX-250023 (preferred)
Entry contents:
50 distinct polypeptide molecules
5 distinct RNA molecules
Macromolecules (55 distinct):
Large ribosomal subunit protein uL2 Chains: E, JB
Molecule details ›
Chains: E, JB
Length: 275 amino acids
Theoretical weight: 30.4 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72I07 (Residues: 2-276; Coverage: 100%)
Gene names: TT_C1325, rplB
Sequence domains:
Large ribosomal subunit protein uL3 Chains: F, KB
Molecule details ›
Chains: F, KB
Length: 206 amino acids
Theoretical weight: 22.45 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72I04 (Residues: 1-206; Coverage: 100%)
Gene names: TT_C1328, rplC
Sequence domains: Ribosomal protein L3
Large ribosomal subunit protein uL4 Chains: G, LB
Molecule details ›
Chains: G, LB
Length: 205 amino acids
Theoretical weight: 22.74 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72I05 (Residues: 1-205; Coverage: 100%)
Gene names: TT_C1327, rplD
Sequence domains: Ribosomal protein L4/L1 family
Large ribosomal subunit protein uL5 Chains: H, MB
Molecule details ›
Chains: H, MB
Length: 182 amino acids
Theoretical weight: 21.08 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72I16 (Residues: 1-182; Coverage: 100%)
Gene names: TT_C1316, rplE
Sequence domains:
Large ribosomal subunit protein uL6 Chains: I, NB
Molecule details ›
Chains: I, NB
Length: 180 amino acids
Theoretical weight: 19.57 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72I19 (Residues: 1-180; Coverage: 100%)
Gene names: TT_C1313, rplF
Sequence domains: Ribosomal protein L6
Large ribosomal subunit protein bL9 Chains: J, OB
Molecule details ›
Chains: J, OB
Length: 148 amino acids
Theoretical weight: 16.44 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72GV5 (Residues: 1-148; Coverage: 100%)
Gene names: TT_C1743, rplI
Sequence domains:
Large ribosomal subunit protein uL13 Chains: K, PB
Molecule details ›
Chains: K, PB
Length: 140 amino acids
Theoretical weight: 15.93 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72IN1 (Residues: 1-140; Coverage: 100%)
Gene names: TT_C1101, rplM
Sequence domains: Ribosomal protein L13
Large ribosomal subunit protein uL14 Chains: L, QB
Molecule details ›
Chains: L, QB
Length: 122 amino acids
Theoretical weight: 13.31 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72I14 (Residues: 1-122; Coverage: 100%)
Gene names: TT_C1318, rplN
Sequence domains: Ribosomal protein L14p/L23e
Large ribosomal subunit protein uL15 Chains: M, RB
Molecule details ›
Chains: M, RB
Length: 150 amino acids
Theoretical weight: 16.32 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72I23 (Residues: 1-150; Coverage: 100%)
Gene names: TT_C1309, rplO
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
Large ribosomal subunit protein uL16 Chains: N, SB
Molecule details ›
Chains: N, SB
Length: 141 amino acids
Theoretical weight: 15.98 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72I11 (Residues: 1-141; Coverage: 100%)
Gene names: TT_C1321, rplP
Sequence domains: Ribosomal protein L16p/L10e
Large ribosomal subunit protein bL17 Chains: O, TB
Molecule details ›
Chains: O, TB
Length: 118 amino acids
Theoretical weight: 13.75 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72I33 (Residues: 1-118; Coverage: 100%)
Gene names: TT_C1299, rplQ
Sequence domains: Ribosomal protein L17
Large ribosomal subunit protein uL18 Chains: P, UB
Molecule details ›
Chains: P, UB
Length: 112 amino acids
Theoretical weight: 12.64 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72I20 (Residues: 1-112; Coverage: 100%)
Gene names: TT_C1312, rplR
Sequence domains: Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
Large ribosomal subunit protein bL19 Chains: Q, VB
Molecule details ›
Chains: Q, VB
Length: 146 amino acids
Theoretical weight: 17.22 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72JU9 (Residues: 1-146; Coverage: 100%)
Gene names: TT_C0669, rplS
Sequence domains: Ribosomal protein L19
Large ribosomal subunit protein bL20 Chains: R, WB
Molecule details ›
Chains: R, WB
Length: 118 amino acids
Theoretical weight: 13.78 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72L76 (Residues: 1-118; Coverage: 100%)
Gene names: TT_C0185, rplT
Sequence domains: Ribosomal protein L20
Large ribosomal subunit protein bL21 Chains: S, XB
Molecule details ›
Chains: S, XB
Length: 101 amino acids
Theoretical weight: 11.07 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72HR2 (Residues: 1-101; Coverage: 100%)
Gene names: TT_C1424, rplU
Sequence domains: Ribosomal prokaryotic L21 protein
Large ribosomal subunit protein uL22 Chains: T, YB
Molecule details ›
Chains: T, YB
Length: 113 amino acids
Theoretical weight: 12.81 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72I09 (Residues: 1-113; Coverage: 100%)
Gene names: TT_C1323, rplV
Sequence domains: Ribosomal protein L22p/L17e
Large ribosomal subunit protein uL23 Chains: U, ZB
Molecule details ›
Chains: U, ZB
Length: 96 amino acids
Theoretical weight: 10.76 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72I06 (Residues: 1-96; Coverage: 100%)
Gene names: TT_C1326, rplW
Sequence domains: Ribosomal protein L23
Large ribosomal subunit protein uL24 Chains: AC, V
Molecule details ›
Chains: AC, V
Length: 110 amino acids
Theoretical weight: 12.09 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72I15 (Residues: 1-110; Coverage: 100%)
Gene names: TT_C1317, rplX
Sequence domains:
Large ribosomal subunit protein bL25 Chains: BC, W
Molecule details ›
Chains: BC, W
Length: 206 amino acids
Theoretical weight: 23.24 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72IA7 (Residues: 1-206; Coverage: 100%)
Gene names: TT_C1225, ctc, rplY
Sequence domains:
Large ribosomal subunit protein bL27 Chains: CC, X
Molecule details ›
Chains: CC, X
Length: 85 amino acids
Theoretical weight: 9.53 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72HR3 (Residues: 1-85; Coverage: 100%)
Gene names: TT_C1423, rpmA
Sequence domains: Ribosomal L27 protein
Large ribosomal subunit protein bL28 Chains: DC, Y
Molecule details ›
Chains: DC, Y
Length: 98 amino acids
Theoretical weight: 11.03 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72G84 (Residues: 1-98; Coverage: 100%)
Gene names: TT_C1964, rpmB
Sequence domains: Ribosomal L28 family
Large ribosomal subunit protein uL29 Chains: EC, Z
Molecule details ›
Chains: EC, Z
Length: 72 amino acids
Theoretical weight: 8.67 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72I12 (Residues: 1-72; Coverage: 100%)
Gene names: TT_C1320, rpmC
Sequence domains: Ribosomal L29 protein
Large ribosomal subunit protein uL30 Chains: AA, FC
Molecule details ›
Chains: AA, FC
Length: 60 amino acids
Theoretical weight: 6.8 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72I22 (Residues: 1-60; Coverage: 100%)
Gene names: TT_C1310, rpmD
Sequence domains: Ribosomal protein L30p/L7e
Large ribosomal subunit protein bL31 Chains: BA, GC
Molecule details ›
Chains: BA, GC
Length: 71 amino acids
Theoretical weight: 8.3 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72JR0 (Residues: 1-71; Coverage: 100%)
Gene names: TT_C0708, rpmE
Sequence domains: Ribosomal protein L31
Large ribosomal subunit protein bL32 Chains: CA, HC
Molecule details ›
Chains: CA, HC
Length: 60 amino acids
Theoretical weight: 6.73 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62652 (Residues: 1-60; Coverage: 100%)
Gene names: TT_C0050, rpl32, rpmF
Sequence domains: Ribosomal L32p protein family
Large ribosomal subunit protein bL33 Chains: DA, IC
Molecule details ›
Chains: DA, IC
Length: 54 amino acids
Theoretical weight: 6.63 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72GW3 (Residues: 1-54; Coverage: 100%)
Gene names: TT_C1735, rpmG
Sequence domains: Ribosomal protein L33
Large ribosomal subunit protein bL34 Chains: EA, JC
Molecule details ›
Chains: EA, JC
Length: 49 amino acids
Theoretical weight: 6.13 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P80340 (Residues: 1-49; Coverage: 100%)
Gene names: TTHA0446, rpl34, rpmH
Sequence domains: Ribosomal protein L34
Large ribosomal subunit protein bL35 Chains: FA, KC
Molecule details ›
Chains: FA, KC
Length: 65 amino acids
Theoretical weight: 7.51 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72L77 (Residues: 1-65; Coverage: 100%)
Gene names: TT_C0184, rpmI
Sequence domains: Ribosomal protein L35
Large ribosomal subunit protein bL36 Chains: GA, LC
Molecule details ›
Chains: GA, LC
Length: 37 amino acids
Theoretical weight: 4.44 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72I28 (Residues: 1-37; Coverage: 100%)
Gene names: TT_C1304, rpmJ
Sequence domains: Ribosomal protein L36
Peptide chain release factor RF1 Chains: JA, KA, OC, PC
Molecule details ›
Chains: JA, KA, OC, PC
Length: 365 amino acids
Theoretical weight: 41.29 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P0A7I0 (Residues: 1-360; Coverage: 99%)
Gene names: JW1202, b1211, prfA, sueB, uar
Sequence domains:
Small ribosomal subunit protein uS2 Chains: LA, QC
Molecule details ›
Chains: LA, QC
Length: 256 amino acids
Theoretical weight: 29.32 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62662 (Residues: 1-256; Coverage: 100%)
Gene names: TT_C0509, rps2, rpsB
Sequence domains: Ribosomal protein S2
Small ribosomal subunit protein uS3 Chains: MA, RC
Molecule details ›
Chains: MA, RC
Length: 239 amino acids
Theoretical weight: 26.75 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62663 (Residues: 1-239; Coverage: 100%)
Gene names: TT_C1322, rps3, rpsC
Sequence domains:
Small ribosomal subunit protein uS4 Chains: NA, SC
Molecule details ›
Chains: NA, SC
Length: 209 amino acids
Theoretical weight: 24.37 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62664 (Residues: 1-209; Coverage: 100%)
Gene names: TT_C1301, rps4, rpsD
Sequence domains:
Small ribosomal subunit protein uS5 Chains: OA, TC
Molecule details ›
Chains: OA, TC
Length: 162 amino acids
Theoretical weight: 17.58 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62665 (Residues: 1-162; Coverage: 100%)
Gene names: TT_C1311, rps5, rpsE
Sequence domains:
Small ribosomal subunit protein bS6 Chains: PA, UC
Molecule details ›
Chains: PA, UC
Length: 101 amino acids
Theoretical weight: 11.99 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62666 (Residues: 1-101; Coverage: 100%)
Gene names: TT_C1740, rps6, rpsF
Sequence domains: Ribosomal protein S6
Small ribosomal subunit protein uS7 Chains: QA, VC
Molecule details ›
Chains: QA, VC
Length: 156 amino acids
Theoretical weight: 18.05 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62667 (Residues: 1-156; Coverage: 100%)
Gene names: TT_C1332, rps7, rpsG
Sequence domains: Ribosomal protein S7p/S5e
Small ribosomal subunit protein uS8 Chains: RA, WC
Molecule details ›
Chains: RA, WC
Length: 138 amino acids
Theoretical weight: 15.87 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62668 (Residues: 1-138; Coverage: 100%)
Gene names: TT_C1314, rps8, rpsH
Sequence domains: Ribosomal protein S8
Small ribosomal subunit protein uS9 Chains: SA, XC
Molecule details ›
Chains: SA, XC
Length: 128 amino acids
Theoretical weight: 14.43 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62669 (Residues: 1-128; Coverage: 100%)
Gene names: TT_C1100, rps9, rpsI
Sequence domains: Ribosomal protein S9/S16
Small ribosomal subunit protein uS10 Chains: TA, YC
Molecule details ›
Chains: TA, YC
Length: 105 amino acids
Theoretical weight: 11.95 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62653 (Residues: 1-105; Coverage: 100%)
Gene names: TT_C1329, rps10, rpsJ
Sequence domains: Ribosomal protein S10p/S20e
Small ribosomal subunit protein uS11 Chains: UA, ZC
Molecule details ›
Chains: UA, ZC
Length: 129 amino acids
Theoretical weight: 13.74 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62654 (Residues: 1-129; Coverage: 100%)
Gene names: TT_C1302, rps11, rpsK
Sequence domains: Ribosomal protein S11
Small ribosomal subunit protein uS12 Chains: AD, VA
Molecule details ›
Chains: AD, VA
Length: 132 amino acids
Theoretical weight: 14.68 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P61941 (Residues: 1-132; Coverage: 100%)
Gene names: TT_C1333, rps12, rpsL
Sequence domains: Ribosomal protein S12/S23
Small ribosomal subunit protein uS13 Chains: BD, WA
Molecule details ›
Chains: BD, WA
Length: 126 amino acids
Theoretical weight: 14.34 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62655 (Residues: 1-126; Coverage: 100%)
Gene names: TT_C1303, rps13, rpsM
Sequence domains: Ribosomal protein S13/S18
Small ribosomal subunit protein uS14 Chains: CD, XA
Molecule details ›
Chains: CD, XA
Length: 61 amino acids
Theoretical weight: 7.16 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62656 (Residues: 1-61; Coverage: 100%)
Gene names: TT_C1315, rps14, rpsN, rpsZ
Sequence domains: Ribosomal protein S14p/S29e
Small ribosomal subunit protein uS15 Chains: DD, YA
Molecule details ›
Chains: DD, YA
Length: 89 amino acids
Theoretical weight: 10.58 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62657 (Residues: 1-89; Coverage: 100%)
Gene names: TT_C0773, rps15, rpsO
Sequence domains: Ribosomal protein S15
Small ribosomal subunit protein bS16 Chains: ED, ZA
Molecule details ›
Chains: ED, ZA
Length: 88 amino acids
Theoretical weight: 10.41 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62238 (Residues: 1-88; Coverage: 100%)
Gene names: TT_C0673, rps16, rpsP
Sequence domains: Ribosomal protein S16
Small ribosomal subunit protein uS17 Chains: AB, FD
Molecule details ›
Chains: AB, FD
Length: 105 amino acids
Theoretical weight: 12.32 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62658 (Residues: 1-105; Coverage: 100%)
Gene names: TT_C1319, rps17, rpsQ
Sequence domains: Ribosomal protein S17
Small ribosomal subunit protein bS18 Chains: BB, GD
Molecule details ›
Chains: BB, GD
Length: 88 amino acids
Theoretical weight: 10.26 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62659 (Residues: 1-88; Coverage: 100%)
Gene names: TT_C1742, rps18, rpsR
Sequence domains: Ribosomal protein S18
Small ribosomal subunit protein uS19 Chains: CB, HD
Molecule details ›
Chains: CB, HD
Length: 93 amino acids
Theoretical weight: 10.61 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62660 (Residues: 1-93; Coverage: 100%)
Gene names: TT_C1324, rps19, rpsS
Sequence domains: Ribosomal protein S19
Small ribosomal subunit protein bS20 Chains: DB, ID
Molecule details ›
Chains: DB, ID
Length: 106 amino acids
Theoretical weight: 11.72 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62661 (Residues: 1-106; Coverage: 100%)
Gene names: TT_C1031, rps20, rpsT
Sequence domains: Ribosomal protein S20
Small ribosomal subunit protein bTHX Chains: EB, JD
Molecule details ›
Chains: EB, JD
Length: 27 amino acids
Theoretical weight: 3.35 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62613 (Residues: 1-27; Coverage: 100%)
Gene names: TT_C1030, rpsU
Sequence domains: 30S ribosomal protein Thx
16S ribosomal RNA Chains: A, FB
Molecule details ›
Chains: A, FB
Length: 1507 nucleotides
Theoretical weight: 489.56 KDa
Sequence domains: Bacterial small subunit ribosomal RNA
23S ribosomal RNA Chains: B, GB
Molecule details ›
Chains: B, GB
Length: 2880 nucleotides
Theoretical weight: 936.79 KDa
Sequence domains: Bacterial large subunit ribosomal RNA
5S ribosomal RNA Chains: C, HB
Molecule details ›
Chains: C, HB
Length: 120 nucleotides
Theoretical weight: 38.88 KDa
Sequence domains: 5S ribosomal RNA
tRNA Chains: D, IA, IB, NC
Molecule details ›
Chains: D, IA, IB, NC
Length: 77 nucleotides
Theoretical weight: 24.85 KDa
Sequence domains: tRNA
Messenger RNA Chains: HA, MC
Molecule details ›
Chains: HA, MC
Length: 27 nucleotides
Theoretical weight: 8.86 KDa

Ligands and Environments

3 bound ligands:
Ligand MG 1428 x MG
Ligand BLS 2 x BLS
Ligand ZN 10 x ZN
14 modified residues:
Ligand PSU 12 x PSU
Ligand 7MG 2 x 7MG
Ligand M2G 2 x M2G
Ligand 5MC 16 x 5MC
Ligand 2MG 2 x 2MG
Ligand 4OC 4 x 4OC
Ligand UR3 2 x UR3
Ligand MA6 4 x MA6
Ligand 5MU 8 x 5MU
Ligand OMG 2 x OMG
Ligand 2MA 2 x 2MA
Ligand 2MU 2 x 2MU
Ligand 4SU 4 x 4SU
Ligand 0TD 2 x 0TD

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-D
Spacegroup: P212121
Unit cell:
a: 209.86Å b: 450.69Å c: 615.88Å
α: 90° β: 90° γ: 90°
Expression system: Escherichia coli

Quick links

Citations

3 review citations

Ribosome Rescue Pathways in Bacteria.
Müller et al. (2021)
2 more

1 mention without citation

Conformational Control of Translation Termination on the 70S Ribosome.
Svidritskiy et al. (2018)