› 6n1d

X-ray diffraction
3.2Å resolution

X-ray Crystal complex showing Spontaneous Ribosomal Translocation of mRNA and tRNAs into a Chimeric Hybrid State

Released:
DOI: 10.2210/pdb6n1d/pdb
PDB entry 6n1d coloured by chain, front view.
PDB entry 6n1d coloured by chain, side view.
PDB entry 6n1d coloured by chain, top view.
Source organisms:
Primary publication:
Spontaneous ribosomal translocation of mRNA and tRNAs into a chimeric hybrid state.
Zhou J, Lancaster L, Donohue JP, Noller HF
Proc Natl Acad Sci U S A 116 7813-7818 (2019)
PMID: 30936299

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
hetero 55-mer
hetero 56-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-219407 (preferred)
Entry contents:
50 distinct polypeptide molecules
6 distinct RNA molecules
Macromolecules (56 distinct):
Large ribosomal subunit protein uL1 Chains: AL01, BL01
Molecule details ›
Chains: AL01, BL01
Length: 228 amino acids
Theoretical weight: 24.74 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: Q72GV9 (Residues: 2-229; Coverage: 100%)
Gene names: TT_C1739, rplA
Sequence domains: Ribosomal protein L1p/L10e family
Large ribosomal subunit protein uL2 Chains: AL02, BL02
Molecule details ›
Chains: AL02, BL02
Length: 276 amino acids
Theoretical weight: 30.53 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72I07 (Residues: 1-276; Coverage: 100%)
Gene names: TT_C1325, rplB
Sequence domains:
Large ribosomal subunit protein uL3 Chains: AL03, BL03
Molecule details ›
Chains: AL03, BL03
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: AL04, BL04
Molecule details ›
Chains: AL04, BL04
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: AL05, BL05
Molecule details ›
Chains: AL05, BL05
Length: 181 amino acids
Theoretical weight: 20.94 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72I16 (Residues: 2-182; Coverage: 100%)
Gene names: TT_C1316, rplE
Sequence domains:
Large ribosomal subunit protein uL6 Chains: AL06, BL06
Molecule details ›
Chains: AL06, BL06
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: AL09, BL09
Molecule details ›
Chains: AL09, BL09
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: AL13, BL13
Molecule details ›
Chains: AL13, BL13
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: AL14, BL14
Molecule details ›
Chains: AL14, BL14
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: AL15, BL15
Molecule details ›
Chains: AL15, BL15
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: AL16, BL16
Molecule details ›
Chains: AL16, BL16
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: AL17, BL17
Molecule details ›
Chains: AL17, BL17
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: AL18, BL18
Molecule details ›
Chains: AL18, BL18
Length: 111 amino acids
Theoretical weight: 12.51 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72I20 (Residues: 2-112; Coverage: 99%)
Gene names: TT_C1312, rplR
Sequence domains: Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
Large ribosomal subunit protein bL19 Chains: AL19, BL19
Molecule details ›
Chains: AL19, BL19
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: AL20, BL20
Molecule details ›
Chains: AL20, BL20
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: AL21, BL21
Molecule details ›
Chains: AL21, BL21
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: AL22, BL22
Molecule details ›
Chains: AL22, BL22
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: AL23, BL23
Molecule details ›
Chains: AL23, BL23
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: AL24, BL24
Molecule details ›
Chains: AL24, BL24
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: AL25, BL25
Molecule details ›
Chains: AL25, BL25
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: AL27, BL27
Molecule details ›
Chains: AL27, BL27
Length: 84 amino acids
Theoretical weight: 9.4 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: Q72HR3 (Residues: 2-85; Coverage: 99%)
Gene names: TT_C1423, rpmA
Sequence domains: Ribosomal L27 protein
Large ribosomal subunit protein bL28 Chains: AL28, BL28
Molecule details ›
Chains: AL28, BL28
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: AL29, BL29
Molecule details ›
Chains: AL29, BL29
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: AL30, BL30
Molecule details ›
Chains: AL30, BL30
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: AL31, BL31
Molecule details ›
Chains: AL31, BL31
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: AL32, BL32
Molecule details ›
Chains: AL32, BL32
Length: 59 amino acids
Theoretical weight: 6.59 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: P62652 (Residues: 2-60; Coverage: 98%)
Gene names: TT_C0050, rpl32, rpmF
Sequence domains: Ribosomal L32p protein family
Large ribosomal subunit protein bL33 Chains: AL33, BL33
Molecule details ›
Chains: AL33, BL33
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: AL34, BL34
Molecule details ›
Chains: AL34, BL34
Length: 49 amino acids
Theoretical weight: 6.13 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: P80340 (Residues: 1-49; Coverage: 100%)
Gene names: TTHA0446, rpl34, rpmH
Sequence domains: Ribosomal protein L34
Large ribosomal subunit protein bL35 Chains: AL35, BL35
Molecule details ›
Chains: AL35, BL35
Length: 64 amino acids
Theoretical weight: 7.37 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72L77 (Residues: 2-65; Coverage: 99%)
Gene names: TT_C0184, rpmI
Sequence domains: Ribosomal protein L35
Large ribosomal subunit protein bL36 Chains: AL36, BL36
Molecule details ›
Chains: AL36, BL36
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
Small ribosomal subunit protein uS2 Chains: AS02, BS02
Molecule details ›
Chains: AS02, BS02
Length: 255 amino acids
Theoretical weight: 29.19 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62662 (Residues: 2-256; Coverage: 100%)
Gene names: TT_C0509, rps2, rpsB
Sequence domains: Ribosomal protein S2
Small ribosomal subunit protein uS3 Chains: AS03, BS03
Molecule details ›
Chains: AS03, BS03
Length: 238 amino acids
Theoretical weight: 26.62 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62663 (Residues: 2-239; Coverage: 100%)
Gene names: TT_C1322, rps3, rpsC
Sequence domains:
Small ribosomal subunit protein uS4 Chains: AS04, BS04
Molecule details ›
Chains: AS04, BS04
Length: 208 amino acids
Theoretical weight: 24.24 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62664 (Residues: 2-209; Coverage: 100%)
Gene names: TT_C1301, rps4, rpsD
Sequence domains:
Small ribosomal subunit protein uS5 Chains: AS05, BS05
Molecule details ›
Chains: AS05, BS05
Length: 161 amino acids
Theoretical weight: 17.45 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62665 (Residues: 2-162; Coverage: 99%)
Gene names: TT_C1311, rps5, rpsE
Sequence domains:
Small ribosomal subunit protein bS6 Chains: AS06, BS06
Molecule details ›
Chains: AS06, BS06
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: AS07, BS07
Molecule details ›
Chains: AS07, BS07
Length: 155 amino acids
Theoretical weight: 17.92 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62667 (Residues: 2-156; Coverage: 99%)
Gene names: TT_C1332, rps7, rpsG
Sequence domains: Ribosomal protein S7p/S5e
Small ribosomal subunit protein uS8 Chains: AS08, BS08
Molecule details ›
Chains: AS08, BS08
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: AS09, BS09
Molecule details ›
Chains: AS09, BS09
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: AS10, BS10
Molecule details ›
Chains: AS10, BS10
Length: 104 amino acids
Theoretical weight: 11.82 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62653 (Residues: 2-105; Coverage: 99%)
Gene names: TT_C1329, rps10, rpsJ
Sequence domains: Ribosomal protein S10p/S20e
Small ribosomal subunit protein uS11 Chains: AS11, BS11
Molecule details ›
Chains: AS11, BS11
Length: 128 amino acids
Theoretical weight: 13.61 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62654 (Residues: 2-129; Coverage: 99%)
Gene names: TT_C1302, rps11, rpsK
Sequence domains: Ribosomal protein S11
Small ribosomal subunit protein uS12 Chains: AS12, BS12
Molecule details ›
Chains: AS12, BS12
Length: 131 amino acids
Theoretical weight: 14.51 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P61941 (Residues: 2-132; Coverage: 99%)
Gene names: TT_C1333, rps12, rpsL
Sequence domains: Ribosomal protein S12/S23
Small ribosomal subunit protein uS13 Chains: AS13, BS13
Molecule details ›
Chains: AS13, BS13
Length: 125 amino acids
Theoretical weight: 14.21 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62655 (Residues: 2-126; Coverage: 99%)
Gene names: TT_C1303, rps13, rpsM
Sequence domains: Ribosomal protein S13/S18
Small ribosomal subunit protein uS14 Chains: AS14, BS14
Molecule details ›
Chains: AS14, BS14
Length: 60 amino acids
Theoretical weight: 7.03 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62656 (Residues: 2-61; Coverage: 98%)
Gene names: TT_C1315, rps14, rpsN, rpsZ
Sequence domains: Ribosomal protein S14p/S29e
Small ribosomal subunit protein uS15 Chains: AS15, BS15
Molecule details ›
Chains: AS15, BS15
Length: 88 amino acids
Theoretical weight: 10.45 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62657 (Residues: 2-89; Coverage: 99%)
Gene names: TT_C0773, rps15, rpsO
Sequence domains: Ribosomal protein S15
Small ribosomal subunit protein bS16 Chains: AS16, BS16
Molecule details ›
Chains: AS16, BS16
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: AS17, BS17
Molecule details ›
Chains: AS17, BS17
Length: 104 amino acids
Theoretical weight: 12.19 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62658 (Residues: 2-105; Coverage: 99%)
Gene names: TT_C1319, rps17, rpsQ
Sequence domains: Ribosomal protein S17
Small ribosomal subunit protein bS18 Chains: AS18, BS18
Molecule details ›
Chains: AS18, BS18
Length: 87 amino acids
Theoretical weight: 10.13 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62659 (Residues: 2-88; Coverage: 99%)
Gene names: TT_C1742, rps18, rpsR
Sequence domains: Ribosomal protein S18
Small ribosomal subunit protein uS19 Chains: AS19, BS19
Molecule details ›
Chains: AS19, BS19
Length: 92 amino acids
Theoretical weight: 10.47 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62660 (Residues: 2-93; Coverage: 99%)
Gene names: TT_C1324, rps19, rpsS
Sequence domains: Ribosomal protein S19
Small ribosomal subunit protein bS20 Chains: AS20, BS20
Molecule details ›
Chains: AS20, BS20
Length: 105 amino acids
Theoretical weight: 11.59 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62661 (Residues: 2-106; Coverage: 99%)
Gene names: TT_C1031, rps20, rpsT
Sequence domains: Ribosomal protein S20
Small ribosomal subunit protein bTHX Chains: ATHX, BTHX
Molecule details ›
Chains: ATHX, BTHX
Length: 26 amino acids
Theoretical weight: 3.22 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62613 (Residues: 2-27; Coverage: 96%)
Gene names: TT_C1030, rpsU
Sequence domains: 30S ribosomal protein Thx
16S ribosomal RNA Chains: A16S, B16S
Molecule details ›
Chains: A16S, B16S
Length: 1518 nucleotides
Theoretical weight: 492.77 KDa
Sequence domains: Bacterial small subunit ribosomal RNA
23S ribosomal RNA Chains: A23S, B23S
Molecule details ›
Chains: A23S, B23S
Length: 2881 nucleotides
Theoretical weight: 937.01 KDa
Sequence domains: Bacterial large subunit ribosomal RNA
5s rRNA Chains: A5S, B5S
Molecule details ›
Chains: A5S, B5S
Length: 119 nucleotides
Theoretical weight: 38.55 KDa
Sequence domains: 5S ribosomal RNA
Messenger RNA Chains: AMRN, BMRN
Molecule details ›
Chains: AMRN, BMRN
Length: 17 nucleotides
Theoretical weight: 5.56 KDa
P-tRNA Chains: APTN, BPTN
Molecule details ›
Chains: APTN, BPTN
Length: 76 nucleotides
Theoretical weight: 24.62 KDa
Sequence domains: tRNA
A tRNA Chain: BATN
Molecule details ›
Chain: BATN
Length: 85 nucleotides
Theoretical weight: 27.54 KDa
Sequence domains: tRNA

Ligands and Environments

2 bound ligands:
Ligand MG 359 x MG
Ligand SF4 2 x SF4
7 modified residues:
Ligand 4SU 2 x 4SU
Ligand 6MZ 2 x 6MZ
Ligand G7M 2 x G7M
Ligand 5MU 3 x 5MU
Ligand PSU 4 x PSU
Ligand QUO 1 x QUO
Ligand MIA 1 x MIA

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-D
Spacegroup: P212121
Unit cell:
a: 207.45Å b: 442.87Å c: 613Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.271 0.268 0.321

Quick links

Citations

8 review citations

Mechanisms and regulation of protein synthesis in mitochondria.
Kummer et al. (2021)
7 more

1 mention without citation

Spontaneous ribosomal translocation of mRNA and tRNAs into a chimeric hybrid state.
Zhou et al. (2019)