› 5uq8

Electron Microscopy
3.2Å resolution

70S ribosome complex with dnaX mRNA stem-loop and E-site tRNA ("out" conformation)

Released:
DOI: 10.2210/pdb5uq8/pdb
PDB entry 5uq8 coloured by chain, front view.
PDB entry 5uq8 coloured by chain, side view.
PDB entry 5uq8 coloured by chain, top view.
Source organism: Thermus thermophilus HB8
Primary publication:
Alternative Mode of E-Site tRNA Binding in the Presence of a Downstream mRNA Stem Loop at the Entrance Channel.
Zhang Y, Hong S, Ruangprasert A, Skiniotis G, Dunham CM
Structure 26 437-445.e3 (2018)
PMID: 29456023
Related structures: EMD-8597

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 56-mer (preferred)
Entry contents:
50 distinct polypeptide molecules
6 distinct RNA molecules
Macromolecules (56 distinct):
Large ribosomal subunit protein uL2 Chain: D
Molecule details ›
Chain: D
Length: 275 amino acids
Theoretical weight: 30.4 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60405 (Residues: 2-276; Coverage: 100%)
Gene names: TTHA1689, rplB
Sequence domains:
Large ribosomal subunit protein uL3 Chain: E
Molecule details ›
Chain: E
Length: 204 amino acids
Theoretical weight: 22.25 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHN8 (Residues: 1-204; Coverage: 99%)
Gene names: TTHA1692, rplC
Sequence domains: Ribosomal protein L3
Large ribosomal subunit protein uL4 Chain: F
Molecule details ›
Chain: F
Length: 203 amino acids
Theoretical weight: 22.51 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHN9 (Residues: 6-208; Coverage: 97%)
Gene names: TTHA1691, rplD
Sequence domains: Ribosomal protein L4/L1 family
Large ribosomal subunit protein uL5 Chain: G
Molecule details ›
Chain: G
Length: 181 amino acids
Theoretical weight: 20.93 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHQ0 (Residues: 2-182; Coverage: 100%)
Gene names: TTHA1680, rplE
Sequence domains:
50S ribosomal protein L6 Chain: H
Molecule details ›
Chain: H
Length: 173 amino acids
Theoretical weight: 18.89 KDa
Source organism: Thermus thermophilus HB8
Large ribosomal subunit protein bL9 Chain: I
Molecule details ›
Chain: I
Length: 146 amino acids
Theoretical weight: 16.16 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SLQ1 (Residues: 1-146; Coverage: 99%)
Gene names: TTHA0242, rplI
Sequence domains:
Large ribosomal subunit protein uL13 Chain: N
Molecule details ›
Chain: N
Length: 140 amino acids
Theoretical weight: 15.93 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60488 (Residues: 1-140; Coverage: 100%)
Gene names: TTHA1465, rplM
Sequence domains: Ribosomal protein L13
Large ribosomal subunit protein uL14 Chain: O
Molecule details ›
Chain: O
Length: 122 amino acids
Theoretical weight: 13.32 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHP8 (Residues: 1-122; Coverage: 100%)
Gene names: TTHA1682, rplN
Sequence domains: Ribosomal protein L14p/L23e
Large ribosomal subunit protein uL15 Chain: P
Molecule details ›
Chain: P
Length: 149 amino acids
Theoretical weight: 16.25 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHQ7 (Residues: 1-149; Coverage: 99%)
Gene names: TTHA1673, rplO
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
Large ribosomal subunit protein uL16 Chain: Q
Molecule details ›
Chain: Q
Length: 141 amino acids
Theoretical weight: 15.99 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60489 (Residues: 1-141; Coverage: 100%)
Gene names: TTHA1685, rplP
Sequence domains: Ribosomal protein L16p/L10e
Large ribosomal subunit protein bL17 Chain: R
Molecule details ›
Chain: R
Length: 118 amino acids
Theoretical weight: 13.75 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q9Z9H5 (Residues: 1-118; Coverage: 100%)
Gene names: TTHA1663, rpl17, rplQ
Sequence domains: Ribosomal protein L17
Large ribosomal subunit protein uL18 Chain: S
Molecule details ›
Chain: S
Length: 110 amino acids
Theoretical weight: 12.44 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHQ4 (Residues: 3-112; Coverage: 98%)
Gene names: TTHA1676, rplR
Sequence domains: Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
Large ribosomal subunit protein bL19 Chain: T
Molecule details ›
Chain: T
Length: 131 amino acids
Theoretical weight: 15.5 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60490 (Residues: 1-131; Coverage: 90%)
Gene names: TTHA1031, rplS
Sequence domains: Ribosomal protein L19
Large ribosomal subunit protein bL20 Chain: U
Molecule details ›
Chain: U
Length: 116 amino acids
Theoretical weight: 13.59 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60491 (Residues: 2-117; Coverage: 98%)
Gene names: TTHA0553, rplT
Sequence domains: Ribosomal protein L20
Large ribosomal subunit protein bL21 Chain: V
Molecule details ›
Chain: V
Length: 101 amino acids
Theoretical weight: 11.07 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60492 (Residues: 1-101; Coverage: 100%)
Gene names: TTHA1783, rplU
Sequence domains: Ribosomal prokaryotic L21 protein
Large ribosomal subunit protein uL22 Chain: W
Molecule details ›
Chain: W
Length: 112 amino acids
Theoretical weight: 12.68 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHP3 (Residues: 1-112; Coverage: 99%)
Gene names: TTHA1687, rplV
Sequence domains: Ribosomal protein L22p/L17e
Large ribosomal subunit protein uL23 Chain: X
Molecule details ›
Chain: X
Length: 95 amino acids
Theoretical weight: 10.65 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHP0 (Residues: 1-95; Coverage: 99%)
Gene names: TTHA1690, rplW
Sequence domains: Ribosomal protein L23
Large ribosomal subunit protein uL24 Chain: Y
Molecule details ›
Chain: Y
Length: 107 amino acids
Theoretical weight: 11.73 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHP9 (Residues: 1-107; Coverage: 97%)
Gene names: TTHA1681, rplX
Sequence domains:
Large ribosomal subunit protein bL25 Chain: Z
Molecule details ›
Chain: Z
Length: 187 amino acids
Theoretical weight: 21.14 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHZ1 (Residues: 1-187; Coverage: 91%)
Gene names: TTHA1589, rpl25, rplY, rptL5
Sequence domains:
Large ribosomal subunit protein bL27 Chain: 0
Molecule details ›
Chain: 0
Length: 77 amino acids
Theoretical weight: 8.69 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60493 (Residues: 8-84; Coverage: 91%)
Gene names: TTHA1782, rpmA
Sequence domains: Ribosomal L27 protein
Large ribosomal subunit protein bL28 Chain: 1
Molecule details ›
Chain: 1
Length: 97 amino acids
Theoretical weight: 10.87 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60494 (Residues: 2-98; Coverage: 99%)
Gene names: TTHA0042, rpmB
Sequence domains: Ribosomal L28 family
Large ribosomal subunit protein uL29 Chain: 2
Molecule details ›
Chain: 2
Length: 70 amino acids
Theoretical weight: 8.49 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHP6 (Residues: 1-70; Coverage: 97%)
Gene names: TTHA1684, rpmC
Sequence domains: Ribosomal L29 protein
Large ribosomal subunit protein uL30 Chain: 3
Molecule details ›
Chain: 3
Length: 59 amino acids
Theoretical weight: 6.67 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHQ6 (Residues: 2-60; Coverage: 98%)
Gene names: TTHA1674, rpmD
Sequence domains: Ribosomal protein L30p/L7e
Large ribosomal subunit protein bL31 Chain: 4
Molecule details ›
Chain: 4
Length: 69 amino acids
Theoretical weight: 8.09 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SJE1 (Residues: 1-69; Coverage: 97%)
Gene names: TTHA1073, rpmE
Sequence domains: Ribosomal protein L31
Large ribosomal subunit protein bL32 Chain: 5
Molecule details ›
Chain: 5
Length: 59 amino acids
Theoretical weight: 6.59 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80339 (Residues: 2-60; Coverage: 98%)
Gene names: TTHA0418, rpl32, rpmF
Sequence domains: Ribosomal L32p protein family
Large ribosomal subunit protein bL33 Chain: 6
Molecule details ›
Chain: 6
Length: 53 amino acids
Theoretical weight: 6.5 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P35871 (Residues: 2-54; Coverage: 98%)
Gene names: TTHA0250, rpl33, rpmG
Sequence domains: Ribosomal protein L33
Large ribosomal subunit protein bL34 Chain: 7
Molecule details ›
Chain: 7
Length: 48 amino acids
Theoretical weight: 5.98 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80340 (Residues: 1-48; Coverage: 98%)
Gene names: TTHA0446, rpl34, rpmH
Sequence domains: Ribosomal protein L34
Large ribosomal subunit protein bL35 Chain: 8
Molecule details ›
Chain: 8
Length: 64 amino acids
Theoretical weight: 7.37 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SKU1 (Residues: 2-65; Coverage: 99%)
Gene names: TTHA0552, rpmI
Sequence domains: Ribosomal protein L35
Large ribosomal subunit protein bL36 Chain: 9
Molecule details ›
Chain: 9
Length: 37 amino acids
Theoretical weight: 4.44 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHR2 (Residues: 1-37; Coverage: 100%)
Gene names: TTHA1668, rpmJ
Sequence domains: Ribosomal protein L36
Small ribosomal subunit protein uS2 Chain: b
Molecule details ›
Chain: b
Length: 231 amino acids
Theoretical weight: 26.65 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80371 (Residues: 7-237; Coverage: 90%)
Gene names: TTHA0861, rps2, rpsB
Sequence domains: Ribosomal protein S2
Small ribosomal subunit protein uS3 Chain: c
Molecule details ›
Chain: c
Length: 206 amino acids
Theoretical weight: 22.86 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80372 (Residues: 2-207; Coverage: 86%)
Gene names: TTHA1686, rps3, rpsC
Sequence domains:
Small ribosomal subunit protein uS4 Chain: d
Molecule details ›
Chain: d
Length: 208 amino acids
Theoretical weight: 24.24 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80373 (Residues: 2-209; Coverage: 100%)
Gene names: TTHA1665, rps4, rpsD
Sequence domains:
Small ribosomal subunit protein uS5 Chain: e
Molecule details ›
Chain: e
Length: 148 amino acids
Theoretical weight: 16.14 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHQ5 (Residues: 5-152; Coverage: 91%)
Gene names: TTHA1675, rpsE
Sequence domains:
Small ribosomal subunit protein bS6 Chain: f
Molecule details ›
Chain: f
Length: 100 amino acids
Theoretical weight: 11.92 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SLP8 (Residues: 1-100; Coverage: 99%)
Gene names: TTHA0245, rpsF
Sequence domains: Ribosomal protein S6
Small ribosomal subunit protein uS7 Chain: g
Molecule details ›
Chain: g
Length: 155 amino acids
Theoretical weight: 17.92 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P17291 (Residues: 2-156; Coverage: 99%)
Gene names: TTHA1696, rps7, rpsG
Sequence domains: Ribosomal protein S7p/S5e
30S ribosomal protein S8 Chain: h
Molecule details ›
Chain: h
Length: 137 amino acids
Theoretical weight: 15.74 KDa
Source organism: Thermus thermophilus HB8
Small ribosomal subunit protein uS9 Chain: i
Molecule details ›
Chain: i
Length: 126 amino acids
Theoretical weight: 14.12 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80374 (Residues: 2-127; Coverage: 98%)
Gene names: TTHA1464, rps9, rpsI
Sequence domains: Ribosomal protein S9/S16
Small ribosomal subunit protein uS10 Chain: j
Molecule details ›
Chain: j
Length: 96 amino acids
Theoretical weight: 11.06 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHN7 (Residues: 5-100; Coverage: 91%)
Gene names: TTHA1693, rpsJ
Sequence domains: Ribosomal protein S10p/S20e
Small ribosomal subunit protein uS11 Chain: k
Molecule details ›
Chain: k
Length: 114 amino acids
Theoretical weight: 12.03 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80376 (Residues: 13-126; Coverage: 88%)
Gene names: TTHA1666, rps11, rpsK
Sequence domains: Ribosomal protein S11
Small ribosomal subunit protein uS12 Chain: l
Molecule details ›
Chain: l
Length: 122 amino acids
Theoretical weight: 13.65 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHN3 (Residues: 2-123; Coverage: 92%)
Gene names: TTHA1697, rpsL
Sequence domains: Ribosomal protein S12/S23
Small ribosomal subunit protein uS13 Chain: m
Molecule details ›
Chain: m
Length: 114 amino acids
Theoretical weight: 13.07 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80377 (Residues: 3-116; Coverage: 91%)
Gene names: TTHA1667, rps13, rpsM
Sequence domains: Ribosomal protein S13/S18
30S ribosomal protein S14 type Z Chain: n
Molecule details ›
Chain: n
Length: 60 amino acids
Theoretical weight: 7.03 KDa
Source organism: Thermus thermophilus HB8
Small ribosomal subunit protein uS15 Chain: o
Molecule details ›
Chain: o
Length: 88 amino acids
Theoretical weight: 10.45 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SJ76 (Residues: 2-89; Coverage: 99%)
Gene names: TTHA1138, rpsO
Sequence domains: Ribosomal protein S15
Small ribosomal subunit protein bS16 Chain: p
Molecule details ›
Chain: p
Length: 82 amino acids
Theoretical weight: 9.8 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SJH3 (Residues: 1-82; Coverage: 93%)
Gene names: TTHA1035, rpsP
Sequence domains: Ribosomal protein S16
30S ribosomal protein S17 Chain: q
Molecule details ›
Chain: q
Length: 99 amino acids
Theoretical weight: 11.72 KDa
Source organism: Thermus thermophilus HB8
Small ribosomal subunit protein bS18 Chain: r
Molecule details ›
Chain: r
Length: 68 amino acids
Theoretical weight: 7.9 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SLQ0 (Residues: 20-87; Coverage: 77%)
Gene names: TTHA0243, rpsR
Sequence domains: Ribosomal protein S18
Small ribosomal subunit protein uS19 Chain: s
Molecule details ›
Chain: s
Length: 83 amino acids
Theoretical weight: 9.46 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHP2 (Residues: 2-84; Coverage: 89%)
Gene names: TTHA1688, rpsS
Sequence domains: Ribosomal protein S19
Small ribosomal subunit protein bS20 Chain: t
Molecule details ›
Chain: t
Length: 98 amino acids
Theoretical weight: 10.88 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80380 (Residues: 6-103; Coverage: 93%)
Gene names: TTHA1397, rps20, rpsT
Sequence domains: Ribosomal protein S20
Small ribosomal subunit protein bTHX Chain: u
Molecule details ›
Chain: u
Length: 23 amino acids
Theoretical weight: 2.83 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SIH3 (Residues: 2-24; Coverage: 85%)
Gene names: TTHA1396, rpsU
Sequence domains: 30S ribosomal protein Thx
Large ribosomal subunit protein uL1 Chain: C
Molecule details ›
Chain: C
Length: 226 amino acids
Theoretical weight: 24.51 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SLP7 (Residues: 3-229; Coverage: 99%)
Gene names: TTHA0246, rplA
Sequence domains: Ribosomal protein L1p/L10e family
23S ribosomal RNA Chain: A
Molecule details ›
Chain: A
Length: 2915 nucleotides
Theoretical weight: 948.04 KDa
Sequence domains: Bacterial large subunit ribosomal RNA
5S ribosomal RNA Chain: B
Molecule details ›
Chain: B
Length: 120 nucleotides
Theoretical weight: 38.88 KDa
Sequence domains: 5S ribosomal RNA
16S ribosomal RNA Chain: a
Molecule details ›
Chain: a
Length: 1521 nucleotides
Theoretical weight: 493.9 KDa
Sequence domains: Bacterial small subunit ribosomal RNA
P-site tRNA fMet Chain: y
Molecule details ›
Chain: y
Length: 77 nucleotides
Theoretical weight: 24.8 KDa
Sequence domains: tRNA
E-site tRNA Phe Chain: z
Molecule details ›
Chain: z
Length: 76 nucleotides
Theoretical weight: 24.49 KDa
Sequence domains: tRNA
Messenger RNA Chain: x
Molecule details ›
Chain: x
Length: 55 nucleotides
Theoretical weight: 17.77 KDa
Sequence domains: DnaX ribosomal frameshifting element

Ligands and Environments

2 bound ligands:
Ligand ZN 6 x ZN
Ligand SF4 1 x SF4
13 modified residues:
Ligand PSU 4 x PSU
Ligand 5MU 2 x 5MU
Ligand 4OC 2 x 4OC
Ligand 5MC 6 x 5MC
Ligand OMG 1 x OMG
Ligand 2MA 1 x 2MA
Ligand 2MU 1 x 2MU
Ligand 7MG 1 x 7MG
Ligand M2G 1 x M2G
Ligand 2MG 1 x 2MG
Ligand UR3 1 x UR3
Ligand MA6 2 x MA6
Ligand 0TD 1 x 0TD

Experiments and Validation Details

Entry percentile scores
Resolution: 3.2Å
Relevant EMDB volumes: EMD-8597

Quick links

Citations

17 citation in other articles

trans-Translation inhibitors bind to a novel site on the ribosome and clear Neisseria gonorrhoeae in vivo.
Aron et al. (2021)
16 more

2 mentions without citation

Alternative Mode of E-Site tRNA Binding in the Presence of a Downstream mRNA Stem Loop at the Entrance Channel.
Zhang et al. (2018)
1 more