› 6q95

Electron Microscopy
3.7Å resolution

Structure of tmRNA SmpB bound in A site of T. thermophilus 70S ribosome

Released:
DOI: 10.2210/pdb6q95/pdb
PDB entry 6q95 coloured by chain, front view.
PDB entry 6q95 coloured by chain, side view.
PDB entry 6q95 coloured by chain, top view.
Source organisms:
Primary publication:
How a circularized tmRNA moves through the ribosome.
Rae CD, Gordiyenko Y, Ramakrishnan V
Science 363 740-744 (2019)
PMID: 30765567
Related structures: EMD-4475

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 61-mer (preferred)
PDBe Complex ID:
PDB-CPX-216286 (preferred)
Entry contents:
53 distinct polypeptide molecules
7 distinct RNA molecules
Macromolecules (60 distinct):
Small ribosomal subunit protein uS2 Chain: g
Molecule details ›
Chain: g
Length: 235 amino acids
Theoretical weight: 27.12 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80371 (Residues: 7-241; Coverage: 92%)
Gene names: TTHA0861, rps2, rpsB
Sequence domains: Ribosomal protein S2
Small ribosomal subunit protein uS3 Chain: h
Molecule details ›
Chain: h
Length: 207 amino acids
Theoretical weight: 22.98 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80372 (Residues: 2-208; Coverage: 87%)
Gene names: TTHA1686, rps3, rpsC
Sequence domains:
Small ribosomal subunit protein uS4 Chain: i
Molecule details ›
Chain: i
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: j
Molecule details ›
Chain: j
Length: 151 amino acids
Theoretical weight: 16.46 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHQ5 (Residues: 5-155; Coverage: 93%)
Gene names: TTHA1675, rpsE
Sequence domains:
Small ribosomal subunit protein bS6 Chain: k
Molecule details ›
Chain: k
Length: 101 amino acids
Theoretical weight: 11.99 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SLP8 (Residues: 1-101; Coverage: 100%)
Gene names: TTHA0245, rpsF
Sequence domains: Ribosomal protein S6
Small ribosomal subunit protein uS7 Chain: l
Molecule details ›
Chain: l
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
Small ribosomal subunit protein uS8 Chain: m
Molecule details ›
Chain: m
Length: 138 amino acids
Theoretical weight: 15.87 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P0DOY9 (Residues: 1-138; Coverage: 100%)
Gene names: TTHA1678, rpsH
Sequence domains: Ribosomal protein S8
Small ribosomal subunit protein uS9 Chain: n
Molecule details ›
Chain: n
Length: 127 amino acids
Theoretical weight: 14.3 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80374 (Residues: 2-128; Coverage: 99%)
Gene names: TTHA1464, rps9, rpsI
Sequence domains: Ribosomal protein S9/S16
Small ribosomal subunit protein uS10 Chain: o
Molecule details ›
Chain: o
Length: 99 amino acids
Theoretical weight: 11.4 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHN7 (Residues: 3-101; Coverage: 94%)
Gene names: TTHA1693, rpsJ
Sequence domains: Ribosomal protein S10p/S20e
Small ribosomal subunit protein uS11 Chain: p
Molecule details ›
Chain: p
Length: 119 amino acids
Theoretical weight: 12.61 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80376 (Residues: 11-129; Coverage: 92%)
Gene names: TTHA1666, rps11, rpsK
Sequence domains: Ribosomal protein S11
Small ribosomal subunit protein uS12 Chain: q
Molecule details ›
Chain: q
Length: 125 amino acids
Theoretical weight: 13.88 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHN3 (Residues: 2-126; Coverage: 95%)
Gene names: TTHA1697, rpsL
Sequence domains: Ribosomal protein S12/S23
Small ribosomal subunit protein uS13 Chain: r
Molecule details ›
Chain: r
Length: 120 amino acids
Theoretical weight: 13.62 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80377 (Residues: 2-121; Coverage: 95%)
Gene names: TTHA1667, rps13, rpsM
Sequence domains: Ribosomal protein S13/S18
Small ribosomal subunit protein uS14 Chain: s
Molecule details ›
Chain: s
Length: 60 amino acids
Theoretical weight: 7.03 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P0DOY6 (Residues: 2-61; Coverage: 98%)
Gene names: TTHA1679, rpsN, rpsZ
Sequence domains: Ribosomal protein S14p/S29e
Small ribosomal subunit protein uS15 Chain: t
Molecule details ›
Chain: t
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: u
Molecule details ›
Chain: u
Length: 84 amino acids
Theoretical weight: 10 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SJH3 (Residues: 1-84; Coverage: 96%)
Gene names: TTHA1035, rpsP
Sequence domains: Ribosomal protein S16
Small ribosomal subunit protein uS17 Chain: v
Molecule details ›
Chain: v
Length: 100 amino acids
Theoretical weight: 11.88 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P0DOY7 (Residues: 2-101; Coverage: 95%)
Gene names: TTHA1683, rpsQ
Sequence domains: Ribosomal protein S17
Small ribosomal subunit protein bS18 Chain: w
Molecule details ›
Chain: w
Length: 70 amino acids
Theoretical weight: 8.16 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SLQ0 (Residues: 19-88; Coverage: 80%)
Gene names: TTHA0243, rpsR
Sequence domains: Ribosomal protein S18
Small ribosomal subunit protein uS19 Chain: x
Molecule details ›
Chain: x
Length: 79 amino acids
Theoretical weight: 9.01 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHP2 (Residues: 4-82; Coverage: 85%)
Gene names: TTHA1688, rpsS
Sequence domains: Ribosomal protein S19
Small ribosomal subunit protein bS20 Chain: y
Molecule details ›
Chain: y
Length: 99 amino acids
Theoretical weight: 10.92 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80380 (Residues: 8-106; Coverage: 93%)
Gene names: TTHA1397, rps20, rpsT
Sequence domains: Ribosomal protein S20
Small ribosomal subunit protein bTHX Chain: z
Molecule details ›
Chain: z
Length: 25 amino acids
Theoretical weight: 3.09 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SIH3 (Residues: 2-26; Coverage: 93%)
Gene names: TTHA1396, rpsU
Sequence domains: 30S ribosomal protein Thx
Large ribosomal subunit protein bL27 Chain: W
Molecule details ›
Chain: W
Length: 85 amino acids
Theoretical weight: 9.53 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60493 (Residues: 1-85; Coverage: 100%)
Gene names: TTHA1782, rpmA
Sequence domains: Ribosomal L27 protein
Large ribosomal subunit protein bL28 Chain: X
Molecule details ›
Chain: X
Length: 89 amino acids
Theoretical weight: 9.99 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60494 (Residues: 8-96; Coverage: 91%)
Gene names: TTHA0042, rpmB
Sequence domains: Ribosomal L28 family
Large ribosomal subunit protein uL29 Chain: Y
Molecule details ›
Chain: Y
Length: 51 amino acids
Theoretical weight: 6.11 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHP6 (Residues: 12-62; Coverage: 71%)
Gene names: TTHA1684, rpmC
Sequence domains: Ribosomal L29 protein
Large ribosomal subunit protein uL30 Chain: Z
Molecule details ›
Chain: Z
Length: 60 amino acids
Theoretical weight: 6.8 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHQ6 (Residues: 1-60; Coverage: 100%)
Gene names: TTHA1674, rpmD
Sequence domains: Ribosomal protein L30p/L7e
Large ribosomal subunit protein bL31 Chain: a
Molecule details ›
Chain: a
Length: 58 amino acids
Theoretical weight: 6.64 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SJE1 (Residues: 2-59; Coverage: 82%)
Gene names: TTHA1073, rpmE
Sequence domains: Ribosomal protein L31
Large ribosomal subunit protein bL32 Chain: b
Molecule details ›
Chain: b
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: c
Molecule details ›
Chain: c
Length: 45 amino acids
Theoretical weight: 5.6 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P35871 (Residues: 9-53; Coverage: 83%)
Gene names: TTHA0250, rpl33, rpmG
Sequence domains: Ribosomal protein L33
Large ribosomal subunit protein bL34 Chain: d
Molecule details ›
Chain: d
Length: 49 amino acids
Theoretical weight: 6.13 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80340 (Residues: 1-49; Coverage: 100%)
Gene names: TTHA0446, rpl34, rpmH
Sequence domains: Ribosomal protein L34
Large ribosomal subunit protein bL35 Chain: e
Molecule details ›
Chain: e
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 uL1 Chain: A
Molecule details ›
Chain: A
Length: 229 amino acids
Theoretical weight: 24.87 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SLP7 (Residues: 1-229; Coverage: 100%)
Gene names: TTHA0246, rplA
Sequence domains: Ribosomal protein L1p/L10e family
Large ribosomal subunit protein uL2 Chain: B
Molecule details ›
Chain: B
Length: 272 amino acids
Theoretical weight: 29.99 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60405 (Residues: 2-273; Coverage: 99%)
Gene names: TTHA1689, rplB
Sequence domains:
Large ribosomal subunit protein uL3 Chain: C
Molecule details ›
Chain: C
Length: 205 amino acids
Theoretical weight: 22.32 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHN8 (Residues: 1-205; Coverage: 100%)
Gene names: TTHA1692, rplC
Sequence domains: Ribosomal protein L3
Large ribosomal subunit protein uL4 Chain: D
Molecule details ›
Chain: D
Length: 208 amino acids
Theoretical weight: 23.07 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHN9 (Residues: 1-208; Coverage: 99%)
Gene names: TTHA1691, rplD
Sequence domains: Ribosomal protein L4/L1 family
Large ribosomal subunit protein uL5 Chain: E
Molecule details ›
Chain: E
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:
Large ribosomal subunit protein uL6 Chain: F
Molecule details ›
Chain: F
Length: 160 amino acids
Theoretical weight: 17.48 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P0DOY8 (Residues: 12-171; Coverage: 89%)
Gene names: TTHA1677, rplF
Sequence domains: Ribosomal protein L6
Large ribosomal subunit protein bL9 Chain: G
Molecule details ›
Chain: G
Length: 60 amino acids
Theoretical weight: 6.54 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SLQ1 (Residues: 1-60; Coverage: 41%)
Gene names: TTHA0242, rplI
Sequence domains: Ribosomal protein L9, N-terminal domain
Large ribosomal subunit protein uL13 Chain: J
Molecule details ›
Chain: J
Length: 139 amino acids
Theoretical weight: 15.83 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60488 (Residues: 1-139; Coverage: 99%)
Gene names: TTHA1465, rplM
Sequence domains: Ribosomal protein L13
Large ribosomal subunit protein uL14 Chain: K
Molecule details ›
Chain: K
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: L
Molecule details ›
Chain: L
Length: 146 amino acids
Theoretical weight: 15.86 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHQ7 (Residues: 5-150; Coverage: 97%)
Gene names: TTHA1673, rplO
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
Large ribosomal subunit protein uL16 Chain: M
Molecule details ›
Chain: M
Length: 136 amino acids
Theoretical weight: 15.36 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60489 (Residues: 6-141; Coverage: 97%)
Gene names: TTHA1685, rplP
Sequence domains: Ribosomal protein L16p/L10e
Large ribosomal subunit protein bL17 Chain: N
Molecule details ›
Chain: N
Length: 117 amino acids
Theoretical weight: 13.62 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q9Z9H5 (Residues: 2-118; Coverage: 99%)
Gene names: TTHA1663, rpl17, rplQ
Sequence domains: Ribosomal protein L17
Large ribosomal subunit protein uL18 Chain: O
Molecule details ›
Chain: O
Length: 99 amino acids
Theoretical weight: 11 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHQ4 (Residues: 11-109; Coverage: 88%)
Gene names: TTHA1676, rplR
Sequence domains: Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
Large ribosomal subunit protein bL19 Chain: P
Molecule details ›
Chain: P
Length: 138 amino acids
Theoretical weight: 16.29 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60490 (Residues: 1-138; Coverage: 95%)
Gene names: TTHA1031, rplS
Sequence domains: Ribosomal protein L19
Large ribosomal subunit protein bL20 Chain: Q
Molecule details ›
Chain: Q
Length: 117 amino acids
Theoretical weight: 13.65 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60491 (Residues: 2-118; Coverage: 99%)
Gene names: TTHA0553, rplT
Sequence domains: Ribosomal protein L20
Large ribosomal subunit protein bL21 Chain: R
Molecule details ›
Chain: R
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: S
Molecule details ›
Chain: S
Length: 113 amino acids
Theoretical weight: 12.81 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHP3 (Residues: 1-113; Coverage: 100%)
Gene names: TTHA1687, rplV
Sequence domains: Ribosomal protein L22p/L17e
Large ribosomal subunit protein uL23 Chain: T
Molecule details ›
Chain: T
Length: 93 amino acids
Theoretical weight: 10.39 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHP0 (Residues: 3-95; Coverage: 97%)
Gene names: TTHA1690, rplW
Sequence domains: Ribosomal protein L23
Large ribosomal subunit protein uL24 Chain: U
Molecule details ›
Chain: U
Length: 101 amino acids
Theoretical weight: 11.18 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHP9 (Residues: 2-102; Coverage: 92%)
Gene names: TTHA1681, rplX
Sequence domains:
Large ribosomal subunit protein bL25 Chain: V
Molecule details ›
Chain: V
Length: 92 amino acids
Theoretical weight: 10.95 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHZ1 (Residues: 3-94; Coverage: 45%)
Gene names: TTHA1589, rpl25, rplY, rptL5
Sequence domains: Ribosomal L25p family
SsrA-binding protein Chain: 5
Molecule details ›
Chain: 5
Length: 144 amino acids
Theoretical weight: 16.79 KDa
Source organism: Thermus thermophilus HB8
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8RR57 (Residues: 1-144; Coverage: 100%)
Gene names: TTHA0902, smpB
Sequence domains: SmpB protein
Nascent peptide MET-ALA Chain: 6
Molecule details ›
Chain: 6
Length: 2 amino acids
Theoretical weight: 220 Da
Source organism: Escherichia coli
Expression system: Escherichia coli
Large ribosomal subunit protein bL36 Chain: f
Molecule details ›
Chain: f
Length: 37 amino acids
Theoretical weight: 4.44 KDa
Source organism: Thermus thermophilus HB27
Expression system: Escherichia coli
UniProt:
  • Canonical: Q5SHR2 (Residues: 1-37; Coverage: 100%)
Gene names: TTHA1668, rpmJ
Sequence domains: Ribosomal protein L36
50S RIBOSOMAL PROTEIN L10 AND L11 Chains: H, I
Molecule details ›
Chains: H, I
Length: 140 amino acids
Theoretical weight: 11.93 KDa
Source organism: Thermus thermophilus HB8
16S ribosomal RNA Chain: 2
Molecule details ›
Chain: 2
Length: 1522 nucleotides
Theoretical weight: 493.96 KDa
Sequence domains: Bacterial small subunit ribosomal RNA
tRNA-fMet Chain: 7
Molecule details ›
Chain: 7
Length: 77 nucleotides
Theoretical weight: 24.82 KDa
Sequence domains: tRNA
tRNA-Phe Chain: 8
Molecule details ›
Chain: 8
Length: 76 nucleotides
Theoretical weight: 24.4 KDa
Sequence domains: tRNA
Messenger RNA Chain: 9
Molecule details ›
Chain: 9
Length: 6 nucleotides
Theoretical weight: 1.85 KDa
23S ribosomal RNA Chain: 1
Molecule details ›
Chain: 1
Length: 2915 nucleotides
Theoretical weight: 947.94 KDa
Sequence domains: Bacterial large subunit ribosomal RNA
5S ribosomal RNA Chain: 3
Molecule details ›
Chain: 3
Length: 119 nucleotides
Theoretical weight: 38.55 KDa
Sequence domains: 5S ribosomal RNA
transfer-messenger RNA (tmRNA) Chain: 4
Molecule details ›
Chain: 4
Length: 349 nucleotides
Theoretical weight: 112.82 KDa
Sequence domains: transfer-messenger RNA

Ligands and Environments

2 bound ligands:
Ligand MG 637 x MG
Ligand ZN 3 x ZN
1 modified residue:
Ligand 5MU 1 x 5MU

Experiments and Validation Details

Entry percentile scores
Resolution: 3.7Å
Relevant EMDB volumes: EMD-4475
Expression system: Escherichia coli

Quick links

Citations

6 review citations

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

2 mentions without citation

The World of Stable Ribonucleoproteins and Its Mapping With Grad-Seq and Related Approaches.
Gerovac et al. (2021)
1 more