PDBe 4v8q

X-ray diffraction
3.1Å resolution

Complex of SmpB, a tmRNA fragment and EF-Tu-GDP-Kirromycin with the 70S ribosome

Released:

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero 60-mer (preferred)
Entry contents:
53 distinct polypeptide molecules
6 distinct RNA molecules
Macromolecules (59 distinct):
50S ribosomal protein L27 Chain: A0
Molecule details ›
Chain: A0
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
50S ribosomal protein L28 Chain: A1
Molecule details ›
Chain: A1
Length: 98 amino acids
Theoretical weight: 11 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60494 (Residues: 1-98; Coverage: 100%)
Gene names: TTHA0042, rpmB
Sequence domains: Ribosomal L28 family
50S ribosomal protein L29 Chain: A2
Molecule details ›
Chain: A2
Length: 72 amino acids
Theoretical weight: 8.67 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHP6 (Residues: 1-72; Coverage: 100%)
Gene names: TTHA1684, rpmC
Sequence domains: Ribosomal L29 protein
50S ribosomal protein L30 Chain: A3
Molecule details ›
Chain: A3
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
50S ribosomal protein L31 Chain: A4
Molecule details ›
Chain: A4
Length: 71 amino acids
Theoretical weight: 8.3 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SJE1 (Residues: 1-71; Coverage: 100%)
Gene names: TTHA1073, rpmE
Sequence domains: Ribosomal protein L31
50S ribosomal protein L32 Chain: A5
Molecule details ›
Chain: A5
Length: 60 amino acids
Theoretical weight: 6.72 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80339 (Residues: 1-60; Coverage: 100%)
Gene names: TTHA0418, rpl32, rpmF
Sequence domains: Ribosomal L32p protein family
50S ribosomal protein L33 Chain: A6
Molecule details ›
Chain: A6
Length: 54 amino acids
Theoretical weight: 6.63 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P35871 (Residues: 1-54; Coverage: 100%)
Gene names: TTHA0250, rpl33, rpmG
Sequence domains: Ribosomal protein L33
50S ribosomal protein L34 Chain: A7
Molecule details ›
Chain: A7
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
50S ribosomal protein L35 Chain: A8
Molecule details ›
Chain: A8
Length: 65 amino acids
Theoretical weight: 7.51 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SKU1 (Residues: 1-65; Coverage: 100%)
Gene names: TTHA0552, rpmI
Sequence domains: Ribosomal protein L35
50S ribosomal protein L36 Chain: A9
Molecule details ›
Chain: A9
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
50S ribosomal protein L1 Chain: AC
Molecule details ›
Chain: AC
Length: 229 amino acids
Theoretical weight: 24.89 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
50S ribosomal protein L2 Chain: AD
Molecule details ›
Chain: AD
Length: 276 amino acids
Theoretical weight: 30.53 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60405 (Residues: 1-276; Coverage: 100%)
Gene names: TTHA1689, rplB
Sequence domains:
50S ribosomal protein L3 Chain: AE
Molecule details ›
Chain: AE
Length: 206 amino acids
Theoretical weight: 22.45 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHN8 (Residues: 1-206; Coverage: 100%)
Gene names: TTHA1692, rplC
Sequence domains: Ribosomal protein L3
50S ribosomal protein L4 Chain: AF
Molecule details ›
Chain: AF
Length: 210 amino acids
Theoretical weight: 23.27 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHN9 (Residues: 1-210; Coverage: 100%)
Gene names: TTHA1691, rplD
Sequence domains: Ribosomal protein L4/L1 family
50S ribosomal protein L5 Chain: AG
Molecule details ›
Chain: AG
Length: 182 amino acids
Theoretical weight: 21.06 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHQ0 (Residues: 1-182; Coverage: 100%)
Gene names: TTHA1680, rplE
Sequence domains:
50S ribosomal protein L6 Chain: AH
Molecule details ›
Chain: AH
Length: 180 amino acids
Theoretical weight: 19.57 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: A0A0M9ADP1 (Residues: 1-180; Coverage: 100%)
Gene names: BVI061214_01035, rplF
Sequence domains: Ribosomal protein L6
50S RIBOSOMAL PROTEIN L10 Chain: AJ
Molecule details ›
Chain: AJ
Length: 130 amino acids
Theoretical weight: 11.08 KDa
Source organism: Thermus thermophilus HB8
50S RIBOSOMAL PROTEIN L11 Chain: AK
Molecule details ›
Chain: AK
Length: 140 amino acids
Theoretical weight: 11.93 KDa
Source organism: Thermus thermophilus HB8
50S ribosomal protein L13 Chain: AN
Molecule details ›
Chain: AN
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
50S ribosomal protein L14 Chain: AO
Molecule details ›
Chain: AO
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
50S ribosomal protein L15 Chain: AP
Molecule details ›
Chain: AP
Length: 150 amino acids
Theoretical weight: 16.32 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHQ7 (Residues: 1-150; Coverage: 100%)
Gene names: TTHA1673, rplO
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
50S ribosomal protein L16 Chain: AQ
Molecule details ›
Chain: AQ
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
50S ribosomal protein L17 Chain: AR
Molecule details ›
Chain: AR
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
50S ribosomal protein L18 Chain: AS
Molecule details ›
Chain: AS
Length: 112 amino acids
Theoretical weight: 12.64 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHQ4 (Residues: 1-112; Coverage: 100%)
Gene names: TTHA1676, rplR
Sequence domains: Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
50S ribosomal protein L19 Chain: AT
Molecule details ›
Chain: AT
Length: 146 amino acids
Theoretical weight: 17.19 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60490 (Residues: 1-146; Coverage: 100%)
Gene names: TTHA1031, rplS
Sequence domains: Ribosomal protein L19
50S ribosomal protein L20 Chain: AU
Molecule details ›
Chain: AU
Length: 118 amino acids
Theoretical weight: 13.78 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60491 (Residues: 1-118; Coverage: 100%)
Gene names: TTHA0553, rplT
Sequence domains: Ribosomal protein L20
50S ribosomal protein L21 Chain: AV
Molecule details ›
Chain: AV
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
50S ribosomal protein L22 Chain: AW
Molecule details ›
Chain: AW
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
50S ribosomal protein L23 Chain: AX
Molecule details ›
Chain: AX
Length: 96 amino acids
Theoretical weight: 10.76 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHP0 (Residues: 1-96; Coverage: 100%)
Gene names: TTHA1690, rplW
Sequence domains: Ribosomal protein L23
50S ribosomal protein L24 Chain: AY
Molecule details ›
Chain: AY
Length: 110 amino acids
Theoretical weight: 12.09 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHP9 (Residues: 1-110; Coverage: 100%)
Gene names: TTHA1681, rplX
Sequence domains:
50S ribosomal protein L25 Chain: AZ
Molecule details ›
Chain: AZ
Length: 206 amino acids
Theoretical weight: 23.24 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHZ1 (Residues: 1-206; Coverage: 100%)
Gene names: TTHA1589, rpl25, rplY, rptL5
Sequence domains:
SsrA-binding protein Chain: B2
Molecule details ›
Chain: B2
Length: 144 amino acids
Theoretical weight: 16.79 KDa
Source organism: Thermus thermophilus HB8
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q8RR57 (Residues: 1-144; Coverage: 100%)
Gene names: TTHA0902, smpB
Sequence domains: SmpB protein
30S ribosomal protein S2 Chain: BB
Molecule details ›
Chain: BB
Length: 256 amino acids
Theoretical weight: 29.32 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80371 (Residues: 1-256; Coverage: 100%)
Gene names: TTHA0861, rps2, rpsB
Sequence domains: Ribosomal protein S2
30S ribosomal protein S3 Chain: BC
Molecule details ›
Chain: BC
Length: 239 amino acids
Theoretical weight: 26.75 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80372 (Residues: 1-239; Coverage: 100%)
Gene names: TTHA1686, rps3, rpsC
Sequence domains:
30S ribosomal protein S4 Chain: BD
Molecule details ›
Chain: BD
Length: 209 amino acids
Theoretical weight: 24.37 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80373 (Residues: 1-209; Coverage: 100%)
Gene names: TTHA1665, rps4, rpsD
Sequence domains:
30S ribosomal protein S5 Chain: BE
Molecule details ›
Chain: BE
Length: 162 amino acids
Theoretical weight: 17.58 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHQ5 (Residues: 1-162; Coverage: 100%)
Gene names: TTHA1675, rpsE
Sequence domains:
30S ribosomal protein S6 Chain: BF
Molecule details ›
Chain: BF
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
30S ribosomal protein S7 Chain: BG
Molecule details ›
Chain: BG
Length: 156 amino acids
Theoretical weight: 18.05 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P17291 (Residues: 1-156; Coverage: 100%)
Gene names: TTHA1696, rps7, rpsG
Sequence domains: Ribosomal protein S7p/S5e
30S ribosomal protein S8 Chain: BH
Molecule details ›
Chain: BH
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
30S ribosomal protein S9 Chain: BI
Molecule details ›
Chain: BI
Length: 128 amino acids
Theoretical weight: 14.43 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80374 (Residues: 1-128; Coverage: 100%)
Gene names: TTHA1464, rps9, rpsI
Sequence domains: Ribosomal protein S9/S16
30S ribosomal protein S10 Chain: BJ
Molecule details ›
Chain: BJ
Length: 105 amino acids
Theoretical weight: 11.95 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHN7 (Residues: 1-105; Coverage: 100%)
Gene names: TTHA1693, rpsJ
Sequence domains: Ribosomal protein S10p/S20e
30S ribosomal protein S11 Chain: BK
Molecule details ›
Chain: BK
Length: 129 amino acids
Theoretical weight: 13.74 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80376 (Residues: 1-129; Coverage: 100%)
Gene names: TTHA1666, rps11, rpsK
Sequence domains: Ribosomal protein S11
30S ribosomal protein S12 Chain: BL
Molecule details ›
Chain: BL
Length: 135 amino acids
Theoretical weight: 14.92 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHN3 (Residues: 2-132; Coverage: 99%)
Gene names: TTHA1697, rpsL
Sequence domains: Ribosomal protein S12/S23
30S ribosomal protein S13 Chain: BM
Molecule details ›
Chain: BM
Length: 126 amino acids
Theoretical weight: 14.34 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80377 (Residues: 1-126; Coverage: 100%)
Gene names: TTHA1667, rps13, rpsM
Sequence domains: Ribosomal protein S13/S18
30S ribosomal protein S14 type Z Chain: BN
Molecule details ›
Chain: BN
Length: 61 amino acids
Theoretical weight: 7.16 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: A0A0N0BLP2 (Residues: 1-61; Coverage: 100%)
Gene names: BVI061214_01033, rpsN, rpsZ
Sequence domains: Ribosomal protein S14p/S29e
30S ribosomal protein S15 Chain: BO
Molecule details ›
Chain: BO
Length: 89 amino acids
Theoretical weight: 10.58 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SJ76 (Residues: 1-89; Coverage: 100%)
Gene names: TTHA1138, rpsO
Sequence domains: Ribosomal protein S15
30S ribosomal protein S16 Chain: BP
Molecule details ›
Chain: BP
Length: 88 amino acids
Theoretical weight: 10.41 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SJH3 (Residues: 1-88; Coverage: 100%)
Gene names: TTHA1035, rpsP
Sequence domains: Ribosomal protein S16
30S ribosomal protein S17 Chain: BQ
Molecule details ›
Chain: BQ
Length: 105 amino acids
Theoretical weight: 12.33 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: A0A0N0BLS5 (Residues: 1-105; Coverage: 100%)
Gene names: BVI061214_01029, rpsQ
Sequence domains: Ribosomal protein S17
30S ribosomal protein S18 Chain: BR
Molecule details ›
Chain: BR
Length: 88 amino acids
Theoretical weight: 10.26 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SLQ0 (Residues: 1-88; Coverage: 100%)
Gene names: TTHA0243, rpsR
Sequence domains: Ribosomal protein S18
30S ribosomal protein S19 Chain: BS
Molecule details ›
Chain: BS
Length: 93 amino acids
Theoretical weight: 10.61 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHP2 (Residues: 1-93; Coverage: 100%)
Gene names: TTHA1688, rpsS
Sequence domains: Ribosomal protein S19
30S ribosomal protein S20 Chain: BT
Molecule details ›
Chain: BT
Length: 106 amino acids
Theoretical weight: 11.74 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80380 (Residues: 1-106; Coverage: 100%)
Gene names: TTHA1397, rps20, rpsT
Sequence domains: Ribosomal protein S20
30S ribosomal protein Thx Chain: BU
Molecule details ›
Chain: BU
Length: 27 amino acids
Theoretical weight: 3.35 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SIH3 (Residues: 1-27; Coverage: 100%)
Gene names: TTHA1396, rpsU
Sequence domains: 30S ribosomal protein Thx
Elongation factor Tu-A Chain: BZ
Molecule details ›
Chain: BZ
Length: 405 amino acids
Theoretical weight: 44.73 KDa
Source organism: Thermus thermophilus HB8
Expression system: Escherichia coli
UniProt:
  • Canonical: Q5SHN6 (Residues: 2-406; Coverage: 100%)
Gene names: TTHA1694, tuf, tufA
Sequence domains:
23S ribosomal RNA Chain: AA
Molecule details ›
Chain: AA
Length: 2915 nucleotides
Theoretical weight: 948 KDa
Sequence domains: Bacterial large subunit ribosomal RNA
5S ribosomal RNA Chain: AB
Molecule details ›
Chain: AB
Length: 122 nucleotides
Theoretical weight: 39.54 KDa
Sequence domains: 5S ribosomal RNA
16S ribosomal RNA Chain: BA
Molecule details ›
Chain: BA
Length: 1522 nucleotides
Theoretical weight: 493.97 KDa
Sequence domains: Bacterial small subunit ribosomal RNA
E-SITE or P-SITE TRNA FMET Chains: BV, BW
Molecule details ›
Chains: BV, BW
Length: 77 nucleotides
Theoretical weight: 24.8 KDa
Sequence domains: tRNA
Messenger RNA Chain: BX
Molecule details ›
Chain: BX
Length: 19 nucleotides
Theoretical weight: 6.23 KDa
TMRNA DELA Chain: BY
Molecule details ›
Chain: BY
Length: 90 nucleotides
Theoretical weight: 28.82 KDa
Sequence domains: transfer-messenger RNA

Ligands and Environments


No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: P21
Unit cell:
a: 202.17Å b: 290.76Å c: 250.65Å
α: 90° β: 97.63° γ: 90°
R-values:
R R work R free
0.23 0.23 0.27
Expression systems:
  • Escherichia coli BL21(DE3)
  • Escherichia coli