PDBe 6cfk

X-ray diffraction
2.7Å resolution

Crystal structure of the Thermus thermophilus 70S ribosome in complex with D-histidyl-CAM and bound to protein Y (YfiA) at 2.7A resolution

Released:

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero 53-mer (preferred)
Entry contents:
50 distinct polypeptide molecules
3 distinct RNA molecules
Macromolecules (53 distinct):
50S ribosomal protein L2 Chains: 1D, 2D
Molecule details ›
Chains: 1D, 2D
Length: 276 amino acids
Theoretical weight: 30.53 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q72I07 (Residues: 1-276; Coverage: 100%)
Gene names: TT_C1325, rplB
Sequence domains:
50S ribosomal protein L3 Chains: 1E, 2E
Molecule details ›
Chains: 1E, 2E
Length: 206 amino acids
Theoretical weight: 22.45 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P52860 (Residues: 1-206; Coverage: 100%)
Gene names: rpl3, rplC
Sequence domains: Ribosomal protein L3
50S ribosomal protein L4 Chains: 1F, 2F
Molecule details ›
Chains: 1F, 2F
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 Chains: 1G, 2G
Molecule details ›
Chains: 1G, 2G
Length: 182 amino acids
Theoretical weight: 21.06 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P41201 (Residues: 1-182; Coverage: 100%)
Gene names: rpl5, rplE
Sequence domains:
50S ribosomal protein L6 Chains: 1H, 2H
Molecule details ›
Chains: 1H, 2H
Length: 180 amino acids
Theoretical weight: 19.57 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P24316 (Residues: 1-180; Coverage: 100%)
Gene names: rpl6, rplF
Sequence domains: Ribosomal protein L6
50S ribosomal protein L9 Chains: 1I, 2I
Molecule details ›
Chains: 1I, 2I
Length: 148 amino acids
Theoretical weight: 16.42 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SLQ1 (Residues: 1-148; Coverage: 100%)
Gene names: TTHA0242, rplI
Sequence domains:
50S ribosomal protein L13 Chains: 1N, 2N
Molecule details ›
Chains: 1N, 2N
Length: 140 amino acids
Theoretical weight: 15.93 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q72IN1 (Residues: 1-140; Coverage: 100%)
Gene names: TT_C1101, rplM
Sequence domains: Ribosomal protein L13
50S ribosomal protein L14 Chains: 1O, 2O
Molecule details ›
Chains: 1O, 2O
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 Chains: 1P, 2P
Molecule details ›
Chains: 1P, 2P
Length: 150 amino acids
Theoretical weight: 16.32 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P74910 (Residues: 1-150; Coverage: 100%)
Gene names: rpl15, rplO
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
50S ribosomal protein L16 Chains: 1Q, 2Q
Molecule details ›
Chains: 1Q, 2Q
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 Chains: 1R, 2R
Molecule details ›
Chains: 1R, 2R
Length: 118 amino acids
Theoretical weight: 13.75 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q72I33 (Residues: 1-118; Coverage: 100%)
Gene names: TT_C1299, rplQ
Sequence domains: Ribosomal protein L17
50S ribosomal protein L18 Chains: 1S, 2S
Molecule details ›
Chains: 1S, 2S
Length: 112 amino acids
Theoretical weight: 12.64 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80320 (Residues: 1-112; Coverage: 100%)
Gene names: rpl18, rplR
Sequence domains: Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
50S ribosomal protein L19 Chains: 1T, 2T
Molecule details ›
Chains: 1T, 2T
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 Chains: 1U, 2U
Molecule details ›
Chains: 1U, 2U
Length: 118 amino acids
Theoretical weight: 13.78 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q72L76 (Residues: 1-118; Coverage: 100%)
Gene names: TT_C0185, rplT
Sequence domains: Ribosomal protein L20
50S ribosomal protein L21 Chains: 1V, 2V
Molecule details ›
Chains: 1V, 2V
Length: 101 amino acids
Theoretical weight: 11.07 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q72HR2 (Residues: 1-101; Coverage: 100%)
Gene names: TT_C1424, rplU
Sequence domains: Ribosomal prokaryotic L21 protein
50S ribosomal protein L22 Chains: 1W, 2W
Molecule details ›
Chains: 1W, 2W
Length: 113 amino acids
Theoretical weight: 12.81 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P48286 (Residues: 1-113; Coverage: 100%)
Gene names: rpl22, rplV
Sequence domains: Ribosomal protein L22p/L17e
50S ribosomal protein L23 Chains: 1X, 2X
Molecule details ›
Chains: 1X, 2X
Length: 96 amino acids
Theoretical weight: 10.76 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q9RA57 (Residues: 1-96; Coverage: 100%)
Gene name: rplW
Sequence domains: Ribosomal protein L23
50S ribosomal protein L24 Chains: 1Y, 2Y
Molecule details ›
Chains: 1Y, 2Y
Length: 110 amino acids
Theoretical weight: 12.09 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q56435 (Residues: 1-110; Coverage: 100%)
Gene names: rpl24, rplX
Sequence domains:
50S ribosomal protein L25 Chains: 1Z, 2Z
Molecule details ›
Chains: 1Z, 2Z
Length: 206 amino acids
Theoretical weight: 23.24 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q72IA7 (Residues: 1-206; Coverage: 100%)
Gene names: TT_C1225, ctc, rplY
Sequence domains:
50S ribosomal protein L27 Chains: 10, 20
Molecule details ›
Chains: 10, 20
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 Chains: 11, 21
Molecule details ›
Chains: 11, 21
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 Chains: 12, 22
Molecule details ›
Chains: 12, 22
Length: 72 amino acids
Theoretical weight: 8.67 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q72I12 (Residues: 1-72; Coverage: 100%)
Gene names: TT_C1320, rpmC
Sequence domains: Ribosomal L29 protein
50S ribosomal protein L30 Chains: 13, 23
Molecule details ›
Chains: 13, 23
Length: 60 amino acids
Theoretical weight: 6.8 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P74909 (Residues: 1-60; Coverage: 100%)
Gene names: rpl30, rpmD
Sequence domains: Ribosomal protein L30p/L7e
50S ribosomal protein L31 Chains: 14, 24
Molecule details ›
Chains: 14, 24
Length: 71 amino acids
Theoretical weight: 8.3 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q72JR0 (Residues: 1-71; Coverage: 100%)
Gene names: TT_C0708, rpmE
Sequence domains: Ribosomal protein L31
50S ribosomal protein L32 Chains: 15, 25
Molecule details ›
Chains: 15, 25
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 Chains: 16, 26
Molecule details ›
Chains: 16, 26
Length: 54 amino acids
Theoretical weight: 6.63 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q72GW3 (Residues: 1-54; Coverage: 100%)
Gene names: TT_C1735, rpmG
Sequence domains: Ribosomal protein L33
50S ribosomal protein L34 Chains: 17, 27
Molecule details ›
Chains: 17, 27
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 Chains: 18, 28
Molecule details ›
Chains: 18, 28
Length: 65 amino acids
Theoretical weight: 7.51 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80341 (Residues: 1-65; Coverage: 100%)
Gene names: rpl35, rpmI
Sequence domains: Ribosomal protein L35
50S ribosomal protein L36 Chains: 19, 29
Molecule details ›
Chains: 19, 29
Length: 37 amino acids
Theoretical weight: 4.44 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80256 (Residues: 1-37; Coverage: 100%)
Gene names: rpl36, rpmJ
Sequence domains: Ribosomal protein L36
30S ribosomal protein S2 Chains: 1b, 2b
Molecule details ›
Chains: 1b, 2b
Length: 256 amino acids
Theoretical weight: 29.32 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P62662 (Residues: 1-256; Coverage: 100%)
Gene names: TT_C0509, rps2, rpsB
Sequence domains: Ribosomal protein S2
30S ribosomal protein S3 Chains: 1c, 2c
Molecule details ›
Chains: 1c, 2c
Length: 239 amino acids
Theoretical weight: 26.75 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P62663 (Residues: 1-239; Coverage: 100%)
Gene names: TT_C1322, rps3, rpsC
Sequence domains:
30S ribosomal protein S4 Chains: 1d, 2d
Molecule details ›
Chains: 1d, 2d
Length: 209 amino acids
Theoretical weight: 24.37 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P62664 (Residues: 1-209; Coverage: 100%)
Gene names: TT_C1301, rps4, rpsD
Sequence domains:
30S ribosomal protein S5 Chains: 1e, 2e
Molecule details ›
Chains: 1e, 2e
Length: 162 amino acids
Theoretical weight: 17.58 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P27152 (Residues: 1-162; Coverage: 100%)
Gene names: rps5, rpsE
Sequence domains:
30S ribosomal protein S6 Chains: 1f, 2f
Molecule details ›
Chains: 1f, 2f
Length: 101 amino acids
Theoretical weight: 11.99 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P23370 (Residues: 1-101; Coverage: 100%)
Gene names: rps6, rpsF
Sequence domains: Ribosomal protein S6
30S ribosomal protein S7 Chains: 1g, 2g
Molecule details ›
Chains: 1g, 2g
Length: 156 amino acids
Theoretical weight: 18.05 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P62667 (Residues: 1-156; Coverage: 100%)
Gene names: TT_C1332, rps7, rpsG
Sequence domains: Ribosomal protein S7p/S5e
30S ribosomal protein S8 Chains: 1h, 2h
Molecule details ›
Chains: 1h, 2h
Length: 138 amino acids
Theoretical weight: 15.87 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P24319 (Residues: 1-138; Coverage: 100%)
Gene names: rps8, rpsH
Sequence domains: Ribosomal protein S8
30S ribosomal protein S9 Chains: 1i, 2i
Molecule details ›
Chains: 1i, 2i
Length: 128 amino acids
Theoretical weight: 14.41 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 Chains: 1j, 2j
Molecule details ›
Chains: 1j, 2j
Length: 105 amino acids
Theoretical weight: 11.95 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80375 (Residues: 1-105; Coverage: 100%)
Gene names: rps10, rpsJ
Sequence domains: Ribosomal protein S10p/S20e
30S ribosomal protein S11 Chains: 1k, 2k
Molecule details ›
Chains: 1k, 2k
Length: 129 amino acids
Theoretical weight: 13.74 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P62654 (Residues: 1-129; Coverage: 100%)
Gene names: TT_C1302, rps11, rpsK
Sequence domains: Ribosomal protein S11
30S ribosomal protein S12 Chains: 1l, 2l
Molecule details ›
Chains: 1l, 2l
Length: 132 amino acids
Theoretical weight: 14.68 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P17293 (Residues: 1-132; Coverage: 100%)
Gene names: rps12, rpsL
Sequence domains: Ribosomal protein S12/S23
30S ribosomal protein S13 Chains: 1m, 2m
Molecule details ›
Chains: 1m, 2m
Length: 126 amino acids
Theoretical weight: 14.34 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P62655 (Residues: 1-126; Coverage: 100%)
Gene names: TT_C1303, rps13, rpsM
Sequence domains: Ribosomal protein S13/S18
30S ribosomal protein S14 type Z Chains: 1n, 2n
Molecule details ›
Chains: 1n, 2n
Length: 61 amino acids
Theoretical weight: 7.16 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P24320 (Residues: 1-61; Coverage: 100%)
Gene names: rps14, rpsN, rpsZ
Sequence domains: Ribosomal protein S14p/S29e
30S ribosomal protein S15 Chains: 1o, 2o
Molecule details ›
Chains: 1o, 2o
Length: 89 amino acids
Theoretical weight: 10.58 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80378 (Residues: 1-89; Coverage: 100%)
Gene names: rps15, rpsO
Sequence domains: Ribosomal protein S15
30S ribosomal protein S16 Chains: 1p, 2p
Molecule details ›
Chains: 1p, 2p
Length: 88 amino acids
Theoretical weight: 10.41 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P62238 (Residues: 1-88; Coverage: 100%)
Gene names: TT_C0673, rps16, rpsP
Sequence domains: Ribosomal protein S16
30S ribosomal protein S17 Chains: 1q, 2q
Molecule details ›
Chains: 1q, 2q
Length: 105 amino acids
Theoretical weight: 12.33 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P0DOY7 (Residues: 1-105; Coverage: 100%)
Gene names: TTHA1683, rpsQ
Sequence domains: Ribosomal protein S17
30S ribosomal protein S18 Chains: 1r, 2r
Molecule details ›
Chains: 1r, 2r
Length: 88 amino acids
Theoretical weight: 10.26 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P62659 (Residues: 1-88; Coverage: 100%)
Gene names: TT_C1742, rps18, rpsR
Sequence domains: Ribosomal protein S18
30S ribosomal protein S19 Chains: 1s, 2s
Molecule details ›
Chains: 1s, 2s
Length: 93 amino acids
Theoretical weight: 10.61 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80381 (Residues: 1-93; Coverage: 100%)
Gene names: rps19, rpsS
Sequence domains: Ribosomal protein S19
30S ribosomal protein S20 Chains: 1t, 2t
Molecule details ›
Chains: 1t, 2t
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 Chains: 1u, 2u
Molecule details ›
Chains: 1u, 2u
Length: 27 amino acids
Theoretical weight: 3.35 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P62612 (Residues: 1-27; Coverage: 100%)
Gene name: rpsU
Sequence domains: 30S ribosomal protein Thx
Ribosome-associated inhibitor A Chains: 1y, 2y
Molecule details ›
Chains: 1y, 2y
Length: 113 amino acids
Theoretical weight: 12.8 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P0AD49 (Residues: 1-113; Coverage: 100%)
Gene names: JW2578, b2597, raiA, yfiA
Sequence domains: Sigma 54 modulation protein / S30EA ribosomal protein
23S ribosomal RNA Chains: 1A, 2A
Molecule details ›
Chains: 1A, 2A
Length: 2915 nucleotides
Theoretical weight: 948.04 KDa
Sequence domains: Bacterial large subunit ribosomal RNA
5S ribosomal RNA Chains: 1B, 2B
Molecule details ›
Chains: 1B, 2B
Length: 121 nucleotides
Theoretical weight: 39.19 KDa
Sequence domains: 5S ribosomal RNA
16S ribosomal RNA Chains: 1a, 2a
Molecule details ›
Chains: 1a, 2a
Length: 1521 nucleotides
Theoretical weight: 493.86 KDa
Sequence domains: Bacterial small subunit ribosomal RNA

Ligands and Environments

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P212121
Unit cell:
a: 210.09Å b: 449.12Å c: 621.91Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.208 0.206 0.253
Expression system: Escherichia coli