› 4xej

X-ray diffraction
3.8Å resolution

IRES bound to bacterial Ribosome

Released:
DOI: 10.2210/pdb4xej/pdb
PDB entry 4xej coloured by chain, front view.
PDB entry 4xej coloured by chain, side view.
PDB entry 4xej coloured by chain, top view.
Source organism: Thermus thermophilus HB27
Primary publication:
Initiation of translation in bacteria by a structured eukaryotic IRES RNA.
Colussi TM, Costantino DA, Zhu J, Donohue JP, Korostelev AA, Jaafar ZA, Plank TD, Noller HF, Kieft JS
Nature 519 110-3 (2015)
PMID: 25652826

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 53-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-158436 (preferred)
Entry contents:
49 distinct polypeptide molecules
4 distinct RNA molecules
Macromolecules (53 distinct):
Large ribosomal subunit protein uL2 Chains: AL02, BL02
Molecule details ›
Chains: AL02, BL02
Length: 271 amino acids
Theoretical weight: 29.83 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72I07 (Residues: 2-272; Coverage: 98%)
Gene names: TT_C1325, rplB
Sequence domains:
Large ribosomal subunit protein uL3 Chains: AL03, BL03
Molecule details ›
Chains: AL03, BL03
Length: 204 amino acids
Theoretical weight: 22.25 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72I04 (Residues: 1-204; Coverage: 99%)
Gene names: TT_C1328, rplC
Sequence domains: Ribosomal protein L3
Large ribosomal subunit protein uL4 Chains: AL04, BL04
Molecule details ›
Chains: AL04, BL04
Length: 202 amino acids
Theoretical weight: 22.49 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72I05 (Residues: 1-202; Coverage: 99%)
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: 159 amino acids
Theoretical weight: 17.36 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72I19 (Residues: 12-170; Coverage: 88%)
Gene names: TT_C1313, rplF
Sequence domains: Ribosomal protein L6
Large ribosomal subunit protein bL9 Chains: AL09, BL09
Molecule details ›
Chains: AL09, BL09
Length: 145 amino acids
Theoretical weight: 16.11 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72GV5 (Residues: 1-145; Coverage: 98%)
Gene names: TT_C1743, rplI
Sequence domains:
Large ribosomal subunit protein uL11 Chains: AL11, BL11
Molecule details ›
Chains: AL11, BL11
Length: 147 amino acids
Theoretical weight: 15.53 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62442 (Residues: 1-147; Coverage: 100%)
Gene names: TT_C1738, rplK
Sequence domains:
Large ribosomal subunit protein uL13 Chains: AL13, BL13
Molecule details ›
Chains: AL13, BL13
Length: 137 amino acids
Theoretical weight: 15.57 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72IN1 (Residues: 2-138; Coverage: 98%)
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: 146 amino acids
Theoretical weight: 15.86 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72I23 (Residues: 5-150; Coverage: 97%)
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: 134 amino acids
Theoretical weight: 15.15 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72I11 (Residues: 6-139; Coverage: 95%)
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: 117 amino acids
Theoretical weight: 13.62 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72I33 (Residues: 2-118; Coverage: 99%)
Gene names: TT_C1299, rplQ
Sequence domains: Ribosomal protein L17
Large ribosomal subunit protein uL18 Chains: AL18, BL18
Molecule details ›
Chains: AL18, BL18
Length: 98 amino acids
Theoretical weight: 10.94 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72I20 (Residues: 11-108; Coverage: 88%)
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: 137 amino acids
Theoretical weight: 16.25 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72JU9 (Residues: 1-137; Coverage: 94%)
Gene names: TT_C0669, rplS
Sequence domains: Ribosomal protein L19
Large ribosomal subunit protein bL20 Chains: AL20, BL20
Molecule details ›
Chains: AL20, BL20
Length: 117 amino acids
Theoretical weight: 13.65 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72L76 (Residues: 2-118; Coverage: 99%)
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: 112 amino acids
Theoretical weight: 12.68 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72I09 (Residues: 1-112; Coverage: 99%)
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: 92 amino acids
Theoretical weight: 10.27 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72I06 (Residues: 3-94; Coverage: 96%)
Gene names: TT_C1326, rplW
Sequence domains: Ribosomal protein L23
Large ribosomal subunit protein uL24 Chains: AL24, BL24
Molecule details ›
Chains: AL24, BL24
Length: 100 amino acids
Theoretical weight: 11.08 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72I15 (Residues: 2-101; Coverage: 91%)
Gene names: TT_C1317, rplX
Sequence domains:
Large ribosomal subunit protein bL25 Chains: AL25, BL25
Molecule details ›
Chains: AL25, BL25
Length: 187 amino acids
Theoretical weight: 21.02 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72IA7 (Residues: 3-189; Coverage: 91%)
Gene names: TT_C1225, ctc, rplY
Sequence domains:
Large ribosomal subunit protein bL27 Chains: AL27, BL27
Molecule details ›
Chains: AL27, BL27
Length: 76 amino acids
Theoretical weight: 8.59 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72HR3 (Residues: 10-85; Coverage: 89%)
Gene names: TT_C1423, rpmA
Sequence domains: Ribosomal L27 protein
Large ribosomal subunit protein bL28 Chains: AL28, BL28
Molecule details ›
Chains: AL28, BL28
Length: 88 amino acids
Theoretical weight: 9.88 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72G84 (Residues: 8-95; Coverage: 90%)
Gene names: TT_C1964, rpmB
Sequence domains: Ribosomal L28 family
Large ribosomal subunit protein uL29 Chains: AL29, BL29
Molecule details ›
Chains: AL29, BL29
Length: 62 amino acids
Theoretical weight: 7.46 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72I12 (Residues: 1-62; Coverage: 86%)
Gene names: TT_C1320, rpmC
Sequence domains: Ribosomal L29 protein
Large ribosomal subunit protein uL30 Chains: AL30, BL30
Molecule details ›
Chains: AL30, BL30
Length: 59 amino acids
Theoretical weight: 6.67 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72I22 (Residues: 1-59; Coverage: 98%)
Gene names: TT_C1310, rpmD
Sequence domains: Ribosomal protein L30p/L7e
Large ribosomal subunit protein bL32 Chains: AL32, BL32
Molecule details ›
Chains: AL32, BL32
Length: 52 amino acids
Theoretical weight: 5.82 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62652 (Residues: 2-53; Coverage: 87%)
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: 44 amino acids
Theoretical weight: 5.47 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72GW3 (Residues: 9-52; Coverage: 82%)
Gene names: TT_C1735, rpmG
Sequence domains: Ribosomal protein L33
Large ribosomal subunit protein bL34 Chains: AL34, BL34
Molecule details ›
Chains: AL34, BL34
Length: 48 amino acids
Theoretical weight: 5.98 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P80340 (Residues: 1-48; Coverage: 98%)
Gene names: TTHA0446, rpl34, rpmH
Sequence domains: Ribosomal protein L34
Large ribosomal subunit protein bL35 Chains: AL35, BL35
Molecule details ›
Chains: AL35, BL35
Length: 63 amino acids
Theoretical weight: 7.25 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72L77 (Residues: 2-64; Coverage: 97%)
Gene names: TT_C0184, rpmI
Sequence domains: Ribosomal protein L35
Small ribosomal subunit protein uS2 Chains: AS02, BS02
Molecule details ›
Chains: AS02, BS02
Length: 234 amino acids
Theoretical weight: 26.99 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62662 (Residues: 7-240; Coverage: 91%)
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: 206 amino acids
Theoretical weight: 22.86 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62663 (Residues: 2-207; Coverage: 86%)
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: 151 amino acids
Theoretical weight: 16.46 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62665 (Residues: 5-155; Coverage: 93%)
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: 127 amino acids
Theoretical weight: 14.3 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62669 (Residues: 2-128; Coverage: 99%)
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: 98 amino acids
Theoretical weight: 11.3 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62653 (Residues: 3-100; Coverage: 93%)
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: 114 amino acids
Theoretical weight: 12.01 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62654 (Residues: 11-124; Coverage: 88%)
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: 122 amino acids
Theoretical weight: 13.6 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P61941 (Residues: 2-123; Coverage: 92%)
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: 117 amino acids
Theoretical weight: 13.31 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62655 (Residues: 2-118; Coverage: 93%)
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: 83 amino acids
Theoretical weight: 9.92 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62238 (Residues: 1-83; Coverage: 94%)
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: 99 amino acids
Theoretical weight: 11.72 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62658 (Residues: 2-100; Coverage: 94%)
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: 70 amino acids
Theoretical weight: 8.16 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62659 (Residues: 19-88; Coverage: 80%)
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: 78 amino acids
Theoretical weight: 8.95 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62660 (Residues: 4-81; Coverage: 84%)
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: 99 amino acids
Theoretical weight: 10.91 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62661 (Residues: 8-106; Coverage: 93%)
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: 24 amino acids
Theoretical weight: 2.96 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62613 (Residues: 2-25; Coverage: 89%)
Gene names: TT_C1030, rpsU
Sequence domains: 30S ribosomal protein Thx
Large ribosomal subunit protein bL31 Chains: AL31, BL31
Molecule details ›
Chains: AL31, BL31
Length: 30 amino acids
Theoretical weight: 3.28 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72JR0 (Residues: 10-39; Coverage: 42%)
Gene names: TT_C0708, rpmE
Sequence domains: Ribosomal protein L31
16S ribosomal RNA Chains: A16S, B16S
Molecule details ›
Chains: A16S, B16S
Length: 1506 nucleotides
Theoretical weight: 489.04 KDa
Sequence domains: Bacterial small subunit ribosomal RNA
23S ribosomal RNA Chains: A23S, B23S
Molecule details ›
Chains: A23S, B23S
Length: 2879 nucleotides
Theoretical weight: 936.3 KDa
Sequence domains: Bacterial large subunit ribosomal RNA
5S ribosomal RNA Chains: A5S, B5S
Molecule details ›
Chains: A5S, B5S
Length: 119 nucleotides
Theoretical weight: 38.55 KDa
Sequence domains: 5S ribosomal RNA
IRES RNA Chains: AIRE, BIRE
Molecule details ›
Chains: AIRE, BIRE
Length: 196 nucleotides
Theoretical weight: 62.74 KDa
Sequence domains: Cripavirus internal ribosome entry site (IRES)

Ligands and Environments

1 bound ligand:
Ligand ZN 4 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-B
Spacegroup: P212121
Unit cell:
a: 209.05Å b: 447.22Å c: 608.96Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.246 0.246 0.284

Quick links

Citations

13 review citations

The expanding biology of the C9orf72 nucleotide repeat expansion in neurodegenerative disease.
Haeusler et al. (2016)
12 more

2 mentions without citation

Initiation of translation in bacteria by a structured eukaryotic IRES RNA.
Colussi et al. (2015)
1 more