PDBe 4v84

X-ray diffraction
3.4Å resolution

Crystal structure of a complex containing domain 3 of CrPV IGR IRES RNA bound to the 70S ribosome.

Released:

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero 53-mer (preferred)
Entry contents:
49 distinct polypeptide molecules
4 distinct RNA molecules
Macromolecules (53 distinct):
30S ribosomal protein S2 Chains: AB, CB
Molecule details ›
Chains: AB, CB
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
30S ribosomal protein S3 Chains: AC, CC
Molecule details ›
Chains: AC, CC
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:
30S ribosomal protein S4 Chains: AD, CD
Molecule details ›
Chains: AD, CD
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:
30S ribosomal protein S5 Chains: AE, CE
Molecule details ›
Chains: AE, CE
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:
30S ribosomal protein S6 Chains: AF, CF
Molecule details ›
Chains: AF, CF
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
30S ribosomal protein S7 Chains: AG, CG
Molecule details ›
Chains: AG, CG
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
30S ribosomal protein S8 Chains: AH, CH
Molecule details ›
Chains: AH, CH
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
30S ribosomal protein S9 Chains: AI, CI
Molecule details ›
Chains: AI, CI
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
30S ribosomal protein S10 Chains: AJ, CJ
Molecule details ›
Chains: AJ, CJ
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
30S ribosomal protein S11 Chains: AK, CK
Molecule details ›
Chains: AK, CK
Length: 119 amino acids
Theoretical weight: 12.61 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62654 (Residues: 11-129; Coverage: 92%)
Gene names: TT_C1302, rps11, rpsK
Sequence domains: Ribosomal protein S11
30S ribosomal protein S12 Chains: AL, CL
Molecule details ›
Chains: AL, CL
Length: 124 amino acids
Theoretical weight: 13.8 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P61941 (Residues: 2-125; Coverage: 94%)
Gene names: TT_C1333, rps12, rpsL
Sequence domains: Ribosomal protein S12/S23
30S ribosomal protein S13 Chains: AM, CM
Molecule details ›
Chains: AM, CM
Length: 116 amino acids
Theoretical weight: 13.24 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62655 (Residues: 2-117; Coverage: 92%)
Gene names: TT_C1303, rps13, rpsM
Sequence domains: Ribosomal protein S13/S18
30S ribosomal protein S14 type Z Chains: AN, CN
Molecule details ›
Chains: AN, CN
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
30S ribosomal protein S15 Chains: AO, CO
Molecule details ›
Chains: AO, CO
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
30S ribosomal protein S16 Chains: AP, CP
Molecule details ›
Chains: AP, CP
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
30S ribosomal protein S17 Chains: AQ, CQ
Molecule details ›
Chains: AQ, CQ
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
30S ribosomal protein S18 Chains: AR, CR
Molecule details ›
Chains: AR, CR
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
30S ribosomal protein S19 Chains: AS, CS
Molecule details ›
Chains: AS, CS
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
30S ribosomal protein S20 Chains: AT, CT
Molecule details ›
Chains: AT, CT
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
30S ribosomal protein Thx Chains: AU, CU
Molecule details ›
Chains: AU, CU
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
50S ribosomal protein L2 Chains: BC, DC
Molecule details ›
Chains: BC, DC
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:
50S ribosomal protein L3 Chains: BD, DD
Molecule details ›
Chains: BD, DD
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
50S ribosomal protein L4 Chains: BE, DE
Molecule details ›
Chains: BE, DE
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
50S ribosomal protein L5 Chains: BF, DF
Molecule details ›
Chains: BF, DF
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:
50S ribosomal protein L6 Chains: BG, DG
Molecule details ›
Chains: BG, DG
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
50S ribosomal protein L9 Chains: BH, DH
Molecule details ›
Chains: BH, DH
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: Ribosomal protein L9, N-terminal domain
50S ribosomal protein L10 Chains: BI, DI
Molecule details ›
Chains: BI, DI
Length: 65 amino acids
Theoretical weight: 7.33 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72GS1 (Residues: 3-67; Coverage: 38%)
Gene names: TT_C1777, rplJ
50S ribosomal protein L13 Chains: BJ, DJ
Molecule details ›
Chains: BJ, DJ
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
50S ribosomal protein L14 Chains: BK, DK
Molecule details ›
Chains: BK, DK
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
50S ribosomal protein L15 Chains: BL, DL
Molecule details ›
Chains: BL, DL
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
50S ribosomal protein L16 Chains: BM, DM
Molecule details ›
Chains: BM, DM
Length: 136 amino acids
Theoretical weight: 15.35 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72I11 (Residues: 6-141; Coverage: 97%)
Gene names: TT_C1321, rplP
50S ribosomal protein L17 Chains: BN, DN
Molecule details ›
Chains: BN, DN
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
50S ribosomal protein L18 Chains: BO, DO
Molecule details ›
Chains: BO, DO
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
50S ribosomal protein L19 Chains: BP, DP
Molecule details ›
Chains: BP, DP
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
50S ribosomal protein L20 Chains: BQ, DQ
Molecule details ›
Chains: BQ, DQ
Length: 116 amino acids
Theoretical weight: 13.5 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72L76 (Residues: 2-118; Coverage: 98%)
Gene names: TT_C0185, rplT
Sequence domains: Ribosomal protein L20
50S ribosomal protein L21 Chains: BR, DR
Molecule details ›
Chains: BR, DR
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
50S ribosomal protein L22 Chains: BS, DS
Molecule details ›
Chains: BS, DS
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
50S ribosomal protein L23 Chains: BT, DT
Molecule details ›
Chains: BT, DT
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
50S ribosomal protein L24 Chains: BU, DU
Molecule details ›
Chains: BU, DU
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: KOW motif
50S ribosomal protein L25 Chains: BV, DV
Molecule details ›
Chains: BV, DV
Length: 188 amino acids
Theoretical weight: 21.15 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72IA7 (Residues: 3-190; Coverage: 91%)
Gene names: TT_C1225, ctc, rplY
Sequence domains:
50S ribosomal protein L27 Chains: BW, DW
Molecule details ›
Chains: BW, DW
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
50S ribosomal protein L28 Chains: BX, DX
Molecule details ›
Chains: BX, DX
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
50S ribosomal protein L29 Chains: BY, DY
Molecule details ›
Chains: BY, DY
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
50S ribosomal protein L30 Chains: BZ, DZ
Molecule details ›
Chains: BZ, DZ
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
50S ribosomal protein L31 Chains: B1, D1
Molecule details ›
Chains: B1, D1
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
50S ribosomal protein L32 Chains: B2, D2
Molecule details ›
Chains: B2, D2
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
50S ribosomal protein L33 Chains: B3, D3
Molecule details ›
Chains: B3, D3
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
50S ribosomal protein L34 Chains: B4, D4
Molecule details ›
Chains: B4, D4
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
50S ribosomal protein L35 Chains: B5, D5
Molecule details ›
Chains: B5, D5
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
16S ribosomal RNA Chains: AA, CA
Molecule details ›
Chains: AA, CA
Length: 1506 nucleotides
Theoretical weight: 489.04 KDa
Sequence domains: Bacterial small subunit ribosomal RNA
RNA (34-MER) Chains: AV, CV
Molecule details ›
Chains: AV, CV
Length: 43 nucleotides
Theoretical weight: 13.79 KDa
23S ribosomal RNA Chains: BA, DA
Molecule details ›
Chains: BA, DA
Length: 2879 nucleotides
Theoretical weight: 936.3 KDa
Sequence domains: Bacterial large subunit ribosomal RNA
5S ribosomal RNA Chains: BB, DB
Molecule details ›
Chains: BB, DB
Length: 119 nucleotides
Theoretical weight: 38.55 KDa
Sequence domains: 5S ribosomal RNA

Ligands and Environments

2 bound ligands:

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-D
Spacegroup: P212121
Unit cell:
a: 210.69Å b: 451.66Å c: 614.25Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.228 0.228 0.266