PDBe 5j4d

X-ray diffraction
3.1Å resolution

E. coli release factor 1 bound to the 70S ribosome in response to a pseudouridylated stop codon

Released:

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero 56-mer (preferred)
Entry contents:
50 distinct polypeptide molecules
5 distinct RNA molecules
Macromolecules (55 distinct):
50S ribosomal protein L2 Chains: E, JB
Molecule details ›
Chains: E, JB
Length: 275 amino acids
Theoretical weight: 30.4 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72I07 (Residues: 2-276; Coverage: 100%)
Gene names: TT_C1325, rplB
Sequence domains:
50S ribosomal protein L3 Chains: F, KB
Molecule details ›
Chains: F, KB
Length: 206 amino acids
Theoretical weight: 22.45 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72I04 (Residues: 1-206; Coverage: 100%)
Gene names: TT_C1328, rplC
Sequence domains: Ribosomal protein L3
50S ribosomal protein L4 Chains: G, LB
Molecule details ›
Chains: G, LB
Length: 205 amino acids
Theoretical weight: 22.74 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72I05 (Residues: 1-205; Coverage: 100%)
Gene names: TT_C1327, rplD
Sequence domains: Ribosomal protein L4/L1 family
50S ribosomal protein L5 Chains: H, MB
Molecule details ›
Chains: H, MB
Length: 182 amino acids
Theoretical weight: 21.08 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72I16 (Residues: 1-182; Coverage: 100%)
Gene names: TT_C1316, rplE
Sequence domains:
50S ribosomal protein L6 Chains: I, NB
Molecule details ›
Chains: I, NB
Length: 180 amino acids
Theoretical weight: 19.57 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72I19 (Residues: 1-180; Coverage: 100%)
Gene names: TT_C1313, rplF
Sequence domains: Ribosomal protein L6
50S ribosomal protein L9 Chains: J, OB
Molecule details ›
Chains: J, OB
Length: 148 amino acids
Theoretical weight: 16.44 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72GV5 (Residues: 1-148; Coverage: 100%)
Gene names: TT_C1743, rplI
Sequence domains:
50S ribosomal protein L13 Chains: K, PB
Molecule details ›
Chains: K, PB
Length: 140 amino acids
Theoretical weight: 15.93 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72IN1 (Residues: 1-140; Coverage: 100%)
Gene names: TT_C1101, rplM
Sequence domains: Ribosomal protein L13
50S ribosomal protein L14 Chains: L, QB
Molecule details ›
Chains: L, QB
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: M, RB
Molecule details ›
Chains: M, RB
Length: 150 amino acids
Theoretical weight: 16.32 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72I23 (Residues: 1-150; Coverage: 100%)
Gene names: TT_C1309, rplO
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
50S ribosomal protein L16 Chains: N, SB
Molecule details ›
Chains: N, SB
Length: 141 amino acids
Theoretical weight: 15.98 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72I11 (Residues: 1-141; Coverage: 100%)
Gene names: TT_C1321, rplP
Sequence domains: Ribosomal protein L16p/L10e
50S ribosomal protein L17 Chains: O, TB
Molecule details ›
Chains: O, TB
Length: 118 amino acids
Theoretical weight: 13.75 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72I33 (Residues: 1-118; Coverage: 100%)
Gene names: TT_C1299, rplQ
Sequence domains: Ribosomal protein L17
50S ribosomal protein L18 Chains: P, UB
Molecule details ›
Chains: P, UB
Length: 112 amino acids
Theoretical weight: 12.64 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72I20 (Residues: 1-112; Coverage: 100%)
Gene names: TT_C1312, rplR
Sequence domains: Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
50S ribosomal protein L19 Chains: Q, VB
Molecule details ›
Chains: Q, VB
Length: 146 amino acids
Theoretical weight: 17.22 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72JU9 (Residues: 1-146; Coverage: 100%)
Gene names: TT_C0669, rplS
Sequence domains: Ribosomal protein L19
50S ribosomal protein L20 Chains: R, WB
Molecule details ›
Chains: R, WB
Length: 118 amino acids
Theoretical weight: 13.78 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72L76 (Residues: 1-118; Coverage: 100%)
Gene names: TT_C0185, rplT
Sequence domains: Ribosomal protein L20
50S ribosomal protein L21 Chains: S, XB
Molecule details ›
Chains: S, XB
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: T, YB
Molecule details ›
Chains: T, YB
Length: 113 amino acids
Theoretical weight: 12.81 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72I09 (Residues: 1-113; Coverage: 100%)
Gene names: TT_C1323, rplV
Sequence domains: Ribosomal protein L22p/L17e
50S ribosomal protein L23 Chains: U, ZB
Molecule details ›
Chains: U, ZB
Length: 96 amino acids
Theoretical weight: 10.76 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72I06 (Residues: 1-96; Coverage: 100%)
Gene names: TT_C1326, rplW
Sequence domains: Ribosomal protein L23
50S ribosomal protein L24 Chains: AC, V
Molecule details ›
Chains: AC, V
Length: 110 amino acids
Theoretical weight: 12.09 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72I15 (Residues: 1-110; Coverage: 100%)
Gene names: TT_C1317, rplX
Sequence domains:
50S ribosomal protein L25 Chains: BC, W
Molecule details ›
Chains: BC, W
Length: 206 amino acids
Theoretical weight: 23.24 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72IA7 (Residues: 1-206; Coverage: 100%)
Gene names: TT_C1225, ctc, rplY
Sequence domains:
50S ribosomal protein L27 Chains: CC, X
Molecule details ›
Chains: CC, X
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: DC, Y
Molecule details ›
Chains: DC, Y
Length: 98 amino acids
Theoretical weight: 11.03 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72G84 (Residues: 1-98; Coverage: 100%)
Gene names: TT_C1964, rpmB
Sequence domains: Ribosomal L28 family
50S ribosomal protein L29 Chains: EC, Z
Molecule details ›
Chains: EC, Z
Length: 72 amino acids
Theoretical weight: 8.67 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72I12 (Residues: 1-72; Coverage: 100%)
Gene names: TT_C1320, rpmC
Sequence domains: Ribosomal L29 protein
50S ribosomal protein L30 Chains: AA, FC
Molecule details ›
Chains: AA, FC
Length: 60 amino acids
Theoretical weight: 6.8 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72I22 (Residues: 1-60; Coverage: 100%)
Gene names: TT_C1310, rpmD
Sequence domains: Ribosomal protein L30p/L7e
50S ribosomal protein L31 Chains: BA, GC
Molecule details ›
Chains: BA, GC
Length: 71 amino acids
Theoretical weight: 8.3 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72JR0 (Residues: 1-71; Coverage: 100%)
Gene names: TT_C0708, rpmE
Sequence domains: Ribosomal protein L31
50S ribosomal protein L32 Chains: CA, HC
Molecule details ›
Chains: CA, HC
Length: 60 amino acids
Theoretical weight: 6.73 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62652 (Residues: 1-60; Coverage: 100%)
Gene names: TT_C0050, rpl32, rpmF
Sequence domains: Ribosomal L32p protein family
50S ribosomal protein L33 Chains: DA, IC
Molecule details ›
Chains: DA, IC
Length: 54 amino acids
Theoretical weight: 6.63 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72GW3 (Residues: 1-54; Coverage: 100%)
Gene names: TT_C1735, rpmG
Sequence domains: Ribosomal protein L33
50S ribosomal protein L34 Chains: EA, JC
Molecule details ›
Chains: EA, JC
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: FA, KC
Molecule details ›
Chains: FA, KC
Length: 65 amino acids
Theoretical weight: 7.51 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72L77 (Residues: 1-65; Coverage: 100%)
Gene names: TT_C0184, rpmI
Sequence domains: Ribosomal protein L35
50S ribosomal protein L36 Chains: GA, LC
Molecule details ›
Chains: GA, LC
Length: 37 amino acids
Theoretical weight: 4.44 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72I28 (Residues: 1-37; Coverage: 100%)
Gene names: TT_C1304, rpmJ
Sequence domains: Ribosomal protein L36
Peptide chain release factor RF1 Chains: JA, OC
Molecule details ›
Chains: JA, OC
Length: 368 amino acids
Theoretical weight: 41.64 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P0A7I0 (Residues: 1-360; Coverage: 100%)
Gene names: JW1202, b1211, prfA, sueB, uar
Sequence domains:
30S ribosomal protein S2 Chains: KA, PC
Molecule details ›
Chains: KA, PC
Length: 256 amino acids
Theoretical weight: 29.32 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62662 (Residues: 1-256; Coverage: 100%)
Gene names: TT_C0509, rps2, rpsB
Sequence domains: Ribosomal protein S2
30S ribosomal protein S3 Chains: LA, QC
Molecule details ›
Chains: LA, QC
Length: 239 amino acids
Theoretical weight: 26.75 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62663 (Residues: 1-239; Coverage: 100%)
Gene names: TT_C1322, rps3, rpsC
Sequence domains:
30S ribosomal protein S4 Chains: MA, RC
Molecule details ›
Chains: MA, RC
Length: 209 amino acids
Theoretical weight: 24.37 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62664 (Residues: 1-209; Coverage: 100%)
Gene names: TT_C1301, rps4, rpsD
Sequence domains:
30S ribosomal protein S5 Chains: NA, SC
Molecule details ›
Chains: NA, SC
Length: 162 amino acids
Theoretical weight: 17.58 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62665 (Residues: 1-162; Coverage: 100%)
Gene names: TT_C1311, rps5, rpsE
Sequence domains:
30S ribosomal protein S6 Chains: OA, TC
Molecule details ›
Chains: OA, TC
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: PA, UC
Molecule details ›
Chains: PA, UC
Length: 156 amino acids
Theoretical weight: 18.05 KDa
Source organism: Thermus thermophilus HB27
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: QA, VC
Molecule details ›
Chains: QA, VC
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: RA, WC
Molecule details ›
Chains: RA, WC
Length: 128 amino acids
Theoretical weight: 14.43 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62669 (Residues: 1-128; Coverage: 100%)
Gene names: TT_C1100, rps9, rpsI
Sequence domains: Ribosomal protein S9/S16
30S ribosomal protein S10 Chains: SA, XC
Molecule details ›
Chains: SA, XC
Length: 105 amino acids
Theoretical weight: 11.95 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62653 (Residues: 1-105; Coverage: 100%)
Gene names: TT_C1329, rps10, rpsJ
Sequence domains: Ribosomal protein S10p/S20e
30S ribosomal protein S11 Chains: TA, YC
Molecule details ›
Chains: TA, YC
Length: 129 amino acids
Theoretical weight: 13.74 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62654 (Residues: 1-129; Coverage: 100%)
Gene names: TT_C1302, rps11, rpsK
Sequence domains: Ribosomal protein S11
30S ribosomal protein S12 Chains: UA, ZC
Molecule details ›
Chains: UA, ZC
Length: 132 amino acids
Theoretical weight: 14.68 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P61941 (Residues: 1-132; Coverage: 100%)
Gene names: TT_C1333, rps12, rpsL
Sequence domains: Ribosomal protein S12/S23
30S ribosomal protein S13 Chains: AD, VA
Molecule details ›
Chains: AD, VA
Length: 126 amino acids
Theoretical weight: 14.34 KDa
Source organism: Thermus thermophilus HB27
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: BD, WA
Molecule details ›
Chains: BD, WA
Length: 61 amino acids
Theoretical weight: 7.16 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62656 (Residues: 1-61; Coverage: 100%)
Gene names: TT_C1315, rps14, rpsN, rpsZ
Sequence domains: Ribosomal protein S14p/S29e
30S ribosomal protein S15 Chains: CD, XA
Molecule details ›
Chains: CD, XA
Length: 89 amino acids
Theoretical weight: 10.58 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62657 (Residues: 1-89; Coverage: 100%)
Gene names: TT_C0773, rps15, rpsO
Sequence domains: Ribosomal protein S15
30S ribosomal protein S16 Chains: DD, YA
Molecule details ›
Chains: DD, YA
Length: 88 amino acids
Theoretical weight: 10.41 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62238 (Residues: 1-88; Coverage: 100%)
Gene names: TT_C0673, rps16, rpsP
Sequence domains: Ribosomal protein S16
30S ribosomal protein S17 Chains: ED, ZA
Molecule details ›
Chains: ED, ZA
Length: 105 amino acids
Theoretical weight: 12.32 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62658 (Residues: 1-105; Coverage: 100%)
Gene names: TT_C1319, rps17, rpsQ
Sequence domains: Ribosomal protein S17
30S ribosomal protein S18 Chains: AB, FD
Molecule details ›
Chains: AB, FD
Length: 88 amino acids
Theoretical weight: 10.26 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62659 (Residues: 1-88; Coverage: 100%)
Gene names: TT_C1742, rps18, rpsR
Sequence domains: Ribosomal protein S18
30S ribosomal protein S19 Chains: BB, GD
Molecule details ›
Chains: BB, GD
Length: 93 amino acids
Theoretical weight: 10.61 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62660 (Residues: 1-93; Coverage: 100%)
Gene names: TT_C1324, rps19, rpsS
Sequence domains: Ribosomal protein S19
30S ribosomal protein S20 Chains: CB, HD
Molecule details ›
Chains: CB, HD
Length: 106 amino acids
Theoretical weight: 11.72 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62661 (Residues: 1-106; Coverage: 100%)
Gene names: TT_C1031, rps20, rpsT
Sequence domains: Ribosomal protein S20
30S ribosomal protein Thx Chains: DB, ID
Molecule details ›
Chains: DB, ID
Length: 27 amino acids
Theoretical weight: 3.35 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62613 (Residues: 1-27; Coverage: 100%)
Gene names: TT_C1030, rpsU
Sequence domains: 30S ribosomal protein Thx
16S ribosomal RNA Chains: A, FB
Molecule details ›
Chains: A, FB
Length: 1507 nucleotides
Theoretical weight: 489.56 KDa
Sequence domains: Bacterial small subunit ribosomal RNA
25S ribosomal RNA Chains: B, GB
Molecule details ›
Chains: B, GB
Length: 2880 nucleotides
Theoretical weight: 936.79 KDa
Sequence domains: Bacterial large subunit ribosomal RNA
5S ribosomal RNA Chains: C, HB
Molecule details ›
Chains: C, HB
Length: 120 nucleotides
Theoretical weight: 38.88 KDa
Sequence domains: 5S ribosomal RNA
tRNA Chains: D, IA, IB, NC
Molecule details ›
Chains: D, IA, IB, NC
Length: 77 nucleotides
Theoretical weight: 24.85 KDa
Sequence domains: tRNA
Messenger RNA Chains: HA, MC
Molecule details ›
Chains: HA, MC
Length: 27 nucleotides
Theoretical weight: 8.86 KDa

Ligands and Environments

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL12-2, APS BEAMLINE 23-ID-D
Spacegroup: P212121
Unit cell:
a: 211.541Å b: 454.397Å c: 619.473Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.222 0.221 0.256
Expression system: Escherichia coli