› 4v4i

X-ray diffraction
3.71Å resolution

Crystal Structure of a 70S Ribosome-tRNA Complex Reveals Functional Interactions and Rearrangements.

Released:
DOI: 10.2210/pdb4v4i/pdb
PDB entry 4v4i coloured by chain, front view.
PDB entry 4v4i coloured by chain, side view.
PDB entry 4v4i coloured by chain, top view.
Source organism: Thermus thermophilus HB27
Primary publication:
Crystal structure of a 70S ribosome-tRNA complex reveals functional interactions and rearrangements.
Korostelev A, Trakhanov S, Laurberg M, Noller HF
Cell 126 1065-77 (2006)
PMID: 16962654

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 54-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-216292 (preferred)
Entry contents:
48 distinct polypeptide molecules
6 distinct RNA molecules
Macromolecules (54 distinct):
Large ribosomal subunit protein uL1 Chain: A
Molecule details ›
Chain: A
Length: 229 amino acids
Theoretical weight: 24.87 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q5SLP7 (Residues: 1-229; Coverage: 100%)
Gene names: TTHA0246, rplA
Sequence domains: Ribosomal protein L1p/L10e family
Large ribosomal subunit protein uL2 Chain: B
Molecule details ›
Chain: B
Length: 276 amino acids
Theoretical weight: 30.53 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P60405 (Residues: 1-276; Coverage: 100%)
Gene names: TTHA1689, rplB
Sequence domains:
Large ribosomal subunit protein uL3 Chain: C
Molecule details ›
Chain: C
Length: 206 amino acids
Theoretical weight: 22.45 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q5SHN8 (Residues: 1-206; Coverage: 100%)
Gene names: TTHA1692, rplC
Sequence domains: Ribosomal protein L3
Large ribosomal subunit protein uL4 Chain: D
Molecule details ›
Chain: D
Length: 205 amino acids
Theoretical weight: 22.74 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q5SHN9 (Residues: 6-210; Coverage: 98%)
Gene names: TTHA1691, rplD
Sequence domains: Ribosomal protein L4/L1 family
Large ribosomal subunit protein uL5 Chain: E
Molecule details ›
Chain: E
Length: 182 amino acids
Theoretical weight: 21.08 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q5SHQ0 (Residues: 1-182; Coverage: 100%)
Gene names: TTHA1680, rplE
Sequence domains:
Large ribosomal subunit protein uL6 Chain: F
Molecule details ›
Chain: F
Length: 180 amino acids
Theoretical weight: 19.57 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P0DOY8 (Residues: 1-180; Coverage: 100%)
Gene names: TTHA1677, rplF
Sequence domains: Ribosomal protein L6
Large ribosomal subunit protein bL9 Chain: G
Molecule details ›
Chain: G
Length: 148 amino acids
Theoretical weight: 16.44 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q5SLQ1 (Residues: 1-148; Coverage: 100%)
Gene names: TTHA0242, rplI
Sequence domains:
Large ribosomal subunit protein uL13 Chain: H
Molecule details ›
Chain: H
Length: 163 amino acids
Theoretical weight: 18.53 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P60488 (Residues: 1-140; Coverage: 100%)
Gene names: TTHA1465, rplM
Sequence domains: Ribosomal protein L13
Large ribosomal subunit protein uL14 Chain: I
Molecule details ›
Chain: I
Length: 122 amino acids
Theoretical weight: 13.31 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q5SHP8 (Residues: 1-122; Coverage: 100%)
Gene names: TTHA1682, rplN
Sequence domains: Ribosomal protein L14p/L23e
Large ribosomal subunit protein uL15 Chain: J
Molecule details ›
Chain: J
Length: 150 amino acids
Theoretical weight: 16.32 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q5SHQ7 (Residues: 1-150; Coverage: 100%)
Gene names: TTHA1673, rplO
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
Large ribosomal subunit protein uL16 Chain: K
Molecule details ›
Chain: K
Length: 141 amino acids
Theoretical weight: 15.98 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P60489 (Residues: 1-141; Coverage: 100%)
Gene names: TTHA1685, rplP
Sequence domains: Ribosomal protein L16p/L10e
Large ribosomal subunit protein bL17 Chain: L
Molecule details ›
Chain: L
Length: 118 amino acids
Theoretical weight: 13.75 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q9Z9H5 (Residues: 1-118; Coverage: 100%)
Gene names: TTHA1663, rpl17, rplQ
Sequence domains: Ribosomal protein L17
Large ribosomal subunit protein uL18 Chain: M
Molecule details ›
Chain: M
Length: 112 amino acids
Theoretical weight: 12.64 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q5SHQ4 (Residues: 1-112; Coverage: 100%)
Gene names: TTHA1676, rplR
Sequence domains: Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
Large ribosomal subunit protein bL19 Chain: N
Molecule details ›
Chain: N
Length: 146 amino acids
Theoretical weight: 17.22 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P60490 (Residues: 1-146; Coverage: 100%)
Gene names: TTHA1031, rplS
Sequence domains: Ribosomal protein L19
Large ribosomal subunit protein bL20 Chain: O
Molecule details ›
Chain: O
Length: 118 amino acids
Theoretical weight: 13.78 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P60491 (Residues: 1-118; Coverage: 100%)
Gene names: TTHA0553, rplT
Sequence domains: Ribosomal protein L20
Large ribosomal subunit protein bL21 Chain: P
Molecule details ›
Chain: P
Length: 101 amino acids
Theoretical weight: 11.07 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P60492 (Residues: 1-101; Coverage: 100%)
Gene names: TTHA1783, rplU
Sequence domains: Ribosomal prokaryotic L21 protein
Large ribosomal subunit protein uL22 Chain: Q
Molecule details ›
Chain: Q
Length: 113 amino acids
Theoretical weight: 12.81 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q5SHP3 (Residues: 1-113; Coverage: 100%)
Gene names: TTHA1687, rplV
Sequence domains: Ribosomal protein L22p/L17e
Large ribosomal subunit protein uL23 Chain: R
Molecule details ›
Chain: R
Length: 96 amino acids
Theoretical weight: 10.76 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q5SHP0 (Residues: 1-96; Coverage: 100%)
Gene names: TTHA1690, rplW
Sequence domains: Ribosomal protein L23
Large ribosomal subunit protein uL24 Chain: S
Molecule details ›
Chain: S
Length: 110 amino acids
Theoretical weight: 12.09 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q5SHP9 (Residues: 1-110; Coverage: 100%)
Gene names: TTHA1681, rplX
Sequence domains:
Large ribosomal subunit protein bL25 Chain: T
Molecule details ›
Chain: T
Length: 206 amino acids
Theoretical weight: 23.24 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q5SHZ1 (Residues: 1-206; Coverage: 100%)
Gene names: TTHA1589, rpl25, rplY, rptL5
Sequence domains:
Large ribosomal subunit protein bL27 Chain: U
Molecule details ›
Chain: U
Length: 85 amino acids
Theoretical weight: 9.5 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P60493 (Residues: 1-85; Coverage: 100%)
Gene names: TTHA1782, rpmA
Sequence domains: Ribosomal L27 protein
Large ribosomal subunit protein bL28 Chain: V
Molecule details ›
Chain: V
Length: 98 amino acids
Theoretical weight: 11.03 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P60494 (Residues: 1-98; Coverage: 100%)
Gene names: TTHA0042, rpmB
Sequence domains: Ribosomal L28 family
Large ribosomal subunit protein uL29 Chain: W
Molecule details ›
Chain: W
Length: 72 amino acids
Theoretical weight: 8.67 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q5SHP6 (Residues: 1-72; Coverage: 100%)
Gene names: TTHA1684, rpmC
Sequence domains: Ribosomal L29 protein
Large ribosomal subunit protein uL30 Chain: X
Molecule details ›
Chain: X
Length: 60 amino acids
Theoretical weight: 6.8 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q5SHQ6 (Residues: 1-60; Coverage: 100%)
Gene names: TTHA1674, rpmD
Sequence domains: Ribosomal protein L30p/L7e
Large ribosomal subunit protein bL32 Chain: Y
Molecule details ›
Chain: Y
Length: 60 amino acids
Theoretical weight: 6.73 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P80339 (Residues: 1-60; Coverage: 100%)
Gene names: TTHA0418, rpl32, rpmF
Sequence domains: Ribosomal L32p protein family
Large ribosomal subunit protein bL34 Chain: Z
Molecule details ›
Chain: Z
Length: 49 amino acids
Theoretical weight: 6.13 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P80340 (Residues: 1-49; Coverage: 100%)
Gene names: TTHA0446, rpl34, rpmH
Sequence domains: Ribosomal protein L34
Large ribosomal subunit protein bL35 Chain: a
Molecule details ›
Chain: a
Length: 65 amino acids
Theoretical weight: 7.51 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q5SKU1 (Residues: 1-65; Coverage: 100%)
Gene names: TTHA0552, rpmI
Sequence domains: Ribosomal protein L35
Large ribosomal subunit protein bL36 Chain: b
Molecule details ›
Chain: b
Length: 37 amino acids
Theoretical weight: 4.44 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q5SHR2 (Residues: 1-37; Coverage: 100%)
Gene names: TTHA1668, rpmJ
Sequence domains: Ribosomal protein L36
Small ribosomal subunit protein uS2 Chain: c
Molecule details ›
Chain: c
Length: 256 amino acids
Theoretical weight: 29.32 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P80371 (Residues: 1-256; Coverage: 100%)
Gene names: TTHA0861, rps2, rpsB
Sequence domains: Ribosomal protein S2
Small ribosomal subunit protein uS3 Chain: d
Molecule details ›
Chain: d
Length: 239 amino acids
Theoretical weight: 26.75 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P80372 (Residues: 1-239; Coverage: 100%)
Gene names: TTHA1686, rps3, rpsC
Sequence domains:
Small ribosomal subunit protein uS4 Chain: e
Molecule details ›
Chain: e
Length: 209 amino acids
Theoretical weight: 24.37 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P80373 (Residues: 1-209; Coverage: 100%)
Gene names: TTHA1665, rps4, rpsD
Sequence domains:
Small ribosomal subunit protein uS5 Chain: f
Molecule details ›
Chain: f
Length: 162 amino acids
Theoretical weight: 17.58 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q5SHQ5 (Residues: 1-162; Coverage: 100%)
Gene names: TTHA1675, rpsE
Sequence domains:
Small ribosomal subunit protein bS6 Chain: g
Molecule details ›
Chain: g
Length: 101 amino acids
Theoretical weight: 11.99 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q5SLP8 (Residues: 1-101; Coverage: 100%)
Gene names: TTHA0245, rpsF
Sequence domains: Ribosomal protein S6
Small ribosomal subunit protein uS7 Chain: h
Molecule details ›
Chain: h
Length: 156 amino acids
Theoretical weight: 18.05 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P17291 (Residues: 1-156; Coverage: 100%)
Gene names: TTHA1696, rps7, rpsG
Sequence domains: Ribosomal protein S7p/S5e
Small ribosomal subunit protein uS8 Chain: i
Molecule details ›
Chain: i
Length: 138 amino acids
Theoretical weight: 15.87 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P0DOY9 (Residues: 1-138; Coverage: 100%)
Gene names: TTHA1678, rpsH
Sequence domains: Ribosomal protein S8
Small ribosomal subunit protein uS9 Chain: j
Molecule details ›
Chain: j
Length: 128 amino acids
Theoretical weight: 14.43 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P80374 (Residues: 1-128; Coverage: 100%)
Gene names: TTHA1464, rps9, rpsI
Sequence domains: Ribosomal protein S9/S16
Small ribosomal subunit protein uS10 Chain: k
Molecule details ›
Chain: k
Length: 105 amino acids
Theoretical weight: 11.95 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q5SHN7 (Residues: 1-105; Coverage: 100%)
Gene names: TTHA1693, rpsJ
Sequence domains: Ribosomal protein S10p/S20e
Small ribosomal subunit protein uS11 Chain: l
Molecule details ›
Chain: l
Length: 129 amino acids
Theoretical weight: 13.74 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P80376 (Residues: 1-129; Coverage: 100%)
Gene names: TTHA1666, rps11, rpsK
Sequence domains: Ribosomal protein S11
Small ribosomal subunit protein uS12 Chain: m
Molecule details ›
Chain: m
Length: 132 amino acids
Theoretical weight: 14.64 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q5SHN3 (Residues: 1-132; Coverage: 100%)
Gene names: TTHA1697, rpsL
Sequence domains: Ribosomal protein S12/S23
Small ribosomal subunit protein uS13 Chain: n
Molecule details ›
Chain: n
Length: 126 amino acids
Theoretical weight: 14.34 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P80377 (Residues: 1-126; Coverage: 100%)
Gene names: TTHA1667, rps13, rpsM
Sequence domains: Ribosomal protein S13/S18
Small ribosomal subunit protein uS14 Chain: o
Molecule details ›
Chain: o
Length: 61 amino acids
Theoretical weight: 7.16 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P0DOY6 (Residues: 1-61; Coverage: 100%)
Gene names: TTHA1679, rpsN, rpsZ
Sequence domains: Ribosomal protein S14p/S29e
Small ribosomal subunit protein uS15 Chain: p
Molecule details ›
Chain: p
Length: 89 amino acids
Theoretical weight: 10.58 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q5SJ76 (Residues: 1-89; Coverage: 100%)
Gene names: TTHA1138, rpsO
Sequence domains: Ribosomal protein S15
Small ribosomal subunit protein bS16 Chain: q
Molecule details ›
Chain: q
Length: 88 amino acids
Theoretical weight: 10.41 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q5SJH3 (Residues: 1-88; Coverage: 100%)
Gene names: TTHA1035, rpsP
Sequence domains: Ribosomal protein S16
Small ribosomal subunit protein uS17 Chain: r
Molecule details ›
Chain: r
Length: 105 amino acids
Theoretical weight: 12.32 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P0DOY7 (Residues: 1-105; Coverage: 100%)
Gene names: TTHA1683, rpsQ
Sequence domains: Ribosomal protein S17
Small ribosomal subunit protein bS18 Chain: s
Molecule details ›
Chain: s
Length: 88 amino acids
Theoretical weight: 10.26 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q5SLQ0 (Residues: 1-88; Coverage: 100%)
Gene names: TTHA0243, rpsR
Sequence domains: Ribosomal protein S18
Small ribosomal subunit protein uS19 Chain: t
Molecule details ›
Chain: t
Length: 93 amino acids
Theoretical weight: 10.61 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q5SHP2 (Residues: 1-93; Coverage: 100%)
Gene names: TTHA1688, rpsS
Sequence domains: Ribosomal protein S19
Small ribosomal subunit protein bS20 Chain: u
Molecule details ›
Chain: u
Length: 106 amino acids
Theoretical weight: 11.72 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P80380 (Residues: 1-106; Coverage: 100%)
Gene names: TTHA1397, rps20, rpsT
Sequence domains: Ribosomal protein S20
Small ribosomal subunit protein bTHX Chain: v
Molecule details ›
Chain: v
Length: 27 amino acids
Theoretical weight: 3.35 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q5SIH3 (Residues: 1-27; Coverage: 100%)
Gene names: TTHA1396, rpsU
Sequence domains: 30S ribosomal protein Thx
23S ribosomal RNA Chain: w
Molecule details ›
Chain: w
Length: 2889 nucleotides
Theoretical weight: 939.56 KDa
Sequence domains: Bacterial large subunit ribosomal RNA
5S ribosomal RNA Chain: x
Molecule details ›
Chain: x
Length: 121 nucleotides
Theoretical weight: 39.21 KDa
Sequence domains: 5S ribosomal RNA
16S ribosomal RNA Chain: y
Molecule details ›
Chain: y
Length: 1522 nucleotides
Theoretical weight: 494.21 KDa
Sequence domains: Bacterial small subunit ribosomal RNA
P-site PHE-tRNA Chain: z
Molecule details ›
Chain: z
Length: 76 nucleotides
Theoretical weight: 24.65 KDa
Sequence domains: tRNA
E-TRNA Chain: 0
Molecule details ›
Chain: 0
Length: 76 nucleotides
Theoretical weight: 24.5 KDa
Sequence domains: tRNA
Messenger RNA Chain: 1
Molecule details ›
Chain: 1
Length: 10 nucleotides
Theoretical weight: 3.15 KDa

Ligands and Environments

No bound ligands
12 modified residues:
Ligand PSU 5 x PSU
Ligand 7MG 2 x 7MG
Ligand M2G 1 x M2G
Ligand 5MC 4 x 5MC
Ligand 2MG 1 x 2MG
Ligand 4OC 1 x 4OC
Ligand UR3 1 x UR3
Ligand MA6 2 x MA6
Ligand 4SU 1 x 4SU
Ligand H2U 2 x H2U
Ligand MIA 1 x MIA
Ligand 5MU 1 x 5MU

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 12.3.1
Spacegroup: I422
Unit cell:
a: 507.81Å b: 507.81Å c: 689.52Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.349 0.348 0.353

Quick links

Citations

78 review citations

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Hinnebusch AG. (2014)
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5 mentions without citation

The tRNA Elbow in Structure, Recognition and Evolution.
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