› 4v79

Electron Microscopy
15Å resolution

E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in intermediate post-translocation state (post3b)

Released:
DOI: 10.2210/pdb4v79/pdb
PDB entry 4v79 coloured by chain, front view.
PDB entry 4v79 coloured by chain, side view.
PDB entry 4v79 coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Energy barriers and driving forces in tRNA translocation through the ribosome.
Bock LV, Blau C, Schröder GF, Davydov II, Fischer N, Stark H, Rodnina MV, Vaiana AC, Grubmüller H
Nat Struct Mol Biol 20 1390-6 (2013)
PMID: 24186064
Related structures: EMD-1723

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 56-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-249835 (preferred)
Entry contents:
50 distinct polypeptide molecules
6 distinct RNA molecules
Macromolecules (56 distinct):
Small ribosomal subunit protein uS2 Chain: AB
Molecule details ›
Chain: AB
Length: 220 amino acids
Theoretical weight: 24.28 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Best match: P0A7V0 (Residues: 9-226)
Gene names: JW0164, b0169, rpsB
Small ribosomal subunit protein uS3 Chain: AC
Molecule details ›
Chain: AC
Length: 208 amino acids
Theoretical weight: 23.21 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Best match: P0A7V3 (Residues: 1-207)
Gene names: JW3276, b3314, rpsC
Small ribosomal subunit protein uS4 Chain: AD
Molecule details ›
Chain: AD
Length: 206 amino acids
Theoretical weight: 23.51 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Best match: P0A7V8 (Residues: 1-206)
Gene names: JW3258, b3296, ramA, rpsD
Small ribosomal subunit protein uS5 Chain: AE
Molecule details ›
Chain: AE
Length: 152 amino acids
Theoretical weight: 15.83 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Best match: P0A7W1 (Residues: 10-159)
Gene names: JW3265, b3303, rpsE, spc
Small ribosomal subunit protein bS6, non-modified isoform Chain: AF
Molecule details ›
Chain: AF
Length: 101 amino acids
Theoretical weight: 11.67 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Best match: P02358 (Residues: 1-100)
Gene names: JW4158, b4200, rpsF
Small ribosomal subunit protein uS7 Chain: AG
Molecule details ›
Chain: AG
Length: 152 amino acids
Theoretical weight: 16.79 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Best match: P02359 (Residues: 3-152)
Gene names: JW3303, b3341, rpsG
Small ribosomal subunit protein uS8 Chain: AH
Molecule details ›
Chain: AH
Length: 130 amino acids
Theoretical weight: 14.15 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Best match: P0A7W7 (Residues: 1-130)
Gene names: JW3268, b3306, rpsH
Small ribosomal subunit protein uS9 Chain: AI
Molecule details ›
Chain: AI
Length: 128 amino acids
Theoretical weight: 14.58 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Best match: P0A7X3 (Residues: 4-130)
Gene names: JW3199, b3230, rpsI
Small ribosomal subunit protein uS10 Chain: AJ
Molecule details ›
Chain: AJ
Length: 100 amino acids
Theoretical weight: 11.22 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Best match: P0A7R5 (Residues: 5-102)
Gene names: JW3283, b3321, nusE, rpsJ
Small ribosomal subunit protein uS11 Chain: AK
Molecule details ›
Chain: AK
Length: 118 amino acids
Theoretical weight: 12.51 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Best match: P0A7R9 (Residues: 13-129)
Gene names: JW3259, b3297, rpsK
Small ribosomal subunit protein uS12 Chain: AL
Molecule details ›
Chain: AL
Length: 124 amino acids
Theoretical weight: 13.77 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Best match: P0A7S3 (Residues: 1-124)
Gene names: JW3304, b3342, rpsL, strA
Small ribosomal subunit protein uS13 Chain: AM
Molecule details ›
Chain: AM
Length: 115 amino acids
Theoretical weight: 12.66 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Best match: P0A7S9 (Residues: 1-114)
Gene names: JW3260, b3298, rpsM
Small ribosomal subunit protein uS14 Chain: AN
Molecule details ›
Chain: AN
Length: 101 amino acids
Theoretical weight: 11.61 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Best match: P0AG59 (Residues: 1-101)
Gene names: JW3269, b3307, rpsN
Small ribosomal subunit protein uS15 Chain: AO
Molecule details ›
Chain: AO
Length: 89 amino acids
Theoretical weight: 10.29 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Best match: P0ADZ4 (Residues: 1-89)
Gene names: JW3134, b3165, rpsO, secC
Small ribosomal subunit protein bS16 Chain: AP
Molecule details ›
Chain: AP
Length: 81 amino acids
Theoretical weight: 9.06 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Best match: P0A7T3 (Residues: 1-80)
Gene names: JW2590, b2609, rpsP
Small ribosomal subunit protein uS17 Chain: AQ
Molecule details ›
Chain: AQ
Length: 82 amino acids
Theoretical weight: 9.29 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Best match: P0AG63 (Residues: 4-83)
Gene names: JW3273, b3311, neaA, rpsQ
Small ribosomal subunit protein bS18 Chain: AR
Molecule details ›
Chain: AR
Length: 57 amino acids
Theoretical weight: 6.49 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Best match: P0A7T7 (Residues: 20-74)
Gene names: JW4160, b4202, rpsR
Small ribosomal subunit protein uS19 Chain: AS
Molecule details ›
Chain: AS
Length: 81 amino acids
Theoretical weight: 9.08 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Best match: P0A7U3 (Residues: 3-81)
Gene names: JW3278, b3316, rpsS
Small ribosomal subunit protein bS20 Chain: AT
Molecule details ›
Chain: AT
Length: 86 amino acids
Theoretical weight: 9.53 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Best match: P0A7U7 (Residues: 3-87)
Gene names: JW0022, b0023, rpsT
Small ribosomal subunit protein bS21 Chain: AU
Molecule details ›
Chain: AU
Length: 53 amino acids
Theoretical weight: 6.09 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Best match: P68679 (Residues: 4-54)
Gene names: JW3037, b3065, rpsU
Large ribosomal subunit protein uL2 Chain: BC
Molecule details ›
Chain: BC
Length: 273 amino acids
Theoretical weight: 29.79 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Best match: P60422 (Residues: 1-272)
Gene names: JW3279, b3317, rplB
Large ribosomal subunit protein uL3 Chain: BD
Molecule details ›
Chain: BD
Length: 209 amino acids
Theoretical weight: 22.28 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Best match: P60438 (Residues: 1-209)
Gene names: JW3282, b3320, rplC
Large ribosomal subunit protein uL4 Chain: BE
Molecule details ›
Chain: BE
Length: 201 amino acids
Theoretical weight: 22.12 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Best match: P60723 (Residues: 1-201)
Gene names: JW3281, b3319, eryA, rplD
Large ribosomal subunit protein uL5 Chain: BF
Molecule details ›
Chain: BF
Length: 179 amino acids
Theoretical weight: 20.33 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Best match: P62399 (Residues: 1-179)
Gene names: JW3270, b3308, rplE
Large ribosomal subunit protein uL6 Chain: BG
Molecule details ›
Chain: BG
Length: 177 amino acids
Theoretical weight: 18.93 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Best match: P0AG55 (Residues: 1-177)
Gene names: JW3267, b3305, rplF
Large ribosomal subunit protein bL9 Chain: BH
Molecule details ›
Chain: BH
Length: 149 amino acids
Theoretical weight: 15.79 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Best match: P0A7R1 (Residues: 1-149)
Gene names: JW4161, b4203, rplI
Large ribosomal subunit protein uL11 Chain: BI
Molecule details ›
Chain: BI
Length: 142 amino acids
Theoretical weight: 14.89 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Best match: P0A7J7 (Residues: 1-142)
Gene names: JW3946, b3983, relC, rplK
Large ribosomal subunit protein uL13 Chain: BJ
Molecule details ›
Chain: BJ
Length: 142 amino acids
Theoretical weight: 16.05 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Best match: P0AA10 (Residues: 1-142)
Gene names: JW3200, b3231, rplM
Large ribosomal subunit protein uL14 Chain: BK
Molecule details ›
Chain: BK
Length: 123 amino acids
Theoretical weight: 13.45 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Best match: P0ADY3 (Residues: 1-122)
Gene names: JW3272, b3310, rplN
Large ribosomal subunit protein uL15 Chain: BL
Molecule details ›
Chain: BL
Length: 144 amino acids
Theoretical weight: 15.01 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Best match: P02413 (Residues: 1-144)
Gene names: JW3263, b3301, rplO
Large ribosomal subunit protein uL16 Chain: BM
Molecule details ›
Chain: BM
Length: 136 amino acids
Theoretical weight: 15.31 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Best match: P0ADY7 (Residues: 1-136)
Gene names: JW3275, b3313, rplP
Large ribosomal subunit protein bL17 Chain: BN
Molecule details ›
Chain: BN
Length: 121 amino acids
Theoretical weight: 13.72 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Best match: P0AG44 (Residues: 1-120)
Gene names: JW3256, b3294, rplQ
Large ribosomal subunit protein uL18 Chain: BO
Molecule details ›
Chain: BO
Length: 117 amino acids
Theoretical weight: 12.79 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Best match: P0C018 (Residues: 1-117)
Gene names: JW3266, b3304, rplR
Large ribosomal subunit protein bL19 Chain: BP
Molecule details ›
Chain: BP
Length: 115 amino acids
Theoretical weight: 13.16 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Best match: P0A7K6 (Residues: 1-115)
Gene names: JW2587, b2606, rplS
Large ribosomal subunit protein bL20 Chain: BQ
Molecule details ›
Chain: BQ
Length: 118 amino acids
Theoretical weight: 13.53 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Best match: P0A7L3 (Residues: 1-118)
Gene names: JW1706, b1716, pdzA, rplT
Large ribosomal subunit protein bL21 Chain: BR
Molecule details ›
Chain: BR
Length: 103 amino acids
Theoretical weight: 11.59 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Best match: P0AG48 (Residues: 1-103)
Gene names: JW3153, b3186, rplU
Large ribosomal subunit protein uL22 Chain: BS
Molecule details ›
Chain: BS
Length: 110 amino acids
Theoretical weight: 12.25 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Best match: P61175 (Residues: 1-110)
Gene names: JW3277, b3315, eryB, rplV
Large ribosomal subunit protein uL23 Chain: BT
Molecule details ›
Chain: BT
Length: 94 amino acids
Theoretical weight: 10.54 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Best match: P0ADZ0 (Residues: 1-93)
Gene names: JW3280, b3318, rplW
Large ribosomal subunit protein uL24 Chain: BU
Molecule details ›
Chain: BU
Length: 104 amino acids
Theoretical weight: 11.21 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Best match: P60624 (Residues: 1-103)
Gene names: JW3271, b3309, rplX
Large ribosomal subunit protein bL25 Chain: BV
Molecule details ›
Chain: BV
Length: 94 amino acids
Theoretical weight: 10.71 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Best match: P68919 (Residues: 1-94)
Gene names: JW2173, b2185, rplY
Large ribosomal subunit protein bL27 Chain: BW
Molecule details ›
Chain: BW
Length: 80 amino acids
Theoretical weight: 8.5 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Best match: P0A7L8 (Residues: 7-85)
Gene names: JW3152, b3185, rpmA
Large ribosomal subunit protein bL28 Chain: BX
Molecule details ›
Chain: BX
Length: 79 amino acids
Theoretical weight: 9.05 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Best match: P0A7M2 (Residues: 1-78)
Gene names: JW3612, b3637, rpmB
Large ribosomal subunit protein uL29 Chain: BY
Molecule details ›
Chain: BY
Length: 63 amino acids
Theoretical weight: 7.29 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Best match: P0A7M6 (Residues: 1-63)
Gene names: JW3274, b3312, rpmC
Large ribosomal subunit protein uL30 Chain: BZ
Molecule details ›
Chain: BZ
Length: 59 amino acids
Theoretical weight: 6.55 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Best match: P0AG51 (Residues: 1-59)
Gene names: JW3264, b3302, rpmD
Large ribosomal subunit protein bL32 Chain: B0
Molecule details ›
Chain: B0
Length: 57 amino acids
Theoretical weight: 6.46 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Best match: P0A7N4 (Residues: 1-57)
Gene names: JW1075, b1089, rpmF
Large ribosomal subunit protein bL33 Chain: B1
Molecule details ›
Chain: B1
Length: 52 amino acids
Theoretical weight: 5.84 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Best match: P0A7N9 (Residues: 4-53)
Gene names: JW3611, b3636, rpmG
Large ribosomal subunit protein bL34 Chain: B2
Molecule details ›
Chain: B2
Length: 46 amino acids
Theoretical weight: 5.4 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Best match: P0A7P5 (Residues: 1-46)
Gene names: JW3680, b3703, rimA, rpmH, ssaF
Large ribosomal subunit protein bL35 Chain: B3
Molecule details ›
Chain: B3
Length: 65 amino acids
Theoretical weight: 7.31 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Best match: P0A7Q1 (Residues: 1-65)
Gene names: JW1707, b1717, rpmI
Large ribosomal subunit protein bL36A Chain: B4
Molecule details ›
Chain: B4
Length: 38 amino acids
Theoretical weight: 4.38 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Best match: P0A7Q6 (Residues: 1-38)
Gene names: JW3261, b3299, rpmJ
Large ribosomal subunit protein uL1 Chain: B5
Molecule details ›
Chain: B5
Length: 234 amino acids
Theoretical weight: 24.77 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Best match: P0A7L0 (Residues: 1-234)
Gene names: JW3947, b3984, rplA
16S ribosomal RNA Chain: AA
Molecule details ›
Chain: AA
Length: 1533 nucleotides
Theoretical weight: 496.89 KDa
Sequence domains: Bacterial small subunit ribosomal RNA
fMet-Val-tRNA-Val Chain: A1
Molecule details ›
Chain: A1
Length: 76 nucleotides
Theoretical weight: 24.62 KDa
Sequence domains: tRNA
5'-R(*AP*CP*UP*AP*UP*GP*GP*UP*UP*UP*UP*UP*AP*UP*U)-3' Chain: A2
Molecule details ›
Chain: A2
Length: 15 nucleotides
Theoretical weight: 4.69 KDa
tRNA-fMet Chain: A3
Molecule details ›
Chain: A3
Length: 77 nucleotides
Theoretical weight: 24.85 KDa
Sequence domains: tRNA
23S ribosomal RNA Chain: BA
Molecule details ›
Chain: BA
Length: 2903 nucleotides
Theoretical weight: 941.31 KDa
Sequence domains: Bacterial large subunit ribosomal RNA
5S ribosomal RNA Chain: BB
Molecule details ›
Chain: BB
Length: 118 nucleotides
Theoretical weight: 38.18 KDa
Sequence domains: 5S ribosomal RNA

Ligands and Environments

2 bound ligands:
Ligand VAL 1 x VAL
Ligand FME 1 x FME
7 modified residues:
Ligand 4SU 2 x 4SU
Ligand 6MZ 1 x 6MZ
Ligand 7MG 1 x 7MG
Ligand 5MU 2 x 5MU
Ligand PSU 2 x PSU
Ligand H2U 1 x H2U
Ligand OMC 1 x OMC

Experiments and Validation Details

Entry percentile scores
Resolution: 15Å
Relevant EMDB volumes: EMD-1723

Quick links

Citations

21 review citations

RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.
Šponer et al. (2018)
20 more

2 mentions without citation

Alternative Mode of E-Site tRNA Binding in the Presence of a Downstream mRNA Stem Loop at the Entrance Channel.
Zhang et al. (2018)
1 more