5WDT image
Deposition Date 2017-07-06
Release Date 2018-04-25
Last Version Date 2025-02-12
Entry Detail
PDB ID:
5WDT
Keywords:
RIBOSOME
Title:
70S ribosome-EF-Tu H84A complex with GppNHp
Biological Source:
Source Organism:
Escherichia coli (Taxon ID: 562)
Host Organism:
Escherichia coli
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.00 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
5WDT validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32
Gene (Uniprot):rpmF
Chain IDs:AA (auth: 0)
Chain Length:55
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7N4 Pfam ID:PF01783
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L33
Gene (Uniprot):rpmG
Chain IDs:BA (auth: 1)
Chain Length:51
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7N9 Pfam ID:PF00471
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L34
Gene (Uniprot):rpmH
Chain IDs:CA (auth: 2)
Chain Length:45
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7P5 Pfam ID:PF00468
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L35
Gene (Uniprot):rpmI
Chain IDs:DA (auth: 3)
Chain Length:64
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7Q1 Pfam ID:PF01632
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L36
Gene (Uniprot):rpmJ
Chain IDs:EA (auth: 4)
Chain Length:38
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7Q6 Pfam ID:PF00444
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L10
Gene (Uniprot):rplJ
Chain IDs:FA (auth: 5)
Chain Length:131
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7J3 Pfam ID:PF00466
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L31
Gene (Uniprot):rpmE
Chain IDs:GA (auth: 6)
Chain Length:66
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7M9 Pfam ID:PF01197
Polymer Type:polyribonucleotide
Molecule:23S rRNA
Chain IDs:A
Chain Length:2903
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:5S rRNA
Chain IDs:B
Chain Length:218
Number of Molecules:1
Biological Source:Escherichia coli
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Gene (Uniprot):rplB
Chain IDs:C
Chain Length:206
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P60422 Pfam ID:PF00181, PF03947
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L3
Gene (Uniprot):rplC
Chain IDs:D
Chain Length:205
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P60438 Pfam ID:PF00297
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4
Gene (Uniprot):rplD
Chain IDs:E
Chain Length:200
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P60723 Pfam ID:PF00573
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5
Gene (Uniprot):rplE
Chain IDs:F
Chain Length:177
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P62399 Pfam ID:PF00281, PF00673
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L6
Gene (Uniprot):rplF
Chain IDs:G
Chain Length:151
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0AG55 Pfam ID:PF00347
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L9
Gene (Uniprot):rplI
Chain IDs:H
Chain Length:149
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7R1 Pfam ID:PF01281, PF03948
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L11
Gene (Uniprot):rplK
Chain IDs:I
Chain Length:127
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7J7 Pfam ID:PF03946, PF00298
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13
Gene (Uniprot):rplM
Chain IDs:J
Chain Length:141
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0AA10 Pfam ID:PF00572
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Gene (Uniprot):rplN
Chain IDs:K
Chain Length:116
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0ADY3 Pfam ID:PF00238
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15
Gene (Uniprot):rplO
Chain IDs:L
Chain Length:121
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P02413 Pfam ID:PF00828
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16
Gene (Uniprot):rplP
Chain IDs:M
Chain Length:115
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0ADY7 Pfam ID:PF00252
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L17
Gene (Uniprot):rplQ
Chain IDs:N
Chain Length:101
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0AG44 Pfam ID:PF01196
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18
Gene (Uniprot):rplR
Chain IDs:O
Chain Length:116
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0C018 Pfam ID:PF00861
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19
Gene (Uniprot):rplS
Chain IDs:P
Chain Length:82
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7K6 Pfam ID:PF01245
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L20
Gene (Uniprot):rplT
Chain IDs:Q
Chain Length:80
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7L3 Pfam ID:PF00453
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L21
Gene (Uniprot):rplU
Chain IDs:R
Chain Length:102
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0AG48 Pfam ID:PF00829
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22
Gene (Uniprot):rplV
Chain IDs:S
Chain Length:109
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P61175 Pfam ID:PF00237
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L23
Gene (Uniprot):rplW
Chain IDs:T
Chain Length:85
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0ADZ0 Pfam ID:PF00276
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24
Gene (Uniprot):rplX
Chain IDs:U
Chain Length:65
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P60624 Pfam ID:PF00467, PF17136
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L25
Gene (Uniprot):rplY
Chain IDs:V
Chain Length:77
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P68919 Pfam ID:PF01386
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Gene (Uniprot):rpmA
Chain IDs:W
Chain Length:75
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7L8 Pfam ID:PF01016
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L28
Gene (Uniprot):rpmB
Chain IDs:X
Chain Length:77
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7M2 Pfam ID:PF00830
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29
Gene (Uniprot):rpmC
Chain IDs:Y
Chain Length:60
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7M6 Pfam ID:PF00831
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L30
Gene (Uniprot):rpmD
Chain IDs:Z
Chain Length:56
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0AG51 Pfam ID:PF00327
Polymer Type:polyribonucleotide
Molecule:16S rRNA
Chain IDs:HA (auth: a)
Chain Length:2903
Number of Molecules:1
Biological Source:Escherichia coli
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Gene (Uniprot):rpsB
Chain IDs:IA (auth: b)
Chain Length:218
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7V0 Pfam ID:PF00318
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S3
Gene (Uniprot):rpsC
Chain IDs:JA (auth: c)
Chain Length:206
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7V3 Pfam ID:PF07650, PF00189
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S4
Gene (Uniprot):rpsD
Chain IDs:KA (auth: d)
Chain Length:205
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7V8 Pfam ID:PF00163, PF01479
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S5
Gene (Uniprot):rpsE
Chain IDs:LA (auth: e)
Chain Length:200
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7W1 Pfam ID:PF00333, PF03719
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S6
Gene (Uniprot):rpsF
Chain IDs:MA (auth: f)
Chain Length:177
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P02358 Pfam ID:PF01250
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S7
Gene (Uniprot):rpsG
Chain IDs:NA (auth: g)
Chain Length:151
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P02359 Pfam ID:PF00177
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S8
Gene (Uniprot):rpsH
Chain IDs:OA (auth: h)
Chain Length:149
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7W7 Pfam ID:PF00410
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S9
Gene (Uniprot):rpsI
Chain IDs:PA (auth: i)
Chain Length:127
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7X3 Pfam ID:PF00380
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S10
Gene (Uniprot):rpsJ
Chain IDs:QA (auth: j)
Chain Length:141
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7R5 Pfam ID:PF00338
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S11
Gene (Uniprot):rpsK
Chain IDs:RA (auth: k)
Chain Length:116
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7R9 Pfam ID:PF00411
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S12
Gene (Uniprot):rpsL
Chain IDs:SA (auth: l)
Chain Length:121
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7S3 Pfam ID:PF00164
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S13
Gene (Uniprot):rpsM
Chain IDs:TA (auth: m)
Chain Length:115
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7S9 Pfam ID:PF00416
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S14
Gene (Uniprot):rpsN
Chain IDs:UA (auth: n)
Chain Length:101
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0AG59 Pfam ID:PF00253
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S15
Gene (Uniprot):rpsO
Chain IDs:VA (auth: o)
Chain Length:116
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0ADZ4 Pfam ID:PF00312
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S16
Gene (Uniprot):rpsP
Chain IDs:WA (auth: p)
Chain Length:82
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7T3 Pfam ID:PF00886
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S17
Gene (Uniprot):rpsQ
Chain IDs:XA (auth: q)
Chain Length:80
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0AG63 Pfam ID:PF00366
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S18
Gene (Uniprot):rpsR
Chain IDs:YA (auth: r)
Chain Length:102
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7T7 Pfam ID:PF01084
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S19
Gene (Uniprot):rpsS
Chain IDs:ZA (auth: s)
Chain Length:109
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7U3 Pfam ID:PF00203
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S20
Gene (Uniprot):rpsT
Chain IDs:AB (auth: t)
Chain Length:85
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7U7 Pfam ID:PF01649
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S21
Gene (Uniprot):rpsU
Chain IDs:BB (auth: u)
Chain Length:65
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P68679 Pfam ID:PF01165
Polymer Type:polyribonucleotide
Molecule:tRNA-fMet
Chain IDs:CB (auth: v), DB (auth: w)
Chain Length:77
Number of Molecules:2
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:mRNA
Chain IDs:EB (auth: x)
Chain Length:77
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:tRNA-Phe
Chain IDs:FB (auth: y)
Chain Length:60
Number of Molecules:1
Biological Source:Escherichia coli
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Elongation factor Tu 2
Gene (Uniprot):tufB
Mutations:H84A
Chain IDs:GB (auth: z)
Chain Length:56
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0CE48 Pfam ID:PF00009, PF03144, PF03143 EC:3.6.5.3
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
1MG A G modified residue
2MA A A modified residue
2MG A G modified residue
3TD A U modified residue
4OC HA C modified residue
4SU CB U modified residue
5MC A C modified residue
5MU A U modified residue
6MZ A A modified residue
7MG A G modified residue
H2U A U modified residue
MA6 HA A modified residue
OMC A C modified residue
OMG A G modified residue
OMU A U modified residue
PSU A U modified residue
UR3 HA U modified residue
Ligand Molecules
FME
GNP
K
MG
PHE
Primary Citation
Cryo-EM shows stages of initial codon selection on the ribosome by aa-tRNA in ternary complex with GTP and the GTPase-deficient EF-TuH84A.
Nucleic Acids Res. 46 5861 5874 (2018)
PMID: 29733411 DOI: 10.1093/nar/gky346

Abstact

The GTPase EF-Tu in ternary complex with GTP and aminoacyl-tRNA (aa-tRNA) promotes rapid and accurate delivery of cognate aa-tRNAs to the ribosomal A site. Here we used cryo-EM to study the molecular origins of the accuracy of ribosome-aided recognition of a cognate ternary complex and the accuracy-amplifying role of the monitoring bases A1492, A1493 and G530 of the 16S rRNA. We used the GTPase-deficient EF-Tu variant H84A with native GTP, rather than non-cleavable GTP analogues, to trap a near-cognate ternary complex in high-resolution ribosomal complexes of varying codon-recognition accuracy. We found that ribosome complexes trapped by GTPase-deficicent ternary complex due to the presence of EF-TuH84A or non-cleavable GTP analogues have very similar structures. We further discuss speed and accuracy of initial aa-tRNA selection in terms of conformational changes of aa-tRNA and stepwise activation of the monitoring bases at the decoding center of the ribosome.

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Protein

Chemical

Disease

Primary Citation of related structures
5WDT