3jcd image
Deposition Date 2015-12-01
Release Date 2016-01-13
Last Version Date 2024-03-20
Entry Detail
PDB ID:
3JCD
Keywords:
RIBOSOME
Title:
Structure of Escherichia coli EF4 in posttranslocational ribosomes (Post EF4)
Biological Source:
Source Organism:
Escherichia coli K-12 (Taxon ID: 83333)
synthetic construct (Taxon ID: 32630)
Host Organism:
Escherichia coli
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.70 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
3jcd validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32
Gene (Uniprot):rpmF
Chain IDs:U (auth: 0)
Chain Length:57
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7N4 Pfam ID:PF01783
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L33
Gene (Uniprot):rpmG
Chain IDs:V (auth: 1)
Chain Length:55
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7N9 Pfam ID:PF00471
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L34
Gene (Uniprot):rpmH
Chain IDs:W (auth: 2)
Chain Length:46
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7P5 Pfam ID:PF00468
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L35
Gene (Uniprot):rpmI
Chain IDs:X (auth: 3)
Chain Length:64
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7Q1 Pfam ID:PF01632
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L36
Gene (Uniprot):rpmJ
Chain IDs:Y (auth: 4)
Chain Length:38
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7Q6 Pfam ID:PF00444
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L1
Gene (Uniprot):rplA
Chain IDs:Z (auth: 5)
Chain Length:234
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7L0 Pfam ID:PF00687
Polymer Type:polyribonucleotide
Molecule:mRNA
Chain IDs:CB (auth: 7)
Chain Length:15
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polyribonucleotide
Molecule:tRNA
Chain IDs:DB (auth: 8), EB (auth: 9)
Chain Length:76
Number of Molecules:2
Biological Source:synthetic construct
Polymer Type:polyribonucleotide
Molecule:23S ribosomal RNA
Chain IDs:AB (auth: A)
Chain Length:1533
Number of Molecules:1
Biological Source:Escherichia coli K-12
Polymer Type:polyribonucleotide
Molecule:5S ribosomal RNA
Chain IDs:BB (auth: B)
Chain Length:241
Number of Molecules:1
Biological Source:Escherichia coli K-12
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Gene (Uniprot):rplB
Chain IDs:AA (auth: C)
Chain Length:233
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P60422 Pfam ID:PF00181, PF03947
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L3
Gene (Uniprot):rplC
Chain IDs:BA (auth: D)
Chain Length:206
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P60438 Pfam ID:PF00297
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4
Gene (Uniprot):rplD
Chain IDs:CA (auth: E)
Chain Length:201
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P60723 Pfam ID:PF00573
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5
Gene (Uniprot):rplE
Chain IDs:DA (auth: F)
Chain Length:135
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P62399 Pfam ID:PF00281, PF00673
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L6
Gene (Uniprot):rplF
Chain IDs:EA (auth: G)
Chain Length:179
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0AG55 Pfam ID:PF00347
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L9
Gene (Uniprot):rplI
Chain IDs:FA (auth: H)
Chain Length:149
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7R1 Pfam ID:PF01281, PF03948
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L11
Gene (Uniprot):rplK
Chain IDs:GA (auth: I)
Chain Length:130
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7J7 Pfam ID:PF03946, PF00298
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13
Gene (Uniprot):rplM
Chain IDs:HA (auth: J)
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0AA10 Pfam ID:PF00572
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Gene (Uniprot):rplN
Chain IDs:IA (auth: K)
Chain Length:129
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0ADY3 Pfam ID:PF00238
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15
Gene (Uniprot):rplO
Chain IDs:JA (auth: L)
Chain Length:144
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P02413 Pfam ID:PF00828
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16
Gene (Uniprot):rplP
Chain IDs:KA (auth: M)
Chain Length:136
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0ADY7 Pfam ID:PF00252
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L17
Gene (Uniprot):rplQ
Chain IDs:LA (auth: N)
Chain Length:101
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0AG44 Pfam ID:PF01196
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18
Gene (Uniprot):rplR
Chain IDs:MA (auth: O)
Chain Length:89
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0C018 Pfam ID:PF00861
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19
Gene (Uniprot):rplS
Chain IDs:NA (auth: P)
Chain Length:82
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7K6 Pfam ID:PF01245
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L20
Gene (Uniprot):rplT
Chain IDs:OA (auth: Q)
Chain Length:118
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7L3 Pfam ID:PF00453
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L21
Gene (Uniprot):rplU
Chain IDs:PA (auth: R)
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0AG48 Pfam ID:PF00829
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22
Gene (Uniprot):rplV
Chain IDs:QA (auth: S)
Chain Length:110
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P61175 Pfam ID:PF00237
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L23
Gene (Uniprot):rplW
Chain IDs:RA (auth: T)
Chain Length:87
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0ADZ0 Pfam ID:PF00276
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24
Gene (Uniprot):rplX
Chain IDs:SA (auth: U)
Chain Length:104
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P60624 Pfam ID:PF00467, PF17136
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L25
Gene (Uniprot):rplY
Chain IDs:TA (auth: V)
Chain Length:94
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P68919 Pfam ID:PF01386
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Gene (Uniprot):rpmA
Chain IDs:UA (auth: W)
Chain Length:85
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7L8 Pfam ID:PF01016
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L28
Gene (Uniprot):rpmB
Chain IDs:VA (auth: X)
Chain Length:599
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7M2 Pfam ID:PF00830
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29
Gene (Uniprot):rpmC
Chain IDs:WA (auth: Y)
Chain Length:63
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7M6 Pfam ID:PF00831
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L30
Gene (Uniprot):rpmD
Chain IDs:XA (auth: Z)
Chain Length:59
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0AG51 Pfam ID:PF00327
Polymer Type:polyribonucleotide
Molecule:16S ribosomal RNA
Chain IDs:ZA (auth: a)
Chain Length:1533
Number of Molecules:1
Biological Source:Escherichia coli K-12
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Gene (Uniprot):rpsB
Chain IDs:A (auth: b)
Chain Length:241
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7V0 Pfam ID:PF00318
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S3
Gene (Uniprot):rpsC
Chain IDs:B (auth: c)
Chain Length:233
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7V3 Pfam ID:PF07650, PF00189
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S4
Gene (Uniprot):rpsD
Chain IDs:C (auth: d)
Chain Length:206
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7V8 Pfam ID:PF00163, PF01479
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S5
Gene (Uniprot):rpsE
Chain IDs:D (auth: e)
Chain Length:201
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7W1 Pfam ID:PF00333, PF03719
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S6
Gene (Uniprot):rpsF
Chain IDs:E (auth: f)
Chain Length:135
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P02358 Pfam ID:PF01250
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S7
Gene (Uniprot):rpsG
Chain IDs:F (auth: g)
Chain Length:179
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P02359 Pfam ID:PF00177
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S8
Gene (Uniprot):rpsH
Chain IDs:G (auth: h)
Chain Length:149
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7W7 Pfam ID:PF00410
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S9
Gene (Uniprot):rpsI
Chain IDs:H (auth: i)
Chain Length:130
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7X3 Pfam ID:PF00380
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S10
Gene (Uniprot):rpsJ
Chain IDs:I (auth: j)
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7R5 Pfam ID:PF00338
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S11
Gene (Uniprot):rpsK
Chain IDs:J (auth: k)
Chain Length:129
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7R9 Pfam ID:PF00411
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S12
Gene (Uniprot):rpsL
Chain IDs:K (auth: l)
Chain Length:144
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7S3 Pfam ID:PF00164
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S13
Gene (Uniprot):rpsM
Chain IDs:L (auth: m)
Chain Length:136
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7S9 Pfam ID:PF00416
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S14
Gene (Uniprot):rpsN
Chain IDs:M (auth: n)
Chain Length:101
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0AG59 Pfam ID:PF00253
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S15
Gene (Uniprot):rpsO
Chain IDs:N (auth: o)
Chain Length:89
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0ADZ4 Pfam ID:PF00312
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S16
Gene (Uniprot):rpsP
Chain IDs:O (auth: p)
Chain Length:82
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7T3 Pfam ID:PF00886
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S17
Gene (Uniprot):rpsQ
Chain IDs:P (auth: q)
Chain Length:118
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0AG63 Pfam ID:PF00366
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S18
Gene (Uniprot):rpsR
Chain IDs:Q (auth: r)
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7T7 Pfam ID:PF01084
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S19
Gene (Uniprot):rpsS
Chain IDs:R (auth: s)
Chain Length:110
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7U3 Pfam ID:PF00203
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S20
Gene (Uniprot):rpsT
Chain IDs:S (auth: t)
Chain Length:87
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7U7 Pfam ID:PF01649
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S21
Gene (Uniprot):rpsU
Chain IDs:T (auth: u)
Chain Length:104
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P68679 Pfam ID:PF01165
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Elongation factor 4
Gene (Uniprot):lepA
Chain IDs:YA (auth: x)
Chain Length:599
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P60785 Pfam ID:PF00009, PF03144, PF00679, PF06421 EC:3.6.5.3
Ligand Molecules
NA
Primary Citation
EF4 disengages the peptidyl-tRNA CCA end and facilitates back-translocation on the 70S ribosome
Nat. Struct. Mol. Biol. 23 125 131 (2016)
PMID: 26809121 DOI: 10.1038/nsmb.3160

Abstact

EF4 catalyzes tRNA back-translocation through an unknown mechanism. We report cryo-EM structures of Escherichia coli EF4 in post- and pretranslocational ribosomes (Post- and Pre-EF4) at 3.7- and 3.2-Å resolution, respectively. In Post-EF4, peptidyl-tRNA occupies the peptidyl (P) site, but the interaction between its CCA end and the P loop is disrupted. In Pre-EF4, the peptidyl-tRNA assumes a unique position near the aminoacyl (A) site, denoted the A site/EF4 bound (A/4) site, with a large displacement at its acceptor arm. Mutagenesis analyses suggest that a specific region in the EF4 C-terminal domain (CTD) interferes with base-pairing between the peptidyl-tRNA 3'-CCA and the P loop, whereas the EF4 CTD enhances peptidyl-tRNA interaction at the A/4 site. Therefore, EF4 induces back-translocation by disengaging the tRNA's CCA end from the peptidyl transferase center of the translating ribosome.

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Protein

Chemical

Disease

Primary Citation of related structures
3JCE