8FZJ image
Deposition Date 2023-01-28
Release Date 2024-07-17
Last Version Date 2025-03-19
Entry Detail
PDB ID:
8FZJ
Keywords:
RIBOSOME
Title:
Cryo-EM structure of an E. coli rotated ribosome bound with RF3-GDPCP and p/E-tRNAPhe (Composite state II-C)
Biological Source:
Source Organism:
Escherichia coli (Taxon ID: 562)
Escherichia phage T4 (Taxon ID: 2681598)
Host Organism:
Escherichia coli HB101
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.00 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
8FZJ validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29
Chain IDs:WA (auth: 1)
Chain Length:63
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
Chain IDs:XA (auth: 2)
Chain Length:59
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0AG51 Pfam ID:PF00327
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L31
Gene (Uniprot):rpmE
Chain IDs:YA (auth: 3)
Chain Length:70
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7M9 Pfam ID:PF01197
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32
Chain IDs:ZA (auth: 4)
Chain Length:57
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
Chain IDs:AB (auth: 5)
Chain Length:55
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
Chain IDs:BB (auth: 6)
Chain Length:46
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:CB (auth: 7)
Chain Length:65
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
Chain IDs:DB (auth: 8)
Chain Length:38
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7Q6 Pfam ID:PF00444
Polymer Type:polyribonucleotide
Molecule:23S Ribosomal RNA
Chain IDs:Y (auth: A)
Chain Length:1542
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:5S Ribosomal RNA
Chain IDs:Z (auth: B)
Chain Length:241
Number of Molecules:1
Biological Source:Escherichia coli
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
UniProt ID:P60422 Pfam ID:PF00181, PF03947
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L3
Chain IDs:BA (auth: D)
Chain Length:206
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
Chain IDs:CA (auth: E)
Chain Length:201
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
Chain IDs:DA (auth: F)
Chain Length:131
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
Chain IDs:EA (auth: G)
Chain Length:156
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0AG55 Pfam ID:PF00347
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L10
Gene (Uniprot):rplJ
Chain IDs:FA (auth: I)
Chain Length:130
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7J3 Pfam ID:PF00466
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L11
Gene (Uniprot):rplK
Chain IDs:GA (auth: J)
Chain Length:142
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
Chain IDs:HA (auth: L)
Chain Length:142
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
Chain IDs:IA (auth: M)
Chain Length:118
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
Chain IDs:JA (auth: N)
Chain Length:144
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
Chain IDs:KA (auth: O)
Chain Length:89
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
Chain IDs:LA (auth: P)
Chain Length:127
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
Chain IDs:MA (auth: Q)
Chain Length:117
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
Chain IDs:NA (auth: R)
Chain Length:115
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
Chain IDs:OA (auth: S)
Chain Length:118
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7L3 Pfam ID:PF00453
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L21
Chain IDs:PA (auth: T)
Chain Length:87
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:QA (auth: U)
Chain Length:110
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
Chain IDs:RA (auth: V)
Chain Length:529
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
Chain IDs:SA (auth: W)
Chain Length:104
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
Chain IDs:TA (auth: X)
Chain Length:94
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:UA (auth: Y)
Chain Length:85
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
Chain IDs:VA (auth: Z)
Chain Length:21
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7M2 Pfam ID:PF00830
Polymer Type:polyribonucleotide
Molecule:16S Ribosomal RNA
Chain IDs:A (auth: a)
Chain Length:1542
Number of Molecules:1
Biological Source:Escherichia coli
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Chain IDs:B (auth: b)
Chain Length:241
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
Chain IDs:C (auth: c)
Chain Length:233
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:D (auth: d)
Chain Length:206
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:E (auth: e)
Chain Length:201
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
Chain IDs:F (auth: f)
Chain Length:131
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:G (auth: g)
Chain Length:156
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
Chain IDs:H (auth: h)
Chain Length:130
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
Chain IDs:I (auth: i)
Chain Length:130
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
Chain IDs:J (auth: j)
Chain Length:142
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
Chain IDs:K (auth: k)
Chain Length:129
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
Chain IDs:L (auth: l)
Chain Length:142
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
Chain IDs:M (auth: m)
Chain Length:118
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
Chain IDs:N (auth: n)
Chain Length:144
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
Chain IDs:O (auth: o)
Chain Length:89
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
Chain IDs:P (auth: p)
Chain Length:127
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
Chain IDs:Q (auth: q)
Chain Length:117
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
Chain IDs:R (auth: r)
Chain Length:115
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
Chain IDs:S (auth: s)
Chain Length:118
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
Chain IDs:T (auth: t)
Chain Length:87
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
Chain IDs:U (auth: u)
Chain Length:110
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P68679 Pfam ID:PF01165
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Peptide chain release factor 3
Chain IDs:X (auth: v)
Chain Length:529
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7I4 Pfam ID:PF00009, PF03144, PF16658
Polymer Type:polyribonucleotide
Molecule:p/E phenylalanyl-tRNA
Chain IDs:V (auth: x)
Chain Length:94
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:F-UAA mRNA
Chain IDs:W (auth: z)
Chain Length:21
Number of Molecules:1
Biological Source:Escherichia phage T4
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
2MG A G modified residue
4D4 KA ARG modified residue
4OC A C modified residue
4SU V U modified residue
5MC A C modified residue
5MU V U modified residue
7MG V G modified residue
D2T L ASP modified residue
G7M A G modified residue
MA6 A A modified residue
MEQ BA GLN modified residue
MIA V A modified residue
PSU A U modified residue
UR3 A U modified residue
Ligand Molecules
GCP
MG
ZN
Primary Citation
The ribosome termination complex remodels release factor RF3 and ejects GDP.
Nat.Struct.Mol.Biol. 31 1909 1920 (2024)
PMID: 39030416 DOI: 10.1038/s41594-024-01360-0

Abstact

Translation termination involves release factors RF1, RF2 and the GTPase RF3 that recycles RF1 and RF2 from the ribosome. RF3 dissociates from the ribosome in the GDP-bound form and must then exchange GDP for GTP. The 70S ribosome termination complex (70S-TC) accelerates GDP exchange in RF3, suggesting that the 70S-TC can function as the guanine nucleotide exchange factor for RF3. Here, we use cryogenic-electron microscopy to elucidate the mechanism of GDP dissociation from RF3 catalyzed by the Escherichia coli 70S-TC. The non-rotated ribosome bound to RF1 remodels RF3 and induces a peptide flip in the phosphate-binding loop, efficiently ejecting GDP. Binding of GTP allows RF3 to dock at the GTPase center, promoting the dissociation of RF1 from the ribosome. The structures recapitulate the functional cycle of RF3 on the ribosome and uncover the mechanism by which the 70S-TC allosterically dismantles the phosphate-binding groove in RF3, a previously overlooked function of the ribosome.

Legend

Protein

Chemical

Disease

Primary Citation of related structures
8FZJ