7SSD image
Deposition Date 2021-11-10
Release Date 2022-02-23
Last Version Date 2024-10-23
Entry Detail
PDB ID:
7SSD
Keywords:
RIBOSOME
Title:
Mid translocation intermediate with EF-G bound with GDP (Structure IV)
Biological Source:
Source Organism:
Escherichia coli 113303 (Taxon ID: 1268978)
Escherichia coli K-12 (Taxon ID: 83333)
Host Organism:
Escherichia coli 'BL21-Gold(DE3)pLysS AG'
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.30 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
7SSD validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:23S rRNA
Chain IDs:B (auth: 1)
Chain Length:2903
Number of Molecules:1
Biological Source:Escherichia coli K-12
Polymer Type:polyribonucleotide
Molecule:5S RNA
Chain IDs:C (auth: 2)
Chain Length:120
Number of Molecules:1
Biological Source:Escherichia coli K-12
Polymer Type:polyribonucleotide
Molecule:16S rRNA
Chain IDs:A (auth: 3)
Chain Length:1539
Number of Molecules:1
Biological Source:Escherichia coli K-12
Polymer Type:polyribonucleotide
Molecule:mRNA
Chain IDs:KA (auth: 4)
Chain Length:39
Number of Molecules:1
Biological Source:Escherichia coli K-12
Polymer Type:polyribonucleotide
Molecule:tRNA Pro
Chain IDs:LA (auth: 5)
Chain Length:77
Number of Molecules:1
Biological Source:Escherichia coli K-12
Polymer Type:polyribonucleotide
Molecule:tRNA fMet
Chain IDs:E (auth: 6)
Chain Length:77
Number of Molecules:1
Biological Source:Escherichia coli K-12
Polymer Type:polypeptide(L)
Molecule:Elongation factor G
Chain IDs:D (auth: 8)
Chain Length:697
Number of Molecules:1
Biological Source:Escherichia coli 113303
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L31
Gene (Uniprot):rpmE
Chain IDs:EA (auth: A)
Chain Length:234
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7M9 Pfam ID:PF01197
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32
Gene (Uniprot):rpmF
Chain IDs:FA (auth: B)
Chain Length:56
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:GA (auth: C)
Chain Length:209
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:HA (auth: D)
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:IA (auth: E)
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:JA (auth: F)
Chain Length:176
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7Q6 Pfam ID:PF00444
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Gene (Uniprot):rpsB
Chain IDs:MA (auth: G)
Chain Length:149
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:NA (auth: H)
Chain Length:206
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:OA (auth: I)
Chain Length:142
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:PA (auth: J)
Chain Length:142
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:QA (auth: K)
Chain Length:122
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:RA (auth: L)
Chain Length:151
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:SA (auth: M)
Chain Length:129
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:TA (auth: N)
Chain Length:120
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:UA (auth: O)
Chain Length:98
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:VA (auth: P)
Chain Length:114
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:WA (auth: Q)
Chain Length:117
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:XA (auth: R)
Chain Length:114
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:YA (auth: S)
Chain Length:110
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:ZA (auth: T)
Chain Length:93
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:AB (auth: U)
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:BB (auth: V)
Chain Length:94
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:CB (auth: W)
Chain Length:65
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:DB (auth: X)
Chain Length:79
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:EB (auth: Y)
Chain Length:85
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:FB (auth: Z)
Chain Length:65
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P68679 Pfam ID:PF01165
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L1
Gene (Uniprot):rplA
Chain IDs:L (auth: a)
Chain Length:234
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0A7L0 Pfam ID:PF00687
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Gene (Uniprot):rplB
Chain IDs:F (auth: b)
Chain Length:56
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:G (auth: c)
Chain Length:209
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:H (auth: d)
Chain Length:46
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:I (auth: e)
Chain Length:64
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:J (auth: f)
Chain Length:176
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:K (auth: g)
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:M (auth: i)
Chain Length:142
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:N (auth: j)
Chain Length:142
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:O (auth: k)
Chain Length:122
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:P (auth: l)
Chain Length:151
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:Q (auth: m)
Chain Length:129
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:R (auth: n)
Chain Length:120
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:S (auth: o)
Chain Length:98
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:T (auth: p)
Chain Length:114
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:U (auth: q)
Chain Length:117
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:V (auth: r)
Chain Length:114
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:W (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:X (auth: t)
Chain Length:93
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:Y (auth: u)
Chain Length:82
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:Z (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:AA (auth: w)
Chain Length:65
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:BA (auth: x)
Chain Length:79
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:CA (auth: y)
Chain Length:85
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:DA (auth: z)
Chain Length:65
Number of Molecules:1
Biological Source:Escherichia coli K-12
UniProt ID:P0AG51 Pfam ID:PF00327
Ligand Molecules
GDP
Primary Citation
Time-resolved cryo-EM visualizes ribosomal translocation with EF-G and GTP.
Nat Commun 12 7236 7236 (2021)
PMID: 34903725 DOI: 10.1038/s41467-021-27415-0

Abstact

During translation, a conserved GTPase elongation factor-EF-G in bacteria or eEF2 in eukaryotes-translocates tRNA and mRNA through the ribosome. EF-G has been proposed to act as a flexible motor that propels tRNA and mRNA movement, as a rigid pawl that biases unidirectional translocation resulting from ribosome rearrangements, or by various combinations of motor- and pawl-like mechanisms. Using time-resolved cryo-EM, we visualized GTP-catalyzed translocation without inhibitors, capturing elusive structures of ribosome•EF-G intermediates at near-atomic resolution. Prior to translocation, EF-G binds near peptidyl-tRNA, while the rotated 30S subunit stabilizes the EF-G GTPase center. Reverse 30S rotation releases Pi and translocates peptidyl-tRNA and EF-G by ~20 Å. An additional 4-Å translocation initiates EF-G dissociation from a transient ribosome state with highly swiveled 30S head. The structures visualize how nearly rigid EF-G rectifies inherent and spontaneous ribosomal dynamics into tRNA-mRNA translocation, whereas GTP hydrolysis and Pi release drive EF-G dissociation.

Legend

Protein

Chemical

Disease

Primary Citation of related structures
7SSD