7PJY image
Entry Detail
PDB ID:
7PJY
EMDB ID:
Keywords:
Title:
Structure of the 70S-EF-G-GDP ribosome complex with tRNAs in chimeric state 1 (CHI1-EF-G-GDP)
Biological Source:
PDB Version:
Deposition Date:
2021-08-24
Release Date:
2021-10-20
Method Details:
Experimental Method:
Resolution:
3.10 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L32
Chain IDs:A (auth: 0)
Chain Length:57
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L33
Chain IDs:B (auth: 1)
Chain Length:55
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L34
Chain IDs:C (auth: 2)
Chain Length:46
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L35
Chain IDs:D (auth: 3)
Chain Length:65
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L36
Chain IDs:E (auth: 4)
Chain Length:38
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L10
Chain IDs:F (auth: 5)
Chain Length:165
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L31
Chain IDs:G (auth: 6)
Chain Length:70
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polyribonucleotide
Description:23S ribosomal RNA
Chain IDs:H (auth: A)
Chain Length:2903
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polyribonucleotide
Description:5S ribosomal RNA
Chain IDs:I (auth: B)
Chain Length:240
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L2
Chain IDs:J (auth: C)
Chain Length:273
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L3
Chain IDs:K (auth: D)
Chain Length:209
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L4
Chain IDs:L (auth: E)
Chain Length:167
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L5
Chain IDs:M (auth: F)
Chain Length:179
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L6
Chain IDs:N (auth: G)
Chain Length:179
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L9
Chain IDs:O (auth: H)
Chain Length:149
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L11
Chain IDs:P (auth: I)
Chain Length:142
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L13
Chain IDs:Q (auth: J)
Chain Length:142
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L14
Chain IDs:R (auth: K)
Chain Length:123
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L15
Chain IDs:S (auth: L)
Chain Length:124
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L16
Chain IDs:T (auth: M)
Chain Length:136
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L17
Chain IDs:U (auth: N)
Chain Length:127
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L18
Chain IDs:V (auth: O)
Chain Length:117
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L19
Chain IDs:W (auth: P)
Chain Length:82
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L20
Chain IDs:X (auth: Q)
Chain Length:84
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L21
Chain IDs:Y (auth: R)
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L22
Chain IDs:Z (auth: S)
Chain Length:92
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L23
Chain IDs:AA (auth: T)
Chain Length:100
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L24
Chain IDs:BA (auth: U)
Chain Length:71
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L25
Chain IDs:CA (auth: V)
Chain Length:94
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L27
Chain IDs:DA (auth: W)
Chain Length:85
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L28
Chain IDs:EA (auth: X)
Chain Length:78
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L29
Chain IDs:FA (auth: Y)
Chain Length:63
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L30
Chain IDs:GA (auth: Z)
Chain Length:33
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polyribonucleotide
Description:16S ribosomal RNA
Chain IDs:HA (auth: a)
Chain Length:2903
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S2
Chain IDs:IA (auth: b)
Chain Length:240
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S3
Chain IDs:JA (auth: c)
Chain Length:273
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S4
Chain IDs:KA (auth: d)
Chain Length:209
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S5
Chain IDs:LA (auth: e)
Chain Length:167
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S6, fully modified isoform
Chain IDs:MA (auth: f)
Chain Length:179
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S7
Chain IDs:NA (auth: g)
Chain Length:179
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S8
Chain IDs:OA (auth: h)
Chain Length:149
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S9
Chain IDs:PA (auth: i)
Chain Length:142
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S10
Chain IDs:QA (auth: j)
Chain Length:142
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S11
Chain IDs:RA (auth: k)
Chain Length:123
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S12
Chain IDs:SA (auth: l)
Chain Length:124
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S13
Chain IDs:TA (auth: m)
Chain Length:136
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S14
Chain IDs:UA (auth: n)
Chain Length:127
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S15
Chain IDs:VA (auth: o)
Chain Length:117
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S16
Chain IDs:WA (auth: p)
Chain Length:82
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S17
Chain IDs:XA (auth: q)
Chain Length:84
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S18
Chain IDs:YA (auth: r)
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S19
Chain IDs:ZA (auth: s)
Chain Length:92
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S20
Chain IDs:AB (auth: t)
Chain Length:100
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S21
Chain IDs:BB (auth: u)
Chain Length:71
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polyribonucleotide
Description:P-site tRNA(fMet)
Chain IDs:CB (auth: v)
Chain Length:94
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polyribonucleotide
Description:P-site fMet-Phe-tRNA(Phe)
Chain IDs:DB (auth: w)
Chain Length:85
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:Elongation factor G
Chain IDs:EB (auth: x)
Chain Length:78
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polypeptide(L)
Description:Dipeptide (FME-PHE)
Chain IDs:FB (auth: y)
Chain Length:63
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Polymer Type:polyribonucleotide
Description:mRNA
Chain IDs:GB (auth: z)
Chain Length:33
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
2MG HA G modified residue
4OC HA C modified residue
4SU CB U modified residue
5MC HA C modified residue
5MU CB U modified residue
G7M HA G modified residue
MA6 HA A modified residue
PSU HA U modified residue
U CB U modified residue
UR3 HA U modified residue
Primary Citation
Structural mechanism of GTPase-powered ribosome-tRNA movement.
Nat Commun 12 5933 5933 (2021)
PMID: 34635670 DOI: 10.1038/s41467-021-26133-x

Abstact

GTPases are regulators of cell signaling acting as molecular switches. The translational GTPase EF-G stands out, as it uses GTP hydrolysis to generate force and promote the movement of the ribosome along the mRNA. The key unresolved question is how GTP hydrolysis drives molecular movement. Here, we visualize the GTPase-powered step of ongoing translocation by time-resolved cryo-EM. EF-G in the active GDP-Pi form stabilizes the rotated conformation of ribosomal subunits and induces twisting of the sarcin-ricin loop of the 23 S rRNA. Refolding of the GTPase switch regions upon Pi release initiates a large-scale rigid-body rotation of EF-G pivoting around the sarcin-ricin loop that facilitates back rotation of the ribosomal subunits and forward swiveling of the head domain of the small subunit, ultimately driving tRNA forward movement. The findings demonstrate how a GTPase orchestrates spontaneous thermal fluctuations of a large RNA-protein complex into force-generating molecular movement.

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Primary Citation of related structures