6N1D image
Deposition Date 2018-11-08
Release Date 2019-04-03
Last Version Date 2024-11-13
Entry Detail
PDB ID:
6N1D
Keywords:
Title:
X-ray Crystal complex showing Spontaneous Ribosomal Translocation of mRNA and tRNAs into a Chimeric Hybrid State
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
3.20 Å
R-Value Free:
0.32
R-Value Work:
0.26
R-Value Observed:
0.27
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:16S rRNA
Chain IDs:A (auth: A16S), DB (auth: B16S)
Chain Length:1518
Number of Molecules:2
Biological Source:Thermus thermophilus HB27
Polymer Type:polyribonucleotide
Molecule:23S rRNA
Chain IDs:B (auth: A23S), EB (auth: B23S)
Chain Length:2881
Number of Molecules:2
Biological Source:Thermus thermophilus HB27
Polymer Type:polyribonucleotide
Molecule:5s rRNA
Chain IDs:C (auth: A5S), FB (auth: B5S)
Chain Length:119
Number of Molecules:2
Biological Source:Thermus thermophilus HB27
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L1
Chain IDs:D (auth: AL01), HB (auth: BL01)
Chain Length:228
Number of Molecules:2
Biological Source:Thermus thermophilus
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Gene (Uniprot):rplB
Chain IDs:E (auth: AL02), IB (auth: BL02)
Chain Length:276
Number of Molecules:2
Biological Source:Thermus thermophilus HB27
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L3
Gene (Uniprot):rplC
Chain IDs:F (auth: AL03), JB (auth: BL03)
Chain Length:206
Number of Molecules:2
Biological Source:Thermus thermophilus HB27
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4
Gene (Uniprot):rplD
Chain IDs:G (auth: AL04), KB (auth: BL04)
Chain Length:205
Number of Molecules:2
Biological Source:Thermus thermophilus HB27
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5
Gene (Uniprot):rplE
Chain IDs:H (auth: AL05), LB (auth: BL05)
Chain Length:181
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L6
Gene (Uniprot):rplF
Chain IDs:I (auth: AL06), MB (auth: BL06)
Chain Length:180
Number of Molecules:2
Biological Source:Thermus thermophilus HB27
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L9
Gene (Uniprot):rplI
Chain IDs:J (auth: AL09), NB (auth: BL09)
Chain Length:148
Number of Molecules:2
Biological Source:Thermus thermophilus HB27
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13
Gene (Uniprot):rplM
Chain IDs:K (auth: AL13), OB (auth: BL13)
Chain Length:140
Number of Molecules:2
Biological Source:Thermus thermophilus HB27
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Gene (Uniprot):rplN
Chain IDs:L (auth: AL14), PB (auth: BL14)
Chain Length:122
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15
Gene (Uniprot):rplO
Chain IDs:M (auth: AL15), QB (auth: BL15)
Chain Length:150
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16
Gene (Uniprot):rplP
Chain IDs:N (auth: AL16), RB (auth: BL16)
Chain Length:141
Number of Molecules:2
Biological Source:Thermus thermophilus HB27
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L17
Gene (Uniprot):rplQ
Chain IDs:O (auth: AL17), SB (auth: BL17)
Chain Length:118
Number of Molecules:2
Biological Source:Thermus thermophilus HB27
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18
Gene (Uniprot):rplR
Chain IDs:P (auth: AL18), TB (auth: BL18)
Chain Length:111
Number of Molecules:2
Biological Source:Thermus thermophilus HB27
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19
Gene (Uniprot):rplS
Chain IDs:Q (auth: AL19), UB (auth: BL19)
Chain Length:146
Number of Molecules:2
Biological Source:Thermus thermophilus HB27
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L20
Gene (Uniprot):rplT
Chain IDs:R (auth: AL20), VB (auth: BL20)
Chain Length:118
Number of Molecules:2
Biological Source:Thermus thermophilus HB27
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L21
Gene (Uniprot):rplU
Chain IDs:S (auth: AL21), WB (auth: BL21)
Chain Length:101
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22
Gene (Uniprot):rplV
Chain IDs:T (auth: AL22), XB (auth: BL22)
Chain Length:113
Number of Molecules:2
Biological Source:Thermus thermophilus HB27
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L23
Gene (Uniprot):rplW
Chain IDs:U (auth: AL23), YB (auth: BL23)
Chain Length:96
Number of Molecules:2
Biological Source:Thermus thermophilus HB27
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24
Gene (Uniprot):rplX
Chain IDs:V (auth: AL24), ZB (auth: BL24)
Chain Length:110
Number of Molecules:2
Biological Source:Thermus thermophilus HB27
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L25
Gene (Uniprot):rplY
Chain IDs:W (auth: AL25), AC (auth: BL25)
Chain Length:206
Number of Molecules:2
Biological Source:Thermus thermophilus HB27
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Chain IDs:X (auth: AL27), BC (auth: BL27)
Chain Length:84
Number of Molecules:2
Biological Source:Thermus thermophilus
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L28
Gene (Uniprot):rpmB
Chain IDs:Y (auth: AL28), CC (auth: BL28)
Chain Length:98
Number of Molecules:2
Biological Source:Thermus thermophilus HB27
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29
Gene (Uniprot):rpmC
Chain IDs:Z (auth: AL29), DC (auth: BL29)
Chain Length:72
Number of Molecules:2
Biological Source:Thermus thermophilus HB27
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L30
Gene (Uniprot):rpmD
Chain IDs:AA (auth: AL30), EC (auth: BL30)
Chain Length:60
Number of Molecules:2
Biological Source:Thermus thermophilus HB27
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L31
Gene (Uniprot):rpmE
Chain IDs:BA (auth: AL31), FC (auth: BL31)
Chain Length:71
Number of Molecules:2
Biological Source:Thermus thermophilus HB27
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32
Chain IDs:CA (auth: AL32), GC (auth: BL32)
Chain Length:59
Number of Molecules:2
Biological Source:Thermus thermophilus
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L33
Gene (Uniprot):rpmG
Chain IDs:DA (auth: AL33), HC (auth: BL33)
Chain Length:54
Number of Molecules:2
Biological Source:Thermus thermophilus HB27
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L34
Gene (Uniprot):rpmH
Chain IDs:EA (auth: AL34), IC (auth: BL34)
Chain Length:49
Number of Molecules:2
Biological Source:Thermus thermophilus
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L35
Gene (Uniprot):rpmI
Chain IDs:FA (auth: AL35), JC (auth: BL35)
Chain Length:64
Number of Molecules:2
Biological Source:Thermus thermophilus HB27
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L36
Gene (Uniprot):rpmJ
Chain IDs:GA (auth: AL36), KC (auth: BL36)
Chain Length:37
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
Polymer Type:polyribonucleotide
Molecule:mRNA
Chain IDs:HA (auth: AMRN), LC (auth: BMRN)
Chain Length:17
Number of Molecules:2
Biological Source:synthetic construct
Polymer Type:polyribonucleotide
Molecule:P-tRNA
Chain IDs:IA (auth: APTN), MC (auth: BPTN)
Chain Length:76
Number of Molecules:2
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Gene (Uniprot):rpsB
Chain IDs:JA (auth: AS02), NC (auth: BS02)
Chain Length:255
Number of Molecules:2
Biological Source:Thermus thermophilus HB27
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S3
Gene (Uniprot):rpsC
Chain IDs:KA (auth: AS03), OC (auth: BS03)
Chain Length:238
Number of Molecules:2
Biological Source:Thermus thermophilus HB27
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S4
Gene (Uniprot):rpsD
Chain IDs:LA (auth: AS04), PC (auth: BS04)
Chain Length:208
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S5
Gene (Uniprot):rpsE
Chain IDs:MA (auth: AS05), QC (auth: BS05)
Chain Length:161
Number of Molecules:2
Biological Source:Thermus thermophilus HB27
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S6
Gene (Uniprot):rpsF
Chain IDs:NA (auth: AS06), RC (auth: BS06)
Chain Length:101
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S7
Gene (Uniprot):rpsG
Chain IDs:OA (auth: AS07), SC (auth: BS07)
Chain Length:155
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S8
Gene (Uniprot):rpsH
Chain IDs:PA (auth: AS08), TC (auth: BS08)
Chain Length:138
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S9
Gene (Uniprot):rpsI
Chain IDs:QA (auth: AS09), UC (auth: BS09)
Chain Length:128
Number of Molecules:2
Biological Source:Thermus thermophilus HB27
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S10
Gene (Uniprot):rpsJ
Chain IDs:RA (auth: AS10), VC (auth: BS10)
Chain Length:104
Number of Molecules:2
Biological Source:Thermus thermophilus HB27
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S11
Gene (Uniprot):rpsK
Chain IDs:SA (auth: AS11), WC (auth: BS11)
Chain Length:128
Number of Molecules:2
Biological Source:Thermus thermophilus HB27
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S12
Gene (Uniprot):rpsL
Chain IDs:TA (auth: AS12), XC (auth: BS12)
Chain Length:131
Number of Molecules:2
Biological Source:Thermus thermophilus HB27
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S13
Gene (Uniprot):rpsM
Chain IDs:UA (auth: AS13), YC (auth: BS13)
Chain Length:125
Number of Molecules:2
Biological Source:Thermus thermophilus HB27
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S14 type Z
Gene (Uniprot):rpsZ
Chain IDs:VA (auth: AS14), ZC (auth: BS14)
Chain Length:60
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S15
Gene (Uniprot):rpsO
Chain IDs:WA (auth: AS15), AD (auth: BS15)
Chain Length:88
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S16
Gene (Uniprot):rpsP
Chain IDs:XA (auth: AS16), BD (auth: BS16)
Chain Length:88
Number of Molecules:2
Biological Source:Thermus thermophilus HB27
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S17
Gene (Uniprot):rpsQ
Chain IDs:YA (auth: AS17), CD (auth: BS17)
Chain Length:104
Number of Molecules:2
Biological Source:Thermus thermophilus HB27
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S18
Gene (Uniprot):rpsR
Chain IDs:ZA (auth: AS18), DD (auth: BS18)
Chain Length:87
Number of Molecules:2
Biological Source:Thermus thermophilus HB27
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S19
Gene (Uniprot):rpsS
Chain IDs:AB (auth: AS19), ED (auth: BS19)
Chain Length:92
Number of Molecules:2
Biological Source:Thermus thermophilus HB27
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S20
Gene (Uniprot):rpsT
Chain IDs:BB (auth: AS20), FD (auth: BS20)
Chain Length:105
Number of Molecules:2
Biological Source:Thermus thermophilus HB27
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein Thx
Gene (Uniprot):rpsU
Chain IDs:CB (auth: ATHX), GD (auth: BTHX)
Chain Length:26
Number of Molecules:2
Biological Source:Thermus thermophilus HB27
Polymer Type:polyribonucleotide
Molecule:A tRNA
Chain IDs:GB (auth: BATN)
Chain Length:85
Number of Molecules:1
Biological Source:Escherichia coli
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
5MU GB U modified residue
MIA GB A modified residue
PSU GB U modified residue
QUO GB G modified residue
Primary Citation
Spontaneous ribosomal translocation of mRNA and tRNAs into a chimeric hybrid state.
Proc. Natl. Acad. Sci. U.S.A. 116 7813 7818 (2019)
PMID: 30936299 DOI: 10.1073/pnas.1901310116

Abstact

The elongation factor G (EF-G)-catalyzed translocation of mRNA and tRNA through the ribosome is essential for vacating the ribosomal A site for the next incoming aminoacyl-tRNA, while precisely maintaining the translational reading frame. Here, the 3.2-Å crystal structure of a ribosome translocation intermediate complex containing mRNA and two tRNAs, formed in the absence of EF-G or GTP, provides insight into the respective roles of EF-G and the ribosome in translocation. Unexpectedly, the head domain of the 30S subunit is rotated by 21°, creating a ribosomal conformation closely resembling the two-tRNA chimeric hybrid state that was previously observed only in the presence of bound EF-G. The two tRNAs have moved spontaneously from their A/A and P/P binding states into ap/P and pe/E states, in which their anticodon loops are bound between the 30S body domain and its rotated head domain, while their acceptor ends have moved fully into the 50S P and E sites, respectively. Remarkably, the A-site tRNA translocates fully into the classical P-site position. Although the mRNA also undergoes movement, codon-anticodon interaction is disrupted in the absence of EF-G, resulting in slippage of the translational reading frame. We conclude that, although movement of both tRNAs and mRNA (along with rotation of the 30S head domain) can occur in the absence of EF-G and GTP, EF-G is essential for enforcing coupled movement of the tRNAs and their mRNA codons to maintain the reading frame.

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Primary Citation of related structures