ISDA

Entry Detail

PDB ID:

4V68

Keywords:

Title:

T. thermophilus 70S ribosome in complex with mRNA, tRNAs and EF-Tu.GDP.kirromycin ternary complex, fitted to a 6.4 A Cryo-EM map.

Biological Source:

Source Organism:

Thermus thermophilus

PDB Version:

Deposition Date:

2008-12-11

Release Date:

2014-07-09

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

6.40 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Polymer Type:polyribonucleotide
Description:MRNA CODON
Chain IDs:Z (auth: A0)
Chain Length:3
Number of Molecules:1
Biological Source:

Polymer Type:polyribonucleotide
Description:16S rRNA
Chain IDs:A (auth: AA)
Chain Length:1504
Number of Molecules:1
Biological Source:Thermus thermophilus

Protein Blast

Polymer Type:polypeptide(L)
Description:30S ribosomal protein S2
Chain IDs:B (auth: AB)
Chain Length:235
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P80371 Pfam ID:PF00318

Protein Blast

Polymer Type:polypeptide(L)
Description:30S ribosomal protein S3
Chain IDs:N (auth: AC)
Chain Length:207
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P80372 Pfam ID:PF07650, PF00189

Protein Blast

Polymer Type:polypeptide(L)
Description:30S ribosomal protein S4
Chain IDs:C (auth: AD)
Chain Length:208
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P80373 Pfam ID:PF00163, PF01479

Protein Blast

Polymer Type:polypeptide(L)
Description:30S ribosomal protein S5
Chain IDs:D (auth: AE)
Chain Length:151
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SHQ5 Pfam ID:PF00333, PF03719

Protein Blast

Polymer Type:polypeptide(L)
Description:30S ribosomal protein S6
Chain IDs:E (auth: AF)
Chain Length:101
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SLP8 Pfam ID:PF01250

Protein Blast

Polymer Type:polypeptide(L)
Description:30S ribosomal protein S7
Chain IDs:O (auth: AG)
Chain Length:155
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P17291 Pfam ID:PF00177

Polymer Type:polypeptide(L)
Description:30S ribosomal protein S8
Chain IDs:F (auth: AH)
Chain Length:138
Number of Molecules:1
Biological Source:Thermus thermophilus

Protein Blast

Polymer Type:polypeptide(L)
Description:30S ribosomal protein S9
Chain IDs:P (auth: AI)
Chain Length:127
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P62669 Pfam ID:PF00380

Protein Blast

Polymer Type:polypeptide(L)
Description:30S ribosomal protein S10
Chain IDs:Q (auth: AJ)
Chain Length:99
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SHN7 Pfam ID:PF00338

Protein Blast

Polymer Type:polypeptide(L)
Description:30S ribosomal protein S11
Chain IDs:G (auth: AK)
Chain Length:119
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P80376 Pfam ID:PF00411

Protein Blast

Polymer Type:polypeptide(L)
Description:30S ribosomal protein S12
Chain IDs:H (auth: AL)
Chain Length:125
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SHN3 Pfam ID:PF00164

Protein Blast

Polymer Type:polypeptide(L)
Description:30S ribosomal protein S13
Chain IDs:R (auth: AM)
Chain Length:125
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P80377 Pfam ID:PF00416

Polymer Type:polypeptide(L)
Description:30S ribosomal protein S14
Chain IDs:S (auth: AN)
Chain Length:60
Number of Molecules:1
Biological Source:Thermus thermophilus

Protein Blast

Polymer Type:polypeptide(L)
Description:30S ribosomal protein S15
Chain IDs:I (auth: AO)
Chain Length:88
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SJ76 Pfam ID:PF00312

Protein Blast

Polymer Type:polypeptide(L)
Description:30S ribosomal protein S16
Chain IDs:J (auth: AP)
Chain Length:84
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SJH3 Pfam ID:PF00886

Polymer Type:polypeptide(L)
Description:30S ribosomal protein S17
Chain IDs:K (auth: AQ)
Chain Length:100
Number of Molecules:1
Biological Source:Thermus thermophilus

Protein Blast

Polymer Type:polypeptide(L)
Description:30S ribosomal protein S18
Chain IDs:L (auth: AR)
Chain Length:70
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SLQ0 Pfam ID:PF01084

Protein Blast

Polymer Type:polypeptide(L)
Description:30S ribosomal protein S19
Chain IDs:T (auth: AS)
Chain Length:79
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SHP2 Pfam ID:PF00203

Protein Blast

Polymer Type:polypeptide(L)
Description:30S ribosomal protein S20
Chain IDs:M (auth: AT)
Chain Length:99
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P80380 Pfam ID:PF01649

Protein Blast

Polymer Type:polypeptide(L)
Description:30S ribosomal protein Thx
Chain IDs:U (auth: AU)
Chain Length:25
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SIH3 Pfam ID:PF17070

Polymer Type:polyribonucleotide
Description:P-SITE TRNA
Chain IDs:V (auth: AV)
Chain Length:77
Number of Molecules:1
Biological Source:Thermus thermophilus

Polymer Type:polyribonucleotide
Description:E-SITE TRNA
Chain IDs:X (auth: AW)
Chain Length:76
Number of Molecules:1
Biological Source:Thermus thermophilus

Polymer Type:polyribonucleotide
Description:SYNTHETIC MRNA
Chain IDs:W (auth: AX)
Chain Length:6
Number of Molecules:1
Biological Source:

Polymer Type:polyribonucleotide
Description:AT-SITE TRNA
Chain IDs:Y (auth: AY)
Chain Length:72
Number of Molecules:1
Biological Source:Thermus thermophilus

Protein Blast

Polymer Type:polypeptide(L)
Description:Elongation factor Tu-A
Chain IDs:AA (auth: AZ)
Chain Length:405
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P60339 Pfam ID:PF00009, PF03144, PF03143

Protein Blast

Polymer Type:polypeptide(L)
Description:50S ribosomal protein L27
Chain IDs:BA (auth: B0)
Chain Length:85
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P60493 Pfam ID:PF01016

Protein Blast

Polymer Type:polypeptide(L)
Description:50S ribosomal protein L28
Chain IDs:CA (auth: B1)
Chain Length:89
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P60494 Pfam ID:PF00830

Protein Blast

Polymer Type:polypeptide(L)
Description:50S ribosomal protein L29
Chain IDs:DA (auth: B2)
Chain Length:51
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SHP6 Pfam ID:PF00831

Protein Blast

Polymer Type:polypeptide(L)
Description:50S ribosomal protein L30
Chain IDs:EA (auth: B3)
Chain Length:60
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SHQ6 Pfam ID:PF00327

Protein Blast

Polymer Type:polypeptide(L)
Description:50S ribosomal protein L31
Chain IDs:FA (auth: B4)
Chain Length:50
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SJE1 Pfam ID:PF01197

Protein Blast

Polymer Type:polypeptide(L)
Description:50S ribosomal protein L32
Chain IDs:GA (auth: B5)
Chain Length:59
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P80339 Pfam ID:PF01783

Protein Blast

Polymer Type:polypeptide(L)
Description:50S ribosomal protein L33
Chain IDs:HA (auth: B6)
Chain Length:45
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P35871 Pfam ID:PF00471

Protein Blast

Polymer Type:polypeptide(L)
Description:50S ribosomal protein L34
Chain IDs:IA (auth: B7)
Chain Length:49
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P80340 Pfam ID:PF00468

Protein Blast

Polymer Type:polypeptide(L)
Description:50S ribosomal protein L35
Chain IDs:JA (auth: B8)
Chain Length:64
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P80341 Pfam ID:PF01632

Protein Blast

Polymer Type:polypeptide(L)
Description:50S ribosomal protein L36
Chain IDs:KA (auth: B9)
Chain Length:35
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q72I28 Pfam ID:PF00444

Polymer Type:polyribonucleotide
Description:23S rRNA
Chain IDs:LA (auth: BA)
Chain Length:2852
Number of Molecules:1
Biological Source:Thermus thermophilus

Polymer Type:polyribonucleotide
Description:5S rRNA
Chain IDs:MA (auth: BB)
Chain Length:119
Number of Molecules:1
Biological Source:Thermus thermophilus

Protein Blast

Polymer Type:polypeptide(L)
Description:50S ribosomal protein L1
Chain IDs:NA (auth: BC)
Chain Length:191
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SLP7 Pfam ID:PF00687

Protein Blast

Polymer Type:polypeptide(L)
Description:50S ribosomal protein L2
Chain IDs:OA (auth: BD)
Chain Length:272
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P60405 Pfam ID:PF00181, PF03947

Protein Blast

Polymer Type:polypeptide(L)
Description:50S ribosomal protein L3
Chain IDs:PA (auth: BE)
Chain Length:205
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SHN8 Pfam ID:PF00297

Protein Blast

Polymer Type:polypeptide(L)
Description:50S ribosomal protein L4
Chain IDs:QA (auth: BF)
Chain Length:208
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SHN9 Pfam ID:PF00573

Protein Blast

Polymer Type:polypeptide(L)
Description:50S ribosomal protein L5
Chain IDs:RA (auth: BG)
Chain Length:181
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SHQ0 Pfam ID:PF00281, PF00673

Polymer Type:polypeptide(L)
Description:50S ribosomal protein L6
Chain IDs:SA (auth: BH)
Chain Length:160
Number of Molecules:1
Biological Source:Thermus thermophilus

Protein Blast

Polymer Type:polypeptide(L)
Description:50S ribosomal protein L9
Chain IDs:TA (auth: BI)
Chain Length:146
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SLQ1 Pfam ID:PF01281, PF03948

Protein Blast

Polymer Type:polypeptide(L)
Description:50S ribosomal protein L11
Chain IDs:UA (auth: BL)
Chain Length:138
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P36238 Pfam ID:PF03946, PF00298

Protein Blast

Polymer Type:polypeptide(L)
Description:50S ribosomal protein L13
Chain IDs:VA (auth: BN)
Chain Length:139
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P60488 Pfam ID:PF00572

Protein Blast

Polymer Type:polypeptide(L)
Description:50S ribosomal protein L14
Chain IDs:WA (auth: BO)
Chain Length:122
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SHP8 Pfam ID:PF00238

Protein Blast

Polymer Type:polypeptide(L)
Description:50S ribosomal protein L15
Chain IDs:XA (auth: BP)
Chain Length:146
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SHQ7 Pfam ID:PF00828

Protein Blast

Polymer Type:polypeptide(L)
Description:50S ribosomal protein L16
Chain IDs:YA (auth: BQ)
Chain Length:136
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P60489 Pfam ID:PF00252

Protein Blast

Polymer Type:polypeptide(L)
Description:50S ribosomal protein L17
Chain IDs:ZA (auth: BR)
Chain Length:117
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q9Z9H5 Pfam ID:PF01196

Protein Blast

Polymer Type:polypeptide(L)
Description:50S ribosomal protein L18
Chain IDs:AB (auth: BS)
Chain Length:99
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SHQ4 Pfam ID:PF00861

Protein Blast

Polymer Type:polypeptide(L)
Description:50S ribosomal protein L19
Chain IDs:BB (auth: BT)
Chain Length:138
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P60490 Pfam ID:PF01245

Protein Blast

Polymer Type:polypeptide(L)
Description:50S ribosomal protein L20
Chain IDs:CB (auth: BU)
Chain Length:117
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P60491 Pfam ID:PF00453

Protein Blast

Polymer Type:polypeptide(L)
Description:50S ribosomal protein L21
Chain IDs:DB (auth: BV)
Chain Length:101
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P60492 Pfam ID:PF00829

Protein Blast

Polymer Type:polypeptide(L)
Description:50S ribosomal protein L22
Chain IDs:EB (auth: BW)
Chain Length:113
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SHP3 Pfam ID:PF00237

Protein Blast

Polymer Type:polypeptide(L)
Description:50S ribosomal protein L23
Chain IDs:FB (auth: BX)
Chain Length:93
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SHP0 Pfam ID:PF00276

Protein Blast

Polymer Type:polypeptide(L)
Description:50S ribosomal protein L24
Chain IDs:GB (auth: BY)
Chain Length:101
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SHP9 Pfam ID:PF00467, PF17136

Protein Blast

Polymer Type:polypeptide(L)
Description:50S ribosomal protein L25
Chain IDs:HB (auth: BZ)
Chain Length:177
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SHZ1 Pfam ID:PF01386, PF14693

Modified Residue

Compound ID	Chain ID	Parent Comp ID	Details
1MA	Y	A	?
2MG	Y	G	2N-METHYLGUANOSINE-5'-MONOPHOSPHATE
5MC	Y	C	5-METHYLCYTIDINE-5'-MONOPHOSPHATE
5MU	V	U	5-METHYLURIDINE 5'-MONOPHOSPHATE
7MG	Y	G	?
M2G	Y	G	N2-DIMETHYLGUANOSINE-5'-MONOPHOSPHATE
OMC	Y	C	O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE
OMG	Y	G	O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE
PSU	Y	U	PSEUDOURIDINE-5'-MONOPHOSPHATE
YG	Y	G	WYBUTOSINE

Ligand Molecules

BME

GDP

MAU

PHA

Primary Citation

GTPase activation of elongation factor EF-Tu by the ribosome during decoding

Schuette, J.C, Murphy, F.V, Kelley, A.C, Weir, J.R, Giesebrecht, J, Connell, S.R, Loerke, J, Mielke, T, Zhang, W, Penczek, P.A, Ramakrishnan, V, Spahn, C.M.Show

Embo J. 28 755 765 (2009)

PMID: 19229291 DOI: 10.1038/emboj.2009.26

Abstact

We have used single-particle reconstruction in cryo-electron microscopy to determine a structure of the Thermus thermophilus ribosome in which the ternary complex of elongation factor Tu (EF-Tu), tRNA and guanine nucleotide has been trapped on the ribosome using the antibiotic kirromycin. This represents the state in the decoding process just after codon recognition by tRNA and the resulting GTP hydrolysis by EF-Tu, but before the release of EF-Tu from the ribosome. Progress in sample purification and image processing made it possible to reach a resolution of 6.4 A. Secondary structure elements in tRNA, EF-Tu and the ribosome, and even GDP and kirromycin, could all be visualized directly. The structure reveals a complex conformational rearrangement of the tRNA in the A/T state and the interactions with the functionally important switch regions of EF-Tu crucial to GTP hydrolysis. Thus, the structure provides insights into the molecular mechanism of signalling codon recognition from the decoding centre of the 30S subunit to the GTPase centre of EF-Tu.

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Protein

Chemical

Disease

Primary Citation of related structures