4V5G image
Entry Detail
PDB ID:
4V5G
Keywords:
Title:
The crystal structure of the 70S ribosome bound to EF-Tu and tRNA
Biological Source:
PDB Version:
Deposition Date:
2009-09-01
Release Date:
2014-07-09
Method Details:
Experimental Method:
Resolution:
3.60 Å
R-Value Free:
0.31
R-Value Work:
0.28
R-Value Observed:
0.28
Space Group:
P 1 21 1
Macromolecular Entities
Polymer Type:polyribonucleotide
Description:16S RIBOSOMAL RNA
Chain IDs:A (auth: AA), HB (auth: CA)
Chain Length:1522
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S2
Chain IDs:B (auth: AB), IB (auth: CB)
Chain Length:256
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S3
Chain IDs:C (auth: AC), JB (auth: CC)
Chain Length:239
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S4
Chain IDs:D (auth: AD), KB (auth: CD)
Chain Length:209
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S5
Chain IDs:E (auth: AE), LB (auth: CE)
Chain Length:162
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S6
Chain IDs:F (auth: AF), MB (auth: CF)
Chain Length:101
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S7
Chain IDs:G (auth: AG), NB (auth: CG)
Chain Length:156
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S8
Chain IDs:H (auth: AH), OB (auth: CH)
Chain Length:138
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S9
Chain IDs:I (auth: AI), PB (auth: CI)
Chain Length:128
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S10
Chain IDs:J (auth: AJ), QB (auth: CJ)
Chain Length:105
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S11
Chain IDs:K (auth: AK), RB (auth: CK)
Chain Length:129
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S12
Chain IDs:L (auth: AL), SB (auth: CL)
Chain Length:135
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S13
Chain IDs:M (auth: AM), TB (auth: CM)
Chain Length:126
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S14 TYPE Z
Chain IDs:N (auth: AN), UB (auth: CN)
Chain Length:61
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S15
Chain IDs:O (auth: AO), VB (auth: CO)
Chain Length:89
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S16
Chain IDs:P (auth: AP), WB (auth: CP)
Chain Length:88
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S17
Chain IDs:Q (auth: AQ), XB (auth: CQ)
Chain Length:105
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S18
Chain IDs:R (auth: AR), YB (auth: CR)
Chain Length:88
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S19
Chain IDs:S (auth: AS), ZB (auth: CS)
Chain Length:93
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S20
Chain IDs:T (auth: AT), AC (auth: CT)
Chain Length:106
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN THX
Chain IDs:U (auth: AU), BC (auth: CU)
Chain Length:27
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polyribonucleotide
Description:E-SITE TRNA PHE OR P-SITE TRNA PHE
Chain IDs:V (auth: AV), W (auth: AW), CC (auth: CV), DC (auth: CW)
Chain Length:76
Number of Molecules:4
Biological Source:ESCHERICHIA COLI
Polymer Type:polyribonucleotide
Description:MRNA
Chain IDs:X (auth: AX), EC (auth: CX)
Chain Length:27
Number of Molecules:2
Biological Source:synthetic construct
Polymer Type:polyribonucleotide
Description:A-SITE TRNA THR
Chain IDs:Y (auth: AY), FC (auth: CY)
Chain Length:77
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:ELONGATION FACTOR TU-A
Chain IDs:Z (auth: AZ), GC (auth: CZ)
Chain Length:406
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L27
Chain IDs:AA (auth: B0), HC (auth: D0)
Chain Length:85
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L28
Chain IDs:BA (auth: B1), IC (auth: D1)
Chain Length:98
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L29
Chain IDs:CA (auth: B2), JC (auth: D2)
Chain Length:72
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L30
Chain IDs:DA (auth: B3), KC (auth: D3)
Chain Length:60
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L31
Chain IDs:EA (auth: B4), LC (auth: D4)
Chain Length:71
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L32
Chain IDs:FA (auth: B5), MC (auth: D5)
Chain Length:60
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L33
Chain IDs:GA (auth: B6), NC (auth: D6)
Chain Length:54
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L34
Chain IDs:HA (auth: B7), OC (auth: D7)
Chain Length:49
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L35
Chain IDs:IA (auth: B8), PC (auth: D8)
Chain Length:65
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L36
Chain IDs:JA (auth: B9), QC (auth: D9)
Chain Length:37
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polyribonucleotide
Description:23S RIBOSOMAL RNA
Chain IDs:KA (auth: BA), RC (auth: DA)
Chain Length:2915
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polyribonucleotide
Description:5S RIBOSOMAL RNA
Chain IDs:LA (auth: BB), SC (auth: DB)
Chain Length:122
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L1
Chain IDs:MA (auth: BC), TC (auth: DC)
Chain Length:229
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L2
Chain IDs:NA (auth: BD), UC (auth: DD)
Chain Length:276
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L3
Chain IDs:OA (auth: BE), VC (auth: DE)
Chain Length:206
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L4
Chain IDs:PA (auth: BF), WC (auth: DF)
Chain Length:210
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L5
Chain IDs:QA (auth: BG), XC (auth: DG)
Chain Length:182
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L6
Chain IDs:RA (auth: BH), YC (auth: DH)
Chain Length:180
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L10
Chain IDs:SA (auth: BJ), ZC (auth: DJ)
Chain Length:173
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L11
Chain IDs:TA (auth: BK), AD (auth: DK)
Chain Length:147
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L13
Chain IDs:UA (auth: BN), BD (auth: DN)
Chain Length:140
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L14
Chain IDs:VA (auth: BO), CD (auth: DO)
Chain Length:122
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L15
Chain IDs:WA (auth: BP), DD (auth: DP)
Chain Length:150
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L16
Chain IDs:XA (auth: BQ), ED (auth: DQ)
Chain Length:141
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L17
Chain IDs:YA (auth: BR), FD (auth: DR)
Chain Length:118
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L18
Chain IDs:ZA (auth: BS), GD (auth: DS)
Chain Length:112
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L19
Chain IDs:AB (auth: BT), HD (auth: DT)
Chain Length:146
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L20
Chain IDs:BB (auth: BU), ID (auth: DU)
Chain Length:118
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L21
Chain IDs:CB (auth: BV), JD (auth: DV)
Chain Length:101
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L22
Chain IDs:DB (auth: BW), KD (auth: DW)
Chain Length:113
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L23
Chain IDs:EB (auth: BX), LD (auth: DX)
Chain Length:96
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L24
Chain IDs:FB (auth: BY), MD (auth: DY)
Chain Length:110
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L25
Chain IDs:GB (auth: BZ), ND (auth: DZ)
Chain Length:206
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
5MU Y U 5-METHYLURIDINE 5'-MONOPHOSPHATE
7MG Y G 7N-METHYL-8-HYDROGUANOSINE-5'-MONOPHOSPHATE
H2U Y U 5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE
PSU Y U PSEUDOURIDINE-5'-MONOPHOSPHATE
YG Y G WYBUTOSINE
Primary Citation
The crystal structure of the ribosome bound to EF-Tu and aminoacyl-tRNA.
Science 326 688 694 (2009)
PMID: 19833920 DOI: 10.1126/science.1179700

Abstact

The ribosome selects a correct transfer RNA (tRNA) for each amino acid added to the polypeptide chain, as directed by messenger RNA. Aminoacyl-tRNA is delivered to the ribosome by elongation factor Tu (EF-Tu), which hydrolyzes guanosine triphosphate (GTP) and releases tRNA in response to codon recognition. The signaling pathway that leads to GTP hydrolysis upon codon recognition is critical to accurate decoding. Here we present the crystal structure of the ribosome complexed with EF-Tu and aminoacyl-tRNA, refined to 3.6 angstrom resolution. The structure reveals details of the tRNA distortion that allows aminoacyl-tRNA to interact simultaneously with the decoding center of the 30S subunit and EF-Tu at the factor binding site. A series of conformational changes in EF-Tu and aminoacyl-tRNA suggests a communication pathway between the decoding center and the guanosine triphosphatase center of EF-Tu.

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