4V5F image
Entry Detail
PDB ID:
4V5F
Keywords:
Title:
The structure of the ribosome with elongation factor G trapped in the post-translocational state
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:
0.26
R-Value Work:
0.22
R-Value Observed:
0.22
Space Group:
P 1 21 1
Macromolecular Entities
Polymer Type:polyribonucleotide
Description:16S ribosomal RNA
Chain IDs:A (auth: AA), KB (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), LB (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), MB (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), NB (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), OB (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), PB (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), QB (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), RB (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), SB (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), TB (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), UB (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), VB (auth: CL)
Chain Length:132
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S13
Chain IDs:M (auth: AM), WB (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), XB (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), YB (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), ZB (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), AC (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), BC (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), CC (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), DC (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), EC (auth: CU)
Chain Length:27
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polyribonucleotide
Description:E-SITE TRNA FMET OR P-SITE TRNA FMET (UNMODIFIED BASES EXCEPT FOR THYMINE 54)
Chain IDs:V (auth: AV), W (auth: AW), FC (auth: CV), GC (auth: CW)
Chain Length:77
Number of Molecules:4
Biological Source:ESCHERICHIA COLI
Polymer Type:polyribonucleotide
Description:MRNA
Chain IDs:X (auth: AX), HC (auth: CX)
Chain Length:25
Number of Molecules:2
Biological Source:synthetic construct
Polymer Type:polypeptide(L)
Description:ELONGATION FACTOR G
Chain IDs:Y (auth: AY), IC (auth: CY)
Chain Length:691
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L27
Chain IDs:Z (auth: B0), JC (auth: D0)
Chain Length:85
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L28
Chain IDs:AA (auth: B1), KC (auth: D1)
Chain Length:98
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L29
Chain IDs:BA (auth: B2), LC (auth: D2)
Chain Length:72
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L30
Chain IDs:CA (auth: B3), MC (auth: D3)
Chain Length:60
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L31
Chain IDs:DA (auth: B4), NC (auth: D4)
Chain Length:71
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L32
Chain IDs:EA (auth: B5), OC (auth: D5)
Chain Length:60
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L33
Chain IDs:FA (auth: B6), PC (auth: D6)
Chain Length:54
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L34
Chain IDs:GA (auth: B7), QC (auth: D7)
Chain Length:49
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L35
Chain IDs:HA (auth: B8), RC (auth: D8)
Chain Length:65
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L36
Chain IDs:IA (auth: B9), SC (auth: D9)
Chain Length:37
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polyribonucleotide
Description:23S RIBOSOMAL RNA
Chain IDs:JA (auth: BA), TC (auth: DA)
Chain Length:2915
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polyribonucleotide
Description:5S RIBOSOMAL RNA
Chain IDs:KA (auth: BB), UC (auth: DB)
Chain Length:122
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L1
Chain IDs:LA (auth: BC), VC (auth: DC)
Chain Length:229
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L2
Chain IDs:MA (auth: BD), WC (auth: DD)
Chain Length:276
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L3
Chain IDs:NA (auth: BE), XC (auth: DE)
Chain Length:206
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L4
Chain IDs:OA (auth: BF), YC (auth: DF)
Chain Length:210
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L5
Chain IDs:PA (auth: BG), ZC (auth: DG)
Chain Length:182
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L6
Chain IDs:QA (auth: BH), AD (auth: DH)
Chain Length:180
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L10
Chain IDs:RA (auth: BJ), BD (auth: DJ)
Chain Length:173
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L11
Chain IDs:SA (auth: BK), CD (auth: DK)
Chain Length:147
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L12
Chain IDs:TA (auth: BL), UA (auth: BM), IB (auth: Bl), JB (auth: Bm), DD (auth: DL), ED (auth: DM), SD (auth: Dl), TD (auth: Dm)
Chain Length:125
Number of Molecules:8
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L13
Chain IDs:VA (auth: BN), FD (auth: DN)
Chain Length:140
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L14
Chain IDs:WA (auth: BO), GD (auth: DO)
Chain Length:122
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L15
Chain IDs:XA (auth: BP), HD (auth: DP)
Chain Length:150
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L16
Chain IDs:YA (auth: BQ), ID (auth: DQ)
Chain Length:141
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L17
Chain IDs:ZA (auth: BR), JD (auth: DR)
Chain Length:118
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L18
Chain IDs:AB (auth: BS), KD (auth: DS)
Chain Length:112
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L19
Chain IDs:BB (auth: BT), LD (auth: DT)
Chain Length:146
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L20
Chain IDs:CB (auth: BU), MD (auth: DU)
Chain Length:118
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L21
Chain IDs:DB (auth: BV), ND (auth: DV)
Chain Length:101
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L22
Chain IDs:EB (auth: BW), OD (auth: DW)
Chain Length:113
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L23
Chain IDs:FB (auth: BX), PD (auth: DX)
Chain Length:96
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L24
Chain IDs:GB (auth: BY), QD (auth: DY)
Chain Length:110
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L25
Chain IDs:HB (auth: BZ), RD (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 V U 5-METHYLURIDINE 5'-MONOPHOSPHATE
Primary Citation
The structure of the ribosome with elongation factor G trapped in the posttranslocational state.
Science 326 694 699 (2009)
PMID: 19833919 DOI: 10.1126/science.1179709

Abstact

Elongation factor G (EF-G) is a guanosine triphosphatase (GTPase) that plays a crucial role in the translocation of transfer RNAs (tRNAs) and messenger RNA (mRNA) during translation by the ribosome. We report a crystal structure refined to 3.6 angstrom resolution of the ribosome trapped with EF-G in the posttranslocational state using the antibiotic fusidic acid. Fusidic acid traps EF-G in a conformation intermediate between the guanosine triphosphate and guanosine diphosphate forms. The interaction of EF-G with ribosomal elements implicated in stimulating catalysis, such as the L10-L12 stalk and the L11 region, and of domain IV of EF-G with the tRNA at the peptidyl-tRNA binding site (P site) and with mRNA shed light on the role of these elements in EF-G function. The stabilization of the mobile stalks of the ribosome also results in a more complete description of its structure.

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