4V8N image
Deposition Date 2013-02-13
Release Date 2014-07-09
Last Version Date 2024-11-13
Entry Detail
PDB ID:
4V8N
Keywords:
RIBOSOME
Title:
The crystal structure of agmatidine tRNA-Ile2 bound to the 70S ribosome in the A and P site.
Biological Source:
Source Organism:
ESCHERICHIA COLI (Taxon ID: 562)
THERMUS THERMOPHILUS (Taxon ID: 300852)
HALOARCULA MARISMORTUI (Taxon ID: 2238)
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
3.10 Å
R-Value Free:
0.28
R-Value Work:
0.25
R-Value Observed:
0.25
Space Group:
P 21 21 21
4V8N validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:16S RRNA
Chain IDs:A (auth: AA), GB (auth: CA)
Chain Length:1522
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S2
Gene (Uniprot):rpsB
Chain IDs:B (auth: AB), HB (auth: CB)
Chain Length:256
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
UniProt ID:P80371 Pfam ID:PF00318
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S3
Gene (Uniprot):rpsC
Chain IDs:C (auth: AC), IB (auth: CC)
Chain Length:239
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
UniProt ID:P80372 Pfam ID:PF07650, PF00189
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S4
Gene (Uniprot):rpsD
Chain IDs:D (auth: AD), JB (auth: CD)
Chain Length:209
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
UniProt ID:P80373 Pfam ID:PF00163, PF01479
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S5
Gene (Uniprot):rpsE
Chain IDs:E (auth: AE), KB (auth: CE)
Chain Length:162
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
UniProt ID:Q5SHQ5 Pfam ID:PF00333, PF03719
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S6
Gene (Uniprot):rpsF
Chain IDs:F (auth: AF), LB (auth: CF)
Chain Length:101
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
UniProt ID:Q5SLP8 Pfam ID:PF01250
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S7
Gene (Uniprot):rpsG
Chain IDs:G (auth: AG), MB (auth: CG)
Chain Length:156
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
UniProt ID:P17291 Pfam ID:PF00177
Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S8
Chain IDs:H (auth: AH), NB (auth: CH)
Chain Length:138
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S9
Gene (Uniprot):rpsI
Chain IDs:I (auth: AI), OB (auth: CI)
Chain Length:128
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
UniProt ID:P80374 Pfam ID:PF00380
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S10
Gene (Uniprot):rpsJ
Chain IDs:J (auth: AJ), PB (auth: CJ)
Chain Length:105
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
UniProt ID:Q5SHN7 Pfam ID:PF00338
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S11
Gene (Uniprot):rpsK
Chain IDs:K (auth: AK), QB (auth: CK)
Chain Length:129
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
UniProt ID:P80376 Pfam ID:PF00411
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S12
Gene (Uniprot):rpsL
Chain IDs:L (auth: AL), RB (auth: CL)
Chain Length:135
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
UniProt ID:Q5SHN3 Pfam ID:PF00164
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S13
Gene (Uniprot):rpsM
Chain IDs:M (auth: AM), SB (auth: CM)
Chain Length:126
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
UniProt ID:P80377 Pfam ID:PF00416
Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S14 TYPE Z
Chain IDs:N (auth: AN), TB (auth: CN)
Chain Length:61
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S15
Gene (Uniprot):rpsO
Chain IDs:O (auth: AO), UB (auth: CO)
Chain Length:89
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
UniProt ID:Q5SJ76 Pfam ID:PF00312
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S16
Gene (Uniprot):rpsP
Chain IDs:P (auth: AP), VB (auth: CP)
Chain Length:88
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
UniProt ID:Q5SJH3 Pfam ID:PF00886
Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S17
Chain IDs:Q (auth: AQ), WB (auth: CQ)
Chain Length:105
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S18
Gene (Uniprot):rpsR
Chain IDs:R (auth: AR), XB (auth: CR)
Chain Length:88
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
UniProt ID:Q5SLQ0 Pfam ID:PF01084
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S19
Gene (Uniprot):rpsS
Chain IDs:S (auth: AS), YB (auth: CS)
Chain Length:93
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
UniProt ID:Q5SHP2 Pfam ID:PF00203
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S20
Gene (Uniprot):rpsT
Chain IDs:T (auth: AT), ZB (auth: CT)
Chain Length:106
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
UniProt ID:P80380 Pfam ID:PF01649
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN THX
Gene (Uniprot):rpsU
Chain IDs:U (auth: AU), AC (auth: CU)
Chain Length:27
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
UniProt ID:Q5SIH3 Pfam ID:PF17070
Polymer Type:polyribonucleotide
Molecule:E-SITE TRNA ILE2 AGMATIDINE OR P-SITE TRNA ILE2 AGMATIDINE
Chain IDs:V (auth: AV), Y (auth: AY), BC (auth: CV), EC (auth: CY)
Chain Length:78
Number of Molecules:4
Biological Source:HALOARCULA MARISMORTUI
Polymer Type:polyribonucleotide
Molecule:A-SITE TRNA ILE2 AGMATIDINE
Chain IDs:W (auth: AW), CC (auth: CW)
Chain Length:78
Number of Molecules:2
Biological Source:HALOARCULA MARISMORTUI
Polymer Type:polyribonucleotide
Molecule:MRNA
Chain IDs:X (auth: AX), DC (auth: CX)
Chain Length:24
Number of Molecules:2
Biological Source:ESCHERICHIA COLI
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L27
Gene (Uniprot):rpmA
Chain IDs:Z (auth: B0), FC (auth: D0)
Chain Length:85
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
UniProt ID:P60493 Pfam ID:PF01016
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L28
Gene (Uniprot):rpmB
Chain IDs:AA (auth: B1), GC (auth: D1)
Chain Length:98
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
UniProt ID:P60494 Pfam ID:PF00830
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L29
Gene (Uniprot):rpmC
Chain IDs:BA (auth: B2), HC (auth: D2)
Chain Length:72
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
UniProt ID:Q5SHP6 Pfam ID:PF00831
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L30
Gene (Uniprot):rpmD
Chain IDs:CA (auth: B3), IC (auth: D3)
Chain Length:60
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
UniProt ID:Q5SHQ6 Pfam ID:PF00327
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L31
Gene (Uniprot):rpmE
Chain IDs:DA (auth: B4), JC (auth: D4)
Chain Length:71
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
UniProt ID:Q5SJE1 Pfam ID:PF01197
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L32
Gene (Uniprot):rpmF
Chain IDs:EA (auth: B5), KC (auth: D5)
Chain Length:60
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
UniProt ID:P80339 Pfam ID:PF01783
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L33
Gene (Uniprot):rpmG
Chain IDs:FA (auth: B6), LC (auth: D6)
Chain Length:54
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
UniProt ID:P35871 Pfam ID:PF00471
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L34
Gene (Uniprot):rpmH
Chain IDs:GA (auth: B7), MC (auth: D7)
Chain Length:49
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
UniProt ID:P80340 Pfam ID:PF00468
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L35
Gene (Uniprot):rpmI
Chain IDs:HA (auth: B8), NC (auth: D8)
Chain Length:65
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
UniProt ID:Q5SKU1 Pfam ID:PF01632
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L36
Gene (Uniprot):rpmJ
Chain IDs:IA (auth: B9), OC (auth: D9)
Chain Length:37
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
UniProt ID:Q5SHR2 Pfam ID:PF00444
Polymer Type:polyribonucleotide
Molecule:23S RIBOSOMAL RNA
Chain IDs:JA (auth: BA), PC (auth: DA)
Chain Length:2915
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polyribonucleotide
Molecule:5S RIBOSOMAL RNA
Chain IDs:KA (auth: BB), QC (auth: DB)
Chain Length:122
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L1
Gene (Uniprot):rplA
Chain IDs:LA (auth: BC), RC (auth: DC)
Chain Length:229
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
UniProt ID:Q5SLP7 Pfam ID:PF00687
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L2
Gene (Uniprot):rplB
Chain IDs:MA (auth: BD), SC (auth: DD)
Chain Length:276
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
UniProt ID:P60405 Pfam ID:PF00181, PF03947
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L3
Gene (Uniprot):rplC
Chain IDs:NA (auth: BE), TC (auth: DE)
Chain Length:206
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
UniProt ID:Q5SHN8 Pfam ID:PF00297
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L4
Gene (Uniprot):rplD
Chain IDs:OA (auth: BF), UC (auth: DF)
Chain Length:210
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
UniProt ID:Q5SHN9 Pfam ID:PF00573
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L5
Gene (Uniprot):rplE
Chain IDs:PA (auth: BG), VC (auth: DG)
Chain Length:182
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
UniProt ID:Q5SHQ0 Pfam ID:PF00281, PF00673
Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L6
Chain IDs:QA (auth: BH), WC (auth: DH)
Chain Length:180
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L9
Gene (Uniprot):rplI
Chain IDs:RA (auth: BI), XC (auth: DI)
Chain Length:148
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
UniProt ID:Q5SLQ1 Pfam ID:PF01281, PF03948
Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L10
Chain IDs:SA (auth: BJ), YC (auth: DJ)
Chain Length:173
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L13
Gene (Uniprot):rplM
Chain IDs:TA (auth: BN), ZC (auth: DN)
Chain Length:140
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
UniProt ID:P60488 Pfam ID:PF00572
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L14
Gene (Uniprot):rplN
Chain IDs:UA (auth: BO), AD (auth: DO)
Chain Length:122
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
UniProt ID:Q5SHP8 Pfam ID:PF00238
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L15
Gene (Uniprot):rplO
Chain IDs:VA (auth: BP), BD (auth: DP)
Chain Length:150
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
UniProt ID:Q5SHQ7 Pfam ID:PF00828
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L16
Gene (Uniprot):rplP
Chain IDs:WA (auth: BQ), CD (auth: DQ)
Chain Length:141
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
UniProt ID:P60489 Pfam ID:PF00252
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L17
Gene (Uniprot):rplQ
Chain IDs:XA (auth: BR), DD (auth: DR)
Chain Length:118
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
UniProt ID:Q9Z9H5 Pfam ID:PF01196
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L18
Gene (Uniprot):rplR
Chain IDs:YA (auth: BS), ED (auth: DS)
Chain Length:112
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
UniProt ID:Q5SHQ4 Pfam ID:PF00861
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L19
Gene (Uniprot):rplS
Chain IDs:ZA (auth: BT), FD (auth: DT)
Chain Length:146
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
UniProt ID:P60490 Pfam ID:PF01245
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L20
Gene (Uniprot):rplT
Chain IDs:AB (auth: BU), GD (auth: DU)
Chain Length:118
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
UniProt ID:P60491 Pfam ID:PF00453
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L21
Gene (Uniprot):rplU
Chain IDs:BB (auth: BV), HD (auth: DV)
Chain Length:101
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
UniProt ID:P60492 Pfam ID:PF00829
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L22
Gene (Uniprot):rplV
Chain IDs:CB (auth: BW), ID (auth: DW)
Chain Length:113
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
UniProt ID:Q5SHP3 Pfam ID:PF00237
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L23
Gene (Uniprot):rplW
Chain IDs:DB (auth: BX), JD (auth: DX)
Chain Length:96
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
UniProt ID:Q5SHP0 Pfam ID:PF00276
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L24
Gene (Uniprot):rplX
Chain IDs:EB (auth: BY), KD (auth: DY)
Chain Length:110
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
UniProt ID:Q5SHP9 Pfam ID:PF00467, PF17136
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L25
Gene (Uniprot):rplY
Chain IDs:FB (auth: BZ), LD (auth: DZ)
Chain Length:206
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS
UniProt ID:Q5SHZ1 Pfam ID:PF01386, PF14693
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
AG9 V C AGMATIDINE
Ligand Molecules
ZN
Primary Citation
The Structural Basis for Specific Decoding of Aua by Isoleucine tRNA on the Ribosome
Nat.Struct.Mol.Biol. 20 641 ? (2013)
PMID: 23542153 DOI: 10.1038/NSMB.2545

Abstact

Decoding of the AUA isoleucine codon in bacteria and archaea requires modification of a C in the anticodon wobble position of the isoleucine tRNA. Here, we report the crystal structure of the archaeal tRNA2(Ile), which contains the modification agmatidine in its anticodon, in complex with the AUA codon on the 70S ribosome. The structure illustrates how agmatidine confers codon specificity for AUA over AUG.

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Protein

Chemical

Disease

Primary Citation of related structures
4V8N
3ZN7
3ZN9
3ZND
3ZNE
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