4V8N | pdb_00004v8n

The crystal structure of agmatidine tRNA-Ile2 bound to the 70S ribosome in the A and P site.

PDB DOI: https://doi.org/10.2210/pdb4V8N/pdb
Entry: 4V8N supersedes: 3ZN7, 3ZN9, 3ZND, 3ZNE
NAKB: 4V8N

Classification: RIBOSOME
Organism(s): Thermus thermophilus HB8, Haloarcula marismortui, Escherichia coli
Mutation(s): No

Deposited: 2013-02-13 Released: 2014-07-09
Deposition Author(s): Voorhees, R.M., Mandal, D., Neubauer, C., Koehrer, C., RajBhandary, U.L., Ramakrishnan, V.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free:
0.280 (Depositor)
R-Value Work:
0.250 (Depositor)
R-Value Observed:
0.250 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

The Structural Basis for Specific Decoding of Aua by Isoleucine tRNA on the Ribosome

Voorhees, R.M., Mandal, D., Neubauer, C., Koehrer, C., Rajbhandary, U.L., Ramakrishnan, V.

(2013) Nat Struct Mol Biol 20: 641

PubMed: 23542153 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/nsmb.2545
Primary Citation Related Structures:
4V8N

PubMed Abstract:
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.

Organizational Affiliation

Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.

Macromolecule Content

Total Structure Weight: 4,584.46 kDa
Atom Count: 298,096
Modeled Residue Count: 21,532
Deposited Residue Count: 22,572
Unique protein chains: 51
Unique nucleic acid chains: 6

Macromolecules

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S2	B [auth AB], HB [auth CB]	256	Thermus thermophilus HB8	Mutation(s): 0
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UniProt Group	P80371
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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S3	C [auth AC], IB [auth CC]	239	Thermus thermophilus HB8	Mutation(s): 0
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UniProt Group	P80372
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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S4	D [auth AD], JB [auth CD]	209	Thermus thermophilus HB8	Mutation(s): 0
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UniProt Group	P80373
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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S5	E [auth AE], KB [auth CE]	162	Thermus thermophilus HB8	Mutation(s): 0
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UniProt Group	Q5SHQ5
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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S6	F [auth AF], LB [auth CF]	101	Thermus thermophilus HB8	Mutation(s): 0
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UniProt Group	Q5SLP8
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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S7	G [auth AG], MB [auth CG]	156	Thermus thermophilus HB8	Mutation(s): 0
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UniProt Group	P17291
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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S8	H [auth AH], NB [auth CH]	138	Thermus thermophilus HB8	Mutation(s): 0
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UniProt Group	P0DOY9
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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S9	I [auth AI], OB [auth CI]	128	Thermus thermophilus HB8	Mutation(s): 0
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UniProt Group	P80374
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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S10	J [auth AJ], PB [auth CJ]	105	Thermus thermophilus HB8	Mutation(s): 0
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Find proteins for Q5SHN7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHN7 Go to UniProtKB: Q5SHN7
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UniProt Group	Q5SHN7
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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S11	K [auth AK], QB [auth CK]	129	Thermus thermophilus HB8	Mutation(s): 0
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Find proteins for P80376 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80376 Go to UniProtKB: P80376
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UniProt Group	P80376
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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S12	L [auth AL], RB [auth CL]	135	Thermus thermophilus HB8	Mutation(s): 0
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Find proteins for Q5SHN3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHN3 Go to UniProtKB: Q5SHN3
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UniProt Group	Q5SHN3
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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S13	M [auth AM], SB [auth CM]	126	Thermus thermophilus HB8	Mutation(s): 0
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UniProt Group	P80377
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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S14 TYPE Z	N [auth AN], TB [auth CN]	61	Thermus thermophilus HB8	Mutation(s): 0
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Find proteins for P0DOY6 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P0DOY6 Go to UniProtKB: P0DOY6
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UniProt Group	P0DOY6
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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S15	O [auth AO], UB [auth CO]	89	Thermus thermophilus HB8	Mutation(s): 0
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Find proteins for Q5SJ76 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SJ76 Go to UniProtKB: Q5SJ76
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UniProt Group	Q5SJ76
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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S16	P [auth AP], VB [auth CP]	88	Thermus thermophilus HB8	Mutation(s): 0
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UniProt Group	Q5SJH3
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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S17	Q [auth AQ], WB [auth CQ]	105	Thermus thermophilus HB8	Mutation(s): 0
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UniProt Group	P0DOY7
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Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S18	R [auth AR], XB [auth CR]	88	Thermus thermophilus HB8	Mutation(s): 0
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Find proteins for Q5SLQ0 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SLQ0 Go to UniProtKB: Q5SLQ0
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UniProt Group	Q5SLQ0
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Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S19	S [auth AS], YB [auth CS]	93	Thermus thermophilus HB8	Mutation(s): 0
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UniProt Group	Q5SHP2
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Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S20	T [auth AT], ZB [auth CT]	106	Thermus thermophilus HB8	Mutation(s): 0
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UniProt Group	P80380
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Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN THX	AC [auth CU], U [auth AU]	27	Thermus thermophilus HB8	Mutation(s): 0
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UniProt Group	Q5SIH3
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Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L27	FC [auth D0], Z [auth B0]	85	Thermus thermophilus HB8	Mutation(s): 0
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Find proteins for P60493 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P60493 Go to UniProtKB: P60493
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UniProt Group	P60493
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Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L28	AA [auth B1], GC [auth D1]	98	Thermus thermophilus HB8	Mutation(s): 0
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Find proteins for P60494 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P60494 Go to UniProtKB: P60494
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UniProt Group	P60494
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Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L29	BA [auth B2], HC [auth D2]	72	Thermus thermophilus HB8	Mutation(s): 0
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Find proteins for Q5SHP6 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHP6 Go to UniProtKB: Q5SHP6
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UniProt Group	Q5SHP6
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Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L30	CA [auth B3], IC [auth D3]	60	Thermus thermophilus HB8	Mutation(s): 0
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UniProt Group	Q5SHQ6
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Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L31	DA [auth B4], JC [auth D4]	71	Thermus thermophilus HB8	Mutation(s): 0
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Find proteins for Q5SJE1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SJE1 Go to UniProtKB: Q5SJE1
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UniProt Group	Q5SJE1
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Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L32	EA [auth B5], KC [auth D5]	60	Thermus thermophilus HB8	Mutation(s): 0
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Find proteins for P80339 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80339 Go to UniProtKB: P80339
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UniProt Group	P80339
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Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L33	FA [auth B6], LC [auth D6]	54	Thermus thermophilus HB8	Mutation(s): 0
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UniProt Group	P35871
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Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L34	GA [auth B7], MC [auth D7]	49	Thermus thermophilus HB8	Mutation(s): 0
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UniProt Group	P80340
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Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L35	HA [auth B8], NC [auth D8]	65	Thermus thermophilus HB8	Mutation(s): 0
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Find proteins for Q5SKU1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SKU1 Go to UniProtKB: Q5SKU1
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UniProt Group	Q5SKU1
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Entity ID: 34
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L36	IA [auth B9], OC [auth D9]	37	Thermus thermophilus HB8	Mutation(s): 0
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Find proteins for Q5SHR2 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHR2 Go to UniProtKB: Q5SHR2
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UniProt Group	Q5SHR2
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Entity ID: 37
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L1	LA [auth BC], RC [auth DC]	229	Thermus thermophilus HB8	Mutation(s): 0
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Find proteins for Q5SLP7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SLP7 Go to UniProtKB: Q5SLP7
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UniProt Group	Q5SLP7
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Entity ID: 38
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L2	MA [auth BD], SC [auth DD]	276	Thermus thermophilus HB8	Mutation(s): 0
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UniProt Group	P60405
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Entity ID: 39
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L3	NA [auth BE], TC [auth DE]	206	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHN8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHN8 Go to UniProtKB: Q5SHN8
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UniProt Group	Q5SHN8
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Entity ID: 40
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L4	OA [auth BF], UC [auth DF]	210	Thermus thermophilus HB8	Mutation(s): 0
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Find proteins for Q5SHN9 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHN9 Go to UniProtKB: Q5SHN9
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UniProt Group	Q5SHN9
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Entity ID: 41
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L5	PA [auth BG], VC [auth DG]	182	Thermus thermophilus HB8	Mutation(s): 0
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Find proteins for Q5SHQ0 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHQ0 Go to UniProtKB: Q5SHQ0
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UniProt Group	Q5SHQ0
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Entity ID: 42
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L6	QA [auth BH], WC [auth DH]	180	Thermus thermophilus HB8	Mutation(s): 0
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Find proteins for P0DOY8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P0DOY8 Go to UniProtKB: P0DOY8
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UniProt Group	P0DOY8
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Entity ID: 43
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L9	RA [auth BI], XC [auth DI]	148	Thermus thermophilus HB8	Mutation(s): 0
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Find proteins for Q5SLQ1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SLQ1 Go to UniProtKB: Q5SLQ1
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UniProt Group	Q5SLQ1
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Entity ID: 44
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L10	SA [auth BJ], YC [auth DJ]	173	Thermus thermophilus HB8	Mutation(s): 0

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Entity ID: 45
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L13	TA [auth BN], ZC [auth DN]	140	Thermus thermophilus HB8	Mutation(s): 0
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Find proteins for P60488 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P60488 Go to UniProtKB: P60488
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UniProt Group	P60488
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Entity ID: 46
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L14	AD [auth DO], UA [auth BO]	122	Thermus thermophilus HB8	Mutation(s): 0
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Find proteins for Q5SHP8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHP8 Go to UniProtKB: Q5SHP8
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UniProt Group	Q5SHP8
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Entity ID: 47
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L15	BD [auth DP], VA [auth BP]	150	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHQ7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHQ7 Go to UniProtKB: Q5SHQ7
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Entity ID: 48
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L16	CD [auth DQ], WA [auth BQ]	141	Thermus thermophilus HB8	Mutation(s): 0
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Find proteins for P60489 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P60489 Go to UniProtKB: P60489
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UniProt Group	P60489
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Entity ID: 49
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L17	DD [auth DR], XA [auth BR]	118	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q9Z9H5 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q9Z9H5 Go to UniProtKB: Q9Z9H5
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UniProt Group	Q9Z9H5
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Entity ID: 50
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L18	ED [auth DS], YA [auth BS]	112	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHQ4 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHQ4 Go to UniProtKB: Q5SHQ4
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UniProt Group	Q5SHQ4
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Entity ID: 51
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L19	FD [auth DT], ZA [auth BT]	146	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P60490 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P60490 Go to UniProtKB: P60490
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UniProt Group	P60490
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Entity ID: 52
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L20	AB [auth BU], GD [auth DU]	118	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P60491 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P60491 Go to UniProtKB: P60491
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UniProt Group	P60491
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Entity ID: 53
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L21	BB [auth BV], HD [auth DV]	101	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P60492 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P60492 Go to UniProtKB: P60492
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UniProt Group	P60492
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Entity ID: 54
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L22	CB [auth BW], ID [auth DW]	113	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHP3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHP3 Go to UniProtKB: Q5SHP3
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UniProt Group	Q5SHP3
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Entity ID: 55
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L23	DB [auth BX], JD [auth DX]	96	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHP0 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHP0 Go to UniProtKB: Q5SHP0
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UniProt Group	Q5SHP0
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Entity ID: 56
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L24	EB [auth BY], KD [auth DY]	110	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHP9 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHP9 Go to UniProtKB: Q5SHP9
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UniProt Group	Q5SHP9
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Entity ID: 57
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L25	FB [auth BZ], LD [auth DZ]	206	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHZ1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHZ1 Go to UniProtKB: Q5SHZ1
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UniProt Group	Q5SHZ1
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Molecule	Chains	Length	Organism
Entity ID: 1
16S RRNA	A [auth AA], GB [auth CA]	1,522	Thermus thermophilus HB8
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Molecule	Chains	Length	Organism
Entity ID: 22
E-SITE TRNA ILE2 AGMATIDINE OR P-SITE TRNA ILE2 AGMATIDINE	BC [auth CV], EC [auth CY], V [auth AV], Y [auth AY]	78	Haloarcula marismortui
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Molecule	Chains	Length	Organism
Entity ID: 23
A-SITE TRNA ILE2 AGMATIDINE	CC [auth CW], W [auth AW]	78	Haloarcula marismortui
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Molecule	Chains	Length	Organism
Entity ID: 24
MRNA	DC [auth CX], X [auth AX]	24	Escherichia coli
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Molecule	Chains	Length	Organism
Entity ID: 35
23S RIBOSOMAL RNA	JA [auth BA], PC [auth DA]	2,915	Thermus thermophilus HB8
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Molecule	Chains	Length	Organism
Entity ID: 36
5S RIBOSOMAL RNA	KA [auth BB], QC [auth DB]	122	Thermus thermophilus HB8
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Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain PD [auth CN] SDF format, chain OD [auth CD] SDF format, chain ND [auth AN] SDF format, chain MD [auth AD] MOL2 format, chain PD [auth CN] MOL2 format, chain OD [auth CD] MOL2 format, chain ND [auth AN] MOL2 format, chain MD [auth AD] mmCIF format, chain PD [auth CN] mmCIF format, chain OD [auth CD] mmCIF format, chain ND [auth AN] mmCIF format, chain MD [auth AD]	MD [auth AD], ND [auth AN], OD [auth CD], PD [auth CN]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain MD [auth AD] Focus chain ND [auth AN] Focus chain OD [auth CD] Focus chain PD [auth CN] Interactions & Density Focus chain MD [auth AD] Focus chain ND [auth AN] Focus chain OD [auth CD] Focus chain PD [auth CN]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.280 (Depositor)
R-Value Work: 0.250 (Depositor)
R-Value Observed: 0.250 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 211.9	α = 90
b = 450.79	β = 90
c = 625.61	γ = 90

Software Package:

Software Name	Purpose
CNS	model building
CNS	refinement
XDS	data reduction
XDS	data scaling
CNS	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2014-07-09

Deposition Author(s):

This entry supersedes: 3ZN7, 3ZN9, 3ZND, 3ZNE

Revision History (Full details and data files)

Version 1.0: 2014-07-09
Type: Initial release
Version 1.1: 2014-12-10
Changes: Other
Version 1.2: 2019-10-30
Changes: Advisory, Data collection, Derived calculations
Version 1.3: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2024-11-13
Changes: Structure summary

RCSB PDB is hosted by

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Nucleic Acid Knowledgebase

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

4V8N | pdb_00004v8n

The crystal structure of agmatidine tRNA-Ile2 bound to the 70S ribosome in the A and P site.

Literature

The Structural Basis for Specific Decoding of Aua by Isoleucine tRNA on the Ribosome

Biological Assembly 1

Biological Assembly 2

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