ISDA: 4V50

Deposition Date 2006-08-16

Release Date 2014-07-09

Last Version Date 2023-09-20

Entry Detail

PDB ID:

4V50

Keywords:

RIBOSOME

Title:

Crystal Structure of Ribosome with messenger RNA and the Anticodon stem-loop of P-site tRNA.

Biological Source:

Source Organism:

Escherichia coli (Taxon ID: 562)

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

3.22 Å

R-Value Free:

0.32

R-Value Work:

0.28

Space Group:

P 21 21 21

Download Validation Report

Macromolecular Entities

Polymer Type:polyribonucleotide
Molecule:16S ribosomal RNA
Chain IDs:A (auth: AA), CB (auth: CA)
Chain Length:1542
Number of Molecules:2
Biological Source:Escherichia coli

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Gene (Uniprot):rpsB
Chain IDs:D (auth: AB), FB (auth: CB)
Chain Length:240
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P0A7V0 Pfam ID:PF00318

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S3
Gene (Uniprot):rpsC
Chain IDs:E (auth: AC), GB (auth: CC)
Chain Length:232
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P0A7V3 Pfam ID:PF00189, PF07650

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S4
Gene (Uniprot):rpsD
Chain IDs:F (auth: AD), HB (auth: CD)
Chain Length:205
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P0A7V8 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:G (auth: AE), IB (auth: CE)
Chain Length:166
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P0A7W1 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:H (auth: AF), JB (auth: CF)
Chain Length:135
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P02358 Pfam ID:PF01250

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S7
Gene (Uniprot):rpsG
Chain IDs:I (auth: AG), KB (auth: CG)
Chain Length:178
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P02359 Pfam ID:PF00177

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S8
Gene (Uniprot):rpsH
Chain IDs:J (auth: AH), LB (auth: CH)
Chain Length:129
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P0A7W7 Pfam ID:PF00410

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S9
Gene (Uniprot):rpsI
Chain IDs:K (auth: AI), MB (auth: CI)
Chain Length:129
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P0A7X3 Pfam ID:PF00380

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S10
Gene (Uniprot):rpsJ
Chain IDs:L (auth: AJ), NB (auth: CJ)
Chain Length:103
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P0A7R5 Pfam ID:PF00338

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S11
Gene (Uniprot):rpsK
Chain IDs:M (auth: AK), OB (auth: CK)
Chain Length:128
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P0A7R9 Pfam ID:PF00411

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S12
Gene (Uniprot):rpsL
Chain IDs:N (auth: AL), PB (auth: CL)
Chain Length:123
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P0A7S3 Pfam ID:PF00164

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S13
Gene (Uniprot):rpsM
Chain IDs:O (auth: AM), QB (auth: CM)
Chain Length:117
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P0A7S9 Pfam ID:PF00416

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S14
Gene (Uniprot):rpsN
Chain IDs:P (auth: AN), RB (auth: CN)
Chain Length:100
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P0AG59 Pfam ID:PF00253

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S15
Gene (Uniprot):rpsO
Chain IDs:Q (auth: AO), SB (auth: CO)
Chain Length:88
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:Q8X9M2 Pfam ID:PF00312

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S16
Gene (Uniprot):rpsP
Chain IDs:R (auth: AP), TB (auth: CP)
Chain Length:82
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P0A7T3 Pfam ID:PF00886

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S17
Gene (Uniprot):rpsQ
Chain IDs:S (auth: AQ), UB (auth: CQ)
Chain Length:83
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P0AG63 Pfam ID:PF00366

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S18
Gene (Uniprot):rpsR
Chain IDs:T (auth: AR), VB (auth: CR)
Chain Length:74
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P0A7T7 Pfam ID:PF01084

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S19
Gene (Uniprot):rpsS
Chain IDs:U (auth: AS), WB (auth: CS)
Chain Length:91
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P0A7U3 Pfam ID:PF00203

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S20
Gene (Uniprot):rpsT
Chain IDs:V (auth: AT), XB (auth: CT)
Chain Length:86
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P0A7U7 Pfam ID:PF01649

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S21
Gene (Uniprot):rpsU
Chain IDs:W (auth: AU), YB (auth: CU)
Chain Length:70
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P68679 Pfam ID:PF01165

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32
Gene (Uniprot):rpmF
Chain IDs:XA (auth: B0), ZC (auth: D0)
Chain Length:56
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P0A7N4 Pfam ID:PF01783

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L33
Gene (Uniprot):rpmG
Chain IDs:YA (auth: B1), AD (auth: D1)
Chain Length:54
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P0A7N9 Pfam ID:PF00471

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L34
Gene (Uniprot):rpmH
Chain IDs:ZA (auth: B2), BD (auth: D2)
Chain Length:46
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P0A7P5 Pfam ID:PF00468

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L35
Gene (Uniprot):rpmI
Chain IDs:AB (auth: B3), CD (auth: D3)
Chain Length:64
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P0A7Q1 Pfam ID:PF01632

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L36
Gene (Uniprot):rpmJ
Chain IDs:BB (auth: B4), DD (auth: D4)
Chain Length:38
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P0A7Q6 Pfam ID:PF00444

Polymer Type:polyribonucleotide
Molecule:5S ribosomal RNA
Chain IDs:X (auth: BA), ZB (auth: DA)
Chain Length:120
Number of Molecules:2
Biological Source:Escherichia coli

Polymer Type:polyribonucleotide
Molecule:23S ribosomal RNA
Chain IDs:Y (auth: BB), AC (auth: DB)
Chain Length:2904
Number of Molecules:2
Biological Source:Escherichia coli

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Gene (Uniprot):rplB
Chain IDs:Z (auth: BC), BC (auth: DC)
Chain Length:272
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P60422 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:AA (auth: BD), CC (auth: DD)
Chain Length:209
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P60438 Pfam ID:PF00297

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4
Gene (Uniprot):rplD
Chain IDs:BA (auth: BE), DC (auth: DE)
Chain Length:201
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P60723 Pfam ID:PF00573

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5
Gene (Uniprot):rplE
Chain IDs:CA (auth: BF), EC (auth: DF)
Chain Length:178
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P62399 Pfam ID:PF00281, PF00673

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L6
Gene (Uniprot):rplF
Chain IDs:DA (auth: BG), FC (auth: DG)
Chain Length:176
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P0AG55 Pfam ID:PF00347

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L9
Gene (Uniprot):rplI
Chain IDs:EA (auth: BH), GC (auth: DH)
Chain Length:149
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P0A7R1 Pfam ID:PF01281, PF03948

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L11
Gene (Uniprot):rplK
Chain IDs:FA (auth: BI), HC (auth: DI)
Chain Length:141
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P0A7J7 Pfam ID:PF03946, PF00298

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13
Gene (Uniprot):rplM
Chain IDs:GA (auth: BJ), IC (auth: DJ)
Chain Length:142
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P0AA10 Pfam ID:PF00572

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Gene (Uniprot):rplN
Chain IDs:HA (auth: BK), JC (auth: DK)
Chain Length:123
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P0ADY3 Pfam ID:PF00238

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15
Gene (Uniprot):rplO
Chain IDs:IA (auth: BL), KC (auth: DL)
Chain Length:144
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P02413 Pfam ID:PF00828

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16
Gene (Uniprot):rplP
Chain IDs:JA (auth: BM), LC (auth: DM)
Chain Length:136
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P0ADY7 Pfam ID:PF00252

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L17
Gene (Uniprot):rplQ
Chain IDs:KA (auth: BN), MC (auth: DN)
Chain Length:127
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P0AG44 Pfam ID:PF01196

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18
Gene (Uniprot):rplR
Chain IDs:LA (auth: BO), NC (auth: DO)
Chain Length:117
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P0C018 Pfam ID:PF00861

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19
Gene (Uniprot):rplS
Chain IDs:MA (auth: BP), OC (auth: DP)
Chain Length:114
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P0A7K6 Pfam ID:PF01245

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L20
Gene (Uniprot):rplT
Chain IDs:NA (auth: BQ), PC (auth: DQ)
Chain Length:117
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P0A7L3 Pfam ID:PF00453

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L21
Gene (Uniprot):rplU
Chain IDs:OA (auth: BR), QC (auth: DR)
Chain Length:103
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P0AG48 Pfam ID:PF00829

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22
Gene (Uniprot):rplV
Chain IDs:PA (auth: BS), RC (auth: DS)
Chain Length:110
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P61175 Pfam ID:PF00237

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L23
Gene (Uniprot):rplW
Chain IDs:QA (auth: BT), SC (auth: DT)
Chain Length:100
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P0ADZ0 Pfam ID:PF00276

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24
Gene (Uniprot):rplX
Chain IDs:RA (auth: BU), TC (auth: DU)
Chain Length:103
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P60624 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:SA (auth: BV), UC (auth: DV)
Chain Length:94
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P68919 Pfam ID:PF01386

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Gene (Uniprot):rpmA
Chain IDs:TA (auth: BW), VC (auth: DW)
Chain Length:84
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P0A7L8 Pfam ID:PF01016

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L28
Gene (Uniprot):rpmB
Chain IDs:UA (auth: BX), WC (auth: DX)
Chain Length:77
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P0A7M2 Pfam ID:PF00830

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29
Gene (Uniprot):rpmC
Chain IDs:VA (auth: BY), XC (auth: DY)
Chain Length:63
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P0A7M6 Pfam ID:PF00831

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L30
Gene (Uniprot):rpmD
Chain IDs:WA (auth: BZ), YC (auth: DZ)
Chain Length:58
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P0AG51 Pfam ID:PF00327

Ligand Molecules

Primary Citation

Structural basis for mRNA and tRNA positioning on the ribosome.

Berk, V, Zhang, W, Pai, R.D, Cate, J.H.D.Show

Proc.Natl.Acad.Sci.Usa 103 15830 15834 (2006)

PMID: 17038497 DOI: 10.1073/pnas.0607541103

Abstact

Protein synthesis requires the accurate positioning of mRNA and tRNA in the peptidyl-tRNA site of the ribosome. Here we describe x-ray crystal structures of the intact bacterial ribosome from Escherichia coli in a complex with mRNA and the anticodon stem-loop of P-site tRNA. At 3.5-A resolution, these structures reveal rearrangements in the intact ribosome that clamp P-site tRNA and mRNA on the small ribosomal subunit. Binding of the anticodon stem-loop of P-site tRNA to the ribosome is sufficient to lock the head of the small ribosomal subunit in a single conformation, thereby preventing movement of mRNA and tRNA before mRNA decoding.

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Protein

Chemical

Disease

Primary Citation of related structures