ISDA: 4V95

Deposition Date 2012-01-27

Release Date 2014-07-09

Last Version Date 2024-11-06

Entry Detail

PDB ID:

4V95

Keywords:

RIBOSOME

Title:

Crystal structure of YAEJ bound to the 70S ribosome

Biological Source:

Source Organism:

Escherichia coli K-12 (Taxon ID: 83333)
synthetic construct (Taxon ID: 32630)
Thermus thermophilus (Taxon ID: 300852)

Host Organism:

Escherichia coli

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

3.20 Å

R-Value Free:

0.24

R-Value Work:

0.18

R-Value Observed:

0.19

Space Group:

P 21 21 21

Download Validation Report

Macromolecular Entities

Polymer Type:polyribonucleotide
Molecule:16S Ribosomal RNA
Chain IDs:A (auth: AA), DB (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), EB (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), FB (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), GB (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), HB (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), IB (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), JB (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), KB (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), LB (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), MB (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), NB (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), OB (auth: CL)
Chain Length:132
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), PB (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
Chain IDs:N (auth: AN), QB (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), RB (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), SB (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), TB (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), UB (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), VB (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), WB (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), XB (auth: CU)
Chain Length:27
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q5SIH3 Pfam ID:PF17070

Polymer Type:polyribonucleotide
Molecule:P-site fMet-tRNA
Chain IDs:W (auth: AV), YB (auth: CV)
Chain Length:77
Number of Molecules:2
Biological Source:Thermus thermophilus

Polymer Type:polyribonucleotide
Molecule:mRNA
Chain IDs:X (auth: AX), ZB (auth: CX)
Chain Length:16
Number of Molecules:2
Biological Source:synthetic construct

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:YAEJ
Gene (Uniprot):arfB
Chain IDs:V (auth: AY)
Chain Length:140
Number of Molecules:1
Biological Source:Escherichia coli K-12

UniProt ID:P40711 Pfam ID:PF00472

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S Ribosomal Protein L27
Gene (Uniprot):rpmA
Chain IDs:TA (auth: B0), VC (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:UA (auth: B1), WC (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:VA (auth: B2), XC (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:WA (auth: B3), YC (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:XA (auth: B4), ZC (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:YA (auth: B5), AD (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:ZA (auth: B6), BD (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:AB (auth: B7), CD (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:BB (auth: B8), DD (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:CB (auth: B9), ED (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:Y (auth: BA), AC (auth: DA)
Chain Length:2915
Number of Molecules:2
Biological Source:Thermus thermophilus

Polymer Type:polyribonucleotide
Molecule:5S Ribosomal RNA
Chain IDs:Z (auth: BB), BC (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 L2
Gene (Uniprot):rplB
Chain IDs:AA (auth: BD), CC (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:BA (auth: BE), DC (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:CA (auth: BF), EC (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:DA (auth: BG), FC (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:EA (auth: BH), GC (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:FA (auth: BI), HC (auth: DI)
Chain Length:148
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q5SLQ1 Pfam ID:PF01281, PF03948

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S Ribosomal Protein L13
Gene (Uniprot):rplM
Chain IDs:GA (auth: BN), IC (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:HA (auth: BO), JC (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:IA (auth: BP), KC (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:JA (auth: BQ), LC (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:KA (auth: BR), MC (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:LA (auth: BS), NC (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:MA (auth: BT), OC (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:NA (auth: BU), PC (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:OA (auth: BV), QC (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:PA (auth: BW), RC (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:QA (auth: BX), SC (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:RA (auth: BY), TC (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:SA (auth: BZ), UC (auth: DZ)
Chain Length:206
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q5SHZ1 Pfam ID:PF01386, PF14693

Ligand Molecules

Primary Citation

Structural basis for the rescue of stalled ribosomes: structure of YaeJ bound to the ribosome.

Gagnon, M.G, Seetharaman, S.V, Bulkley, D, Steitz, T.A.Show

Science 335 1370 1372 (2012)

PMID: 22422986 DOI: 10.1126/science.1217443

Abstact

In bacteria, the hybrid transfer-messenger RNA (tmRNA) rescues ribosomes stalled on defective messenger RNAs (mRNAs). However, certain gram-negative bacteria have evolved proteins that are capable of rescuing stalled ribosomes in a tmRNA-independent manner. Here, we report a 3.2 angstrom-resolution crystal structure of the rescue factor YaeJ bound to the Thermus thermophilus 70S ribosome in complex with the initiator tRNA(i)(fMet) and a short mRNA. The structure reveals that the C-terminal tail of YaeJ functions as a sensor to discriminate between stalled and actively translating ribosomes by binding in the mRNA entry channel downstream of the A site between the head and shoulder of the 30S subunit. This allows the N-terminal globular domain to sample different conformations, so that its conserved GGQ motif is optimally positioned to catalyze the hydrolysis of peptidyl-tRNA. This structure gives insights into the mechanism of YaeJ function and provides a basis for understanding how it rescues stalled ribosomes.

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Protein

Chemical

Disease

Primary Citation of related structures