ISDA

Deposition Date 2016-07-05

Release Date 2016-09-28

Last Version Date 2024-10-23

Entry Detail

PDB ID:

5KPX

Keywords:

RIBOSOME

Title:

Structure of RelA bound to ribosome in presence of A/R tRNA (Structure IV)

Biological Source:

Source Organism:

Escherichia coli (strain K12) (Taxon ID: 83333)

Host Organism:

Escherichia coli BL21

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

3.90 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32
Gene (Uniprot):rpmF
Chain IDs:AA (auth: 1)
Chain Length:57
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7N4 Pfam ID:PF01783

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S6
Gene (Uniprot):rpsF
Chain IDs:JA (auth: 10)
Chain Length:135
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P02358 Pfam ID:PF01250

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S7
Gene (Uniprot):rpsG
Chain IDs:KA (auth: 11)
Chain Length:179
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P02359 Pfam ID:PF00177

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S8
Gene (Uniprot):rpsH
Chain IDs:LA (auth: 12)
Chain Length:130
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7W7 Pfam ID:PF00410

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S9
Gene (Uniprot):rpsI
Chain IDs:MA (auth: 13)
Chain Length:130
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7X3 Pfam ID:PF00380

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S10
Gene (Uniprot):rpsJ
Chain IDs:NA (auth: 14)
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7R5 Pfam ID:PF00338

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S11
Gene (Uniprot):rpsK
Chain IDs:OA (auth: 15)
Chain Length:129
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7R9 Pfam ID:PF00411

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S12
Gene (Uniprot):rpsL
Chain IDs:PA (auth: 16)
Chain Length:124
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7S3 Pfam ID:PF00164

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S13
Gene (Uniprot):rpsM
Chain IDs:QA (auth: 17)
Chain Length:118
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7S9 Pfam ID:PF00416

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S14
Gene (Uniprot):rpsN
Chain IDs:RA (auth: 18)
Chain Length:101
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0AG59 Pfam ID:PF00253

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S15
Gene (Uniprot):rpsO
Chain IDs:SA (auth: 19)
Chain Length:89
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0ADZ4 Pfam ID:PF00312

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L33
Gene (Uniprot):rpmG
Chain IDs:BA (auth: 2)
Chain Length:55
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7N9 Pfam ID:PF00471

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S16
Gene (Uniprot):rpsP
Chain IDs:TA (auth: 20)
Chain Length:82
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7T3 Pfam ID:PF00886

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S17
Gene (Uniprot):rpsQ
Chain IDs:UA (auth: 21)
Chain Length:84
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0AG63 Pfam ID:PF00366

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S18
Gene (Uniprot):rpsR
Chain IDs:VA (auth: 22)
Chain Length:75
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7T7 Pfam ID:PF01084

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S19
Gene (Uniprot):rpsS
Chain IDs:WA (auth: 23)
Chain Length:92
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7U3 Pfam ID:PF00203

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S20
Gene (Uniprot):rpsT
Chain IDs:XA (auth: 24)
Chain Length:87
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7U7 Pfam ID:PF01649

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S21
Gene (Uniprot):rpsU
Chain IDs:YA (auth: 25)
Chain Length:71
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P68679 Pfam ID:PF01165

Polymer Type:polyribonucleotide
Molecule:16S ribosomal RNA
Chain IDs:ZA (auth: 26)
Chain Length:1539
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

Polymer Type:polyribonucleotide
Molecule:23S ribosomal RNA
Chain IDs:AB (auth: 27)
Chain Length:2903
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

Polymer Type:polyribonucleotide
Molecule:5S ribosomal RNA
Chain IDs:BB (auth: 28)
Chain Length:120
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

Polymer Type:polyribonucleotide
Molecule:mRNA
Chain IDs:CB (auth: 29)
Chain Length:20
Number of Molecules:1
Biological Source:Escherichia coli K-12

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L34
Gene (Uniprot):rpmH
Chain IDs:CA (auth: 3)
Chain Length:46
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7P5 Pfam ID:PF00468

Polymer Type:polyribonucleotide
Molecule:A-site tRNAPhe
Chain IDs:DB (auth: 30)
Chain Length:76
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

Polymer Type:polyribonucleotide
Molecule:P-site tRNAfMet
Chain IDs:EB (auth: 31)
Chain Length:77
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

Polymer Type:polyribonucleotide
Molecule:E-site tRNAfMet
Chain IDs:FB (auth: 32)
Chain Length:77
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

Protein Blast

Polymer Type:polypeptide(L)
Molecule:GTP pyrophosphokinase
Gene (Uniprot):relA
Chain IDs:GB (auth: 33)
Chain Length:750
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0AG20 Pfam ID:PF13328, PF04607, PF02824, PF19296, PF13291 EC:2.7.6.5

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L35
Gene (Uniprot):rpmI
Chain IDs:DA (auth: 4)
Chain Length:65
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7Q1 Pfam ID:PF01632

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L36
Gene (Uniprot):rpmJ
Chain IDs:EA (auth: 5)
Chain Length:38
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7Q6 Pfam ID:PF00444

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Gene (Uniprot):rpsB
Chain IDs:FA (auth: 6)
Chain Length:241
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7V0 Pfam ID:PF00318

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S3
Gene (Uniprot):rpsC
Chain IDs:GA (auth: 7)
Chain Length:233
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7V3 Pfam ID:PF07650, PF00189

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S4
Gene (Uniprot):rpsD
Chain IDs:HA (auth: 8)
Chain Length:206
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7V8 Pfam ID:PF00163, PF01479

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S5
Gene (Uniprot):rpsE
Chain IDs:IA (auth: 9)
Chain Length:167
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7W1 Pfam ID:PF00333, PF03719

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Gene (Uniprot):rplB
Chain IDs:A
Chain Length:273
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P60422 Pfam ID:PF00181, PF03947

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L3
Gene (Uniprot):rplC
Chain IDs:B
Chain Length:209
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P60438 Pfam ID:PF00297

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4
Gene (Uniprot):rplD
Chain IDs:C
Chain Length:201
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P60723 Pfam ID:PF00573

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5
Gene (Uniprot):rplE
Chain IDs:D
Chain Length:179
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P62399 Pfam ID:PF00281, PF00673

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L6
Gene (Uniprot):rplF
Chain IDs:E
Chain Length:177
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0AG55 Pfam ID:PF00347

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L9
Gene (Uniprot):rplI
Chain IDs:F
Chain Length:149
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7R1 Pfam ID:PF01281, PF03948

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L10
Gene (Uniprot):rplJ
Chain IDs:G
Chain Length:165
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7J3 Pfam ID:PF00466

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L11
Gene (Uniprot):rplK
Chain IDs:H
Chain Length:142
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7J7 Pfam ID:PF03946, PF00298

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13
Gene (Uniprot):rplM
Chain IDs:I
Chain Length:142
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0AA10 Pfam ID:PF00572

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Gene (Uniprot):rplN
Chain IDs:J
Chain Length:123
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0ADY3 Pfam ID:PF00238

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15
Gene (Uniprot):rplO
Chain IDs:K
Chain Length:144
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P02413 Pfam ID:PF00828

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16
Gene (Uniprot):rplP
Chain IDs:L
Chain Length:136
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0ADY7 Pfam ID:PF00252

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L17
Gene (Uniprot):rplQ
Chain IDs:M
Chain Length:127
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0AG44 Pfam ID:PF01196

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18
Gene (Uniprot):rplR
Chain IDs:N
Chain Length:117
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0C018 Pfam ID:PF00861

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19
Gene (Uniprot):rplS
Chain IDs:O
Chain Length:115
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7K6 Pfam ID:PF01245

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L20
Gene (Uniprot):rplT
Chain IDs:P
Chain Length:118
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7L3 Pfam ID:PF00453

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L21
Gene (Uniprot):rplU
Chain IDs:Q
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0AG48 Pfam ID:PF00829

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22
Gene (Uniprot):rplV
Chain IDs:R
Chain Length:110
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P61175 Pfam ID:PF00237

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L23
Gene (Uniprot):rplW
Chain IDs:S
Chain Length:100
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0ADZ0 Pfam ID:PF00276

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24
Gene (Uniprot):rplX
Chain IDs:T
Chain Length:104
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P60624 Pfam ID:PF00467, PF17136

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L25
Gene (Uniprot):rplY
Chain IDs:U
Chain Length:94
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P68919 Pfam ID:PF01386

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Gene (Uniprot):rpmA
Chain IDs:V
Chain Length:85
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7L8 Pfam ID:PF01016

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L28
Gene (Uniprot):rpmB
Chain IDs:W
Chain Length:78
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7M2 Pfam ID:PF00830

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29
Gene (Uniprot):rpmC
Chain IDs:X
Chain Length:63
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7M6 Pfam ID:PF00831

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L30
Gene (Uniprot):rpmD
Chain IDs:Y
Chain Length:59
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0AG51 Pfam ID:PF00327

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L31
Gene (Uniprot):rpmE
Chain IDs:Z
Chain Length:70
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7M9 Pfam ID:PF01197

Ligand Molecules

Primary Citation

Ribosome•RelA structures reveal the mechanism of stringent response activation.

Loveland, A.B, Bah, E, Madireddy, R, Zhang, Y, Brilot, A.F, Grigorieff, N, Korostelev, A.A.Show

Elife 5 ? ? (2016)

PMID: 27434674 DOI: 10.7554/eLife.17029

Abstact

Stringent response is a conserved bacterial stress response underlying virulence and antibiotic resistance. RelA/SpoT-homolog proteins synthesize transcriptional modulators (p)ppGpp, allowing bacteria to adapt to stress. RelA is activated during amino-acid starvation, when cognate deacyl-tRNA binds to the ribosomal A (aminoacyl-tRNA) site. We report four cryo-EM structures of E. coli RelA bound to the 70S ribosome, in the absence and presence of deacyl-tRNA accommodating in the 30S A site. The boomerang-shaped RelA with a wingspan of more than 100 Å wraps around the A/R (30S A-site/RelA-bound) tRNA. The CCA end of the A/R tRNA pins the central TGS domain against the 30S subunit, presenting the (p)ppGpp-synthetase domain near the 30S spur. The ribosome and A/R tRNA are captured in three conformations, revealing hitherto elusive states of tRNA engagement with the ribosomal decoding center. Decoding-center rearrangements are coupled with the step-wise 30S-subunit 'closure', providing insights into the dynamics of high-fidelity tRNA decoding.

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Protein

Chemical

Disease

Primary Citation of related structures