ISDA

Deposition Date 2021-04-08

Release Date 2022-02-02

Last Version Date 2024-10-23

Entry Detail

PDB ID:

7O5B

Keywords:

RIBOSOME

Title:

Cryo-EM structure of a Bacillus subtilis MifM-stalled ribosome-nascent chain complex with (p)ppGpp-SRP bound

Biological Source:

Source Organism:

Bacillus subtilis subsp. subtilis str. 168 (Taxon ID: 224308)

Host Organism:

Escherichia coli

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

3.33 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:EA (auth: 0)
Chain Length:59
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168

UniProt ID:O34687 Pfam ID:PF01783

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L33 1
Gene (Uniprot):rpmGA
Chain IDs:FA (auth: 1)
Chain Length:49
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168

UniProt ID:P56849 Pfam ID:PF00471

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L34
Gene (Uniprot):rpmH
Chain IDs:GA (auth: 2)
Chain Length:44
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168

UniProt ID:P05647 Pfam ID:PF00468

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L35
Gene (Uniprot):rpmI
Chain IDs:HA (auth: 3)
Chain Length:66
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168

UniProt ID:P55874 Pfam ID:PF01632

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L36
Gene (Uniprot):rpmJ
Chain IDs:IA (auth: 4)
Chain Length:37
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168

UniProt ID:P20278 Pfam ID:PF00444

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L31
Gene (Uniprot):rpmE
Chain IDs:JA (auth: 6)
Chain Length:66
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168

UniProt ID:Q03223 Pfam ID:PF01197

Polymer Type:polyribonucleotide
Molecule:16S rRNA (1533-MER)
Chain IDs:KA (auth: A)
Chain Length:1533
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Gene (Uniprot):rpsB
Chain IDs:LA (auth: B)
Chain Length:246
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168

UniProt ID:P21464 Pfam ID:PF00318

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S3
Gene (Uniprot):rpsC
Chain IDs:MA (auth: C)
Chain Length:179
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168

UniProt ID:P21465 Pfam ID:PF07650, PF00189

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S4
Gene (Uniprot):rpsD
Chain IDs:NA (auth: D)
Chain Length:200
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168

UniProt ID:P21466 Pfam ID:PF00163, PF01479

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S5
Gene (Uniprot):rpsE
Chain IDs:OA (auth: E)
Chain Length:166
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168

UniProt ID:P21467 Pfam ID:PF00333, PF03719

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S6
Gene (Uniprot):rpsF
Chain IDs:PA (auth: F)
Chain Length:122
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168

UniProt ID:P21468 Pfam ID:PF01250

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S7
Gene (Uniprot):rpsG
Chain IDs:QA (auth: G)
Chain Length:447
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168

UniProt ID:P21469 Pfam ID:PF00177

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S8
Gene (Uniprot):rpsH
Chain IDs:RA (auth: H)
Chain Length:96
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168

UniProt ID:P12879 Pfam ID:PF00410

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S9
Gene (Uniprot):rpsI
Chain IDs:SA (auth: I)
Chain Length:130
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168

UniProt ID:P21470 Pfam ID:PF00380

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S10
Gene (Uniprot):rpsJ
Chain IDs:TA (auth: J)
Chain Length:144
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168

UniProt ID:P21471 Pfam ID:PF00338

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S11
Gene (Uniprot):rpsK
Chain IDs:UA (auth: K)
Chain Length:131
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168

UniProt ID:P04969 Pfam ID:PF00411

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S12
Gene (Uniprot):rpsL
Chain IDs:VA (auth: L)
Chain Length:120
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168

UniProt ID:P21472 Pfam ID:PF00164

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S13
Gene (Uniprot):rpsM
Chain IDs:WA (auth: M)
Chain Length:115
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168

UniProt ID:P20282 Pfam ID:PF00416

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S14
Gene (Uniprot):rpsN1
Chain IDs:XA (auth: N)
Chain Length:61
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168

UniProt ID:P12878 Pfam ID:PF00253

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S15
Gene (Uniprot):rpsO
Chain IDs:YA (auth: O)
Chain Length:102
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168

UniProt ID:P21473 Pfam ID:PF00312

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S16
Gene (Uniprot):rpsP
Chain IDs:ZA (auth: P)
Chain Length:166
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168

UniProt ID:P21474 Pfam ID:PF00886

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S17
Gene (Uniprot):rpsQ
Chain IDs:AB (auth: Q)
Chain Length:141
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168

UniProt ID:P12874 Pfam ID:PF00366

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S18
Gene (Uniprot):rpsR
Chain IDs:BB (auth: R)
Chain Length:113
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168

UniProt ID:P21475 Pfam ID:PF01084

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S19
Gene (Uniprot):rpsS
Chain IDs:CB (auth: S)
Chain Length:92
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168

UniProt ID:P21476 Pfam ID:PF00203

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S20
Gene (Uniprot):rpsT
Chain IDs:DB (auth: T)
Chain Length:103
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168

UniProt ID:P21477 Pfam ID:PF01649

Polymer Type:polyribonucleotide
Molecule:tRNA
Chain IDs:A (auth: U)
Chain Length:94
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168

Polymer Type:polyribonucleotide
Molecule:mRNA
Chain IDs:B (auth: V)
Chain Length:62
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168

Polymer Type:polyribonucleotide
Molecule:SRP RNA (266-MER)
Chain IDs:C (auth: W)
Chain Length:266
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168

Polymer Type:polyribonucleotide
Molecule:23S rRNA (2887-MER)
Chain IDs:H (auth: X)
Chain Length:59
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168

Polymer Type:polyribonucleotide
Molecule:5S rRNA (112-MER)
Chain IDs:I (auth: Y)
Chain Length:112
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Gene (Uniprot):rplB
Chain IDs:J (auth: Z)
Chain Length:277
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168

UniProt ID:P42919 Pfam ID:PF00181, PF03947

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L3
Gene (Uniprot):rplC
Chain IDs:K (auth: a)
Chain Length:1533
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168

UniProt ID:P42920 Pfam ID:PF00297

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4
Gene (Uniprot):rplD
Chain IDs:L (auth: b)
Chain Length:246
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168

UniProt ID:P42921 Pfam ID:PF00573

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5
Gene (Uniprot):rplE
Chain IDs:M (auth: c)
Chain Length:179
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168

UniProt ID:P12877 Pfam ID:PF00281, PF00673

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L6
Gene (Uniprot):rplF
Chain IDs:N (auth: d)
Chain Length:200
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168

UniProt ID:P46898 Pfam ID:PF00347

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13
Gene (Uniprot):rplM
Chain IDs:O (auth: e)
Chain Length:166
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168

UniProt ID:P70974 Pfam ID:PF00572

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Gene (Uniprot):rplN
Chain IDs:P (auth: f)
Chain Length:122
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168

UniProt ID:P12875 Pfam ID:PF00238

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Signal recognition particle protein
Gene (Uniprot):ffh
Chain IDs:D (auth: g)
Chain Length:447
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168

UniProt ID:P37105 Pfam ID:PF02881, PF00448, PF02978

Polymer Type:polypeptide(L)
Molecule:MifM-stalling construct
Chain IDs:E (auth: h)
Chain Length:96
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15
Gene (Uniprot):rplO
Chain IDs:Q (auth: i)
Chain Length:130
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168

UniProt ID:P19946 Pfam ID:PF00828

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16
Gene (Uniprot):rplP
Chain IDs:R (auth: j)
Chain Length:144
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168

UniProt ID:P14577 Pfam ID:PF00252

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L17
Gene (Uniprot):rplQ
Chain IDs:S (auth: k)
Chain Length:131
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168

UniProt ID:P20277 Pfam ID:PF01196

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18
Gene (Uniprot):rplR
Chain IDs:T (auth: l)
Chain Length:120
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168

UniProt ID:P46899 Pfam ID:PF00861

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19
Gene (Uniprot):rplS
Chain IDs:U (auth: m)
Chain Length:115
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168

UniProt ID:O31742 Pfam ID:PF01245

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L20
Gene (Uniprot):rplT
Chain IDs:V (auth: n)
Chain Length:61
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168

UniProt ID:P55873 Pfam ID:PF00453

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L21
Gene (Uniprot):rplU
Chain IDs:W (auth: o)
Chain Length:102
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168

UniProt ID:P26908 Pfam ID:PF00829

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L10
Gene (Uniprot):rplJ
Chain IDs:F (auth: p)
Chain Length:166
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168

UniProt ID:P42923 Pfam ID:PF00466

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L11
Gene (Uniprot):rplK
Chain IDs:G (auth: q)
Chain Length:141
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168

UniProt ID:Q06796 Pfam ID:PF03946, PF00298

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22
Gene (Uniprot):rplV
Chain IDs:X (auth: r)
Chain Length:113
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168

UniProt ID:P42060 Pfam ID:PF00237

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L23
Gene (Uniprot):rplW
Chain IDs:Y (auth: s)
Chain Length:92
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168

UniProt ID:P42924 Pfam ID:PF00276

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24
Gene (Uniprot):rplX
Chain IDs:Z (auth: t)
Chain Length:103
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168

UniProt ID:P0CI78 Pfam ID:PF00467, PF17136

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Gene (Uniprot):rpmA
Chain IDs:AA (auth: u)
Chain Length:94
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168

UniProt ID:P05657 Pfam ID:PF01016

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L28
Gene (Uniprot):rpmB
Chain IDs:BA (auth: v)
Chain Length:62
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168

UniProt ID:P37807 Pfam ID:PF00830

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29
Gene (Uniprot):rpmC
Chain IDs:CA (auth: w)
Chain Length:266
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168

UniProt ID:P12873 Pfam ID:PF00831

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L30
Gene (Uniprot):rpmD
Chain IDs:DA (auth: x)
Chain Length:59
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168

UniProt ID:P19947 Pfam ID:PF00327

Ligand Molecules

G4P

Primary Citation

Inhibition of SRP-dependent protein secretion by the bacterial alarmone (p)ppGpp.

Czech, L, Mais, C.N, Kratzat, H, Sarmah, P, Giammarinaro, P, Freibert, S.A, Esser, H.F, Musial, J, Berninghausen, O, Steinchen, W, Beckmann, R, Koch, H.G, Bange, G.Show

Nat Commun 13 1069 1069 (2022)

PMID: 35217658 DOI: 10.1038/s41467-022-28675-0

Abstact

The stringent response enables bacteria to respond to nutrient limitation and other stress conditions through production of the nucleotide-based second messengers ppGpp and pppGpp, collectively known as (p)ppGpp. Here, we report that (p)ppGpp inhibits the signal recognition particle (SRP)-dependent protein targeting pathway, which is essential for membrane protein biogenesis and protein secretion. More specifically, (p)ppGpp binds to the SRP GTPases Ffh and FtsY, and inhibits the formation of the SRP receptor-targeting complex, which is central for the coordinated binding of the translating ribosome to the SecYEG translocon. Cryo-EM analysis of SRP bound to translating ribosomes suggests that (p)ppGpp may induce a distinct conformational stabilization of the NG domain of Ffh and FtsY in Bacillus subtilis but not in E. coli.

Legend

Protein

Chemical

Disease

Primary Citation of related structures