ISDA: 8PHJ

Deposition Date 2023-06-20

Release Date 2023-12-13

Last Version Date 2025-03-12

Entry Detail

PDB ID:

8PHJ

Keywords:

RIBOSOME

Title:

cA4-bound Cami1 in complex with 70S ribosome

Biological Source:

Source Organism:

Allochromatium vinosum (Taxon ID: 1049)
synthetic construct (Taxon ID: 32630)
Streptococcus thermophilus (Taxon ID: 1308)
Escherichia coli (Taxon ID: 562)

Host Organism:

Escherichia coli

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

3.67 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL33
Gene (Uniprot):rpmG
Chain IDs:A (auth: 0)
Chain Length:55
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7N9 Pfam ID:PF00471

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL34
Gene (Uniprot):rpmH
Chain IDs:B (auth: 1)
Chain Length:46
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7P5 Pfam ID:PF00468

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL35
Gene (Uniprot):rpmI
Chain IDs:C (auth: 2)
Chain Length:65
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7Q1 Pfam ID:PF01632

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL36A
Gene (Uniprot):rpmJ
Chain IDs:D (auth: 3)
Chain Length:38
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7Q6 Pfam ID:PF00444

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL31A
Gene (Uniprot):rpmE
Chain IDs:E (auth: 4)
Chain Length:70
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7M9 Pfam ID:PF01197

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL10
Gene (Uniprot):rplJ
Chain IDs:F (auth: 5)
Chain Length:165
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7J3 Pfam ID:PF00466

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL11
Gene (Uniprot):rplK
Chain IDs:G (auth: 6)
Chain Length:142
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7J7 Pfam ID:PF03946, PF00298

Polymer Type:polyribonucleotide
Molecule:fMet-tRNA(fMet)
Chain IDs:H (auth: 7), I (auth: 8)
Chain Length:77
Number of Molecules:2
Biological Source:Escherichia coli

Polymer Type:polyribonucleotide
Molecule:mRNA
Chain IDs:J (auth: 9)
Chain Length:31
Number of Molecules:1
Biological Source:synthetic construct

Polymer Type:polyribonucleotide
Molecule:16S rRNA
Chain IDs:K (auth: A)
Chain Length:2904
Number of Molecules:1
Biological Source:Escherichia coli

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS2
Gene (Uniprot):rpsB
Chain IDs:L (auth: B)
Chain Length:120
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7V0 Pfam ID:PF00318

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS3
Gene (Uniprot):rpsC
Chain IDs:M (auth: C)
Chain Length:273
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7V3 Pfam ID:PF07650, PF00189

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS4
Gene (Uniprot):rpsD
Chain IDs:N (auth: D)
Chain Length:209
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7V8 Pfam ID:PF00163, PF01479

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS5
Gene (Uniprot):rpsE
Chain IDs:O (auth: E)
Chain Length:201
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7W1 Pfam ID:PF00333, PF03719

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein bS6, fully modified isoform
Gene (Uniprot):rpsF
Chain IDs:P (auth: F)
Chain Length:135
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P02358 Pfam ID:PF01250

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS7
Gene (Uniprot):rpsG
Chain IDs:Q (auth: G)
Chain Length:177
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P02359 Pfam ID:PF00177

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS8
Gene (Uniprot):rpsH
Chain IDs:R (auth: H)
Chain Length:149
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7W7 Pfam ID:PF00410

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS9
Gene (Uniprot):rpsI
Chain IDs:S (auth: I)
Chain Length:130
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7X3 Pfam ID:PF00380

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS10
Gene (Uniprot):rpsJ
Chain IDs:T (auth: J)
Chain Length:123
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7R5 Pfam ID:PF00338

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS11
Gene (Uniprot):rpsK
Chain IDs:U (auth: K)
Chain Length:144
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7R9 Pfam ID:PF00411

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS12
Gene (Uniprot):rpsL
Chain IDs:V (auth: L)
Chain Length:124
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7S3 Pfam ID:PF00164

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS13
Gene (Uniprot):rpsM
Chain IDs:W (auth: M)
Chain Length:127
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7S9 Pfam ID:PF00416

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS14
Gene (Uniprot):rpsN
Chain IDs:X (auth: N)
Chain Length:117
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0AG59 Pfam ID:PF00253

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS15
Gene (Uniprot):rpsO
Chain IDs:Y (auth: O)
Chain Length:89
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0ADZ4 Pfam ID:PF00312

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein bS16
Gene (Uniprot):rpsP
Chain IDs:Z (auth: P)
Chain Length:118
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7T3 Pfam ID:PF00886

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS17
Gene (Uniprot):rpsQ
Chain IDs:AA (auth: Q)
Chain Length:84
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0AG63 Pfam ID:PF00366

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein bS18
Gene (Uniprot):rpsR
Chain IDs:BA (auth: R)
Chain Length:110
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7T7 Pfam ID:PF01084

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS19
Gene (Uniprot):rpsS
Chain IDs:CA (auth: S)
Chain Length:92
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7U3 Pfam ID:PF00203

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein bS20
Gene (Uniprot):rpsT
Chain IDs:DA (auth: T)
Chain Length:87
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7U7 Pfam ID:PF01649

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein bS21
Gene (Uniprot):rpsU
Chain IDs:EA (auth: U)
Chain Length:71
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P68679 Pfam ID:PF01165

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL12
Gene (Uniprot):rplL
Chain IDs:FA (auth: W)
Chain Length:78
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7K2 Pfam ID:PF16320, PF00542

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:CRISPR-associated protein, APE2256 family
Gene (Uniprot):Alvin_3127
Chain IDs:GA (auth: X), HA (auth: Y)
Chain Length:63
Number of Molecules:2
Biological Source:Allochromatium vinosum

UniProt ID:D3RW14 Pfam ID:PF09651

Polymer Type:polyribonucleotide
Molecule:Cyclic tetraadenosine monophosphate (cA4)
Chain IDs:IB (auth: Z)
Chain Length:4
Number of Molecules:1
Biological Source:Streptococcus thermophilus

Polymer Type:polyribonucleotide
Molecule:23S rRNA (2862-MER)
Chain IDs:IA (auth: a)
Chain Length:2904
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polyribonucleotide
Molecule:5S rRNA
Chain IDs:JA (auth: b)
Chain Length:120
Number of Molecules:1
Biological Source:Escherichia coli

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL2
Gene (Uniprot):rplB
Chain IDs:KA (auth: c)
Chain Length:273
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P60422 Pfam ID:PF00181, PF03947

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL3
Gene (Uniprot):rplC
Chain IDs:LA (auth: d)
Chain Length:209
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P60438 Pfam ID:PF00297

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL4
Gene (Uniprot):rplD
Chain IDs:MA (auth: e)
Chain Length:201
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P60723 Pfam ID:PF00573

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL5
Gene (Uniprot):rplE
Chain IDs:NA (auth: f)
Chain Length:135
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P62399 Pfam ID:PF00281, PF00673

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL6
Gene (Uniprot):rplF
Chain IDs:OA (auth: g)
Chain Length:177
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0AG55 Pfam ID:PF00347

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL9
Gene (Uniprot):rplI
Chain IDs:PA (auth: h)
Chain Length:149
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7R1 Pfam ID:PF01281, PF03948

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL13
Gene (Uniprot):rplM
Chain IDs:QA (auth: i)
Chain Length:130
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0AA10 Pfam ID:PF00572

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL14
Gene (Uniprot):rplN
Chain IDs:RA (auth: j)
Chain Length:123
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0ADY3 Pfam ID:PF00238

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL15
Gene (Uniprot):rplO
Chain IDs:SA (auth: k)
Chain Length:144
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P02413 Pfam ID:PF00828

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL16
Gene (Uniprot):rplP
Chain IDs:TA (auth: l)
Chain Length:124
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0ADY7 Pfam ID:PF00252

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL17
Gene (Uniprot):rplQ
Chain IDs:UA (auth: m)
Chain Length:127
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0AG44 Pfam ID:PF01196

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL18
Gene (Uniprot):rplR
Chain IDs:VA (auth: n)
Chain Length:117
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0C018 Pfam ID:PF00861

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL19
Gene (Uniprot):rplS
Chain IDs:WA (auth: o)
Chain Length:89
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7K6 Pfam ID:PF01245

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL20
Gene (Uniprot):rplT
Chain IDs:XA (auth: p)
Chain Length:118
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7L3 Pfam ID:PF00453

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL21
Gene (Uniprot):rplU
Chain IDs:YA (auth: q)
Chain Length:84
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0AG48 Pfam ID:PF00829

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL22
Gene (Uniprot):rplV
Chain IDs:ZA (auth: r)
Chain Length:110
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P61175 Pfam ID:PF00237

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL23
Gene (Uniprot):rplW
Chain IDs:AB (auth: s)
Chain Length:92
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0ADZ0 Pfam ID:PF00276

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL24
Gene (Uniprot):rplX
Chain IDs:BB (auth: t)
Chain Length:87
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P60624 Pfam ID:PF00467, PF17136

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL25
Gene (Uniprot):rplY
Chain IDs:CB (auth: u)
Chain Length:71
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P68919 Pfam ID:PF01386

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL27
Gene (Uniprot):rpmA
Chain IDs:DB (auth: v)
Chain Length:85
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7L8 Pfam ID:PF01016

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL28
Gene (Uniprot):rpmB
Chain IDs:EB (auth: w)
Chain Length:78
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7M2 Pfam ID:PF00830

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL29
Gene (Uniprot):rpmC
Chain IDs:FB (auth: x)
Chain Length:63
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7M6 Pfam ID:PF00831

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL30
Gene (Uniprot):rpmD
Chain IDs:GB (auth: y)
Chain Length:406
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0AG51 Pfam ID:PF00327

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL32
Gene (Uniprot):rpmF
Chain IDs:HB (auth: z)
Chain Length:4
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7N4 Pfam ID:PF01783

Modified Residue

Compound ID	Chain ID	Parent Comp ID	Details
2MG	K	G	modified residue
4OC	H	C	modified residue
4SU	H	U	modified residue
5MC	K	C	modified residue
5MU	H	U	modified residue
G7M	K	G	modified residue
H2U	H	U	modified residue
MA6	K	A	modified residue
MEQ	LA	GLN	modified residue
PSU	H	U	modified residue
UR3	K	U	modified residue

Ligand Molecules

Peptide-like Molecules

PRD_002431

Primary Citation

Ribosomal stalk-captured CARF-RelE ribonuclease inhibits translation following CRISPR signaling.

Mogila, I, Tamulaitiene, G, Keda, K, Timinskas, A, Ruksenaite, A, Sasnauskas, G, Venclovas, C, Siksnys, V, Tamulaitis, G.Show

Science 382 1036 1041 (2023)

PMID: 38033086 DOI: 10.1126/science.adj2107

Abstact

Prokaryotic type III CRISPR-Cas antiviral systems employ cyclic oligoadenylate (cAn) signaling to activate a diverse range of auxiliary proteins that reinforce the CRISPR-Cas defense. Here we characterize a class of cAn-dependent effector proteins named CRISPR-Cas-associated messenger RNA (mRNA) interferase 1 (Cami1) consisting of a CRISPR-associated Rossmann fold sensor domain fused to winged helix-turn-helix and a RelE-family mRNA interferase domain. Upon activation by cyclic tetra-adenylate (cA4), Cami1 cleaves mRNA exposed at the ribosomal A-site thereby depleting mRNA and leading to cell growth arrest. The structures of apo-Cami1 and the ribosome-bound Cami1-cA4 complex delineate the conformational changes that lead to Cami1 activation and the mechanism of Cami1 binding to a bacterial ribosome, revealing unexpected parallels with eukaryotic ribosome-inactivating proteins.

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Protein

Chemical

Disease

Primary Citation of related structures