ISDA: 9IOT

Deposition Date 2024-07-09

Release Date 2025-07-30

Last Version Date 2026-09-23

Entry Detail

PDB ID:

9IOT

Keywords:

RIBOSOME

Title:

Cryo-EM structure of Escherichia coli hibernating ribosome with RNase I mutant

Biological Source:

Source Organism(s):

Escherichia coli (Taxon ID: 562)

Expression System(s):

Escherichia coli bl21(de3)

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

2.70 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Structures with similar UniProt ID

Structural Superimposition Protein Blast

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

UniProt ID:P0A7M6 Pfam ID:PF00831

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpmD
Chain IDs:B (auth: 1)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0AG51 Pfam ID:PF00327

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpmE
Chain IDs:DA (auth: 2)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7M9 Pfam ID:PF01197

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpmF
Chain IDs:C (auth: 3)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7N4 Pfam ID:PF01783

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpmG
Chain IDs:D (auth: 4)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7N9 Pfam ID:PF00471

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L34
Gene (Uniprot):rpmH
Chain IDs:E (auth: 5)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7P5 Pfam ID:PF00468

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpmI
Chain IDs:F (auth: 6)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7Q1 Pfam ID:PF01632

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L36
Gene (Uniprot):rpmJ
Chain IDs:G (auth: 7)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7Q6 Pfam ID:PF00444

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsA
Chain IDs:DB (auth: 8)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0AG67 Pfam ID:PF00575

Polymer Type:polyribonucleotide
Molecule:23S rRNA
Chain IDs:EA (auth: A)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polyribonucleotide
Molecule:5S rRNA
Chain IDs:H (auth: B)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplB
Chain IDs:I (auth: D)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P60422 Pfam ID:PF00181, PF03947

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L3
Gene (Uniprot):rplC
Chain IDs:J (auth: E)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P60438 Pfam ID:PF00297

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4
Gene (Uniprot):rplD
Chain IDs:K (auth: F)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P60723 Pfam ID:PF00573

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplE
Chain IDs:L (auth: G)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P62399 Pfam ID:PF00281, PF00673

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplF
Chain IDs:M (auth: H)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0AG55 Pfam ID:PF00347

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplI
Chain IDs:N (auth: I)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7R1 Pfam ID:PF01281

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13
Gene (Uniprot):rplM
Chain IDs:O (auth: L)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0AA10 Pfam ID:PF00572

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Gene (Uniprot):rplN
Chain IDs:P (auth: M)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0ADY3 Pfam ID:PF00238

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplO
Chain IDs:Q (auth: N)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:A7ZSJ0 Pfam ID:PF00828

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplP
Chain IDs:R (auth: O)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0ADY7 Pfam ID:PF00252

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplQ
Chain IDs:S (auth: P)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0AG44 Pfam ID:PF01196

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplR
Chain IDs:T (auth: Q)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0C018 Pfam ID:PF00861

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplS
Chain IDs:U (auth: R)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7K6 Pfam ID:PF01245

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplT
Chain IDs:V (auth: S)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7L3 Pfam ID:PF00453

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L21
Gene (Uniprot):rplU
Chain IDs:W (auth: T)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0AG48 Pfam ID:PF00829

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22
Gene (Uniprot):rplV
Chain IDs:X (auth: U)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P61175 Pfam ID:PF00237

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplW
Chain IDs:Y (auth: V)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0ADZ0 Pfam ID:PF00276

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplX
Chain IDs:Z (auth: W)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P60624 Pfam ID:PF00467, PF17136

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L25
Gene (Uniprot):rplY
Chain IDs:AA (auth: X)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P68919 Pfam ID:PF01386

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpmA
Chain IDs:BA (auth: Y)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7L8 Pfam ID:PF01016

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpmB
Chain IDs:CA (auth: Z)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7M2 Pfam ID:PF00830

Polymer Type:polyribonucleotide
Molecule:16S rRNA
Chain IDs:FA (auth: a)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsB
Chain IDs:GA (auth: b)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:A7ZHQ9 Pfam ID:PF00318

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsC
Chain IDs:HA (auth: c)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7V3 Pfam ID:PF07650, PF00189

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsD
Chain IDs:IA (auth: d)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7V8 Pfam ID:PF00163, PF01479

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsE
Chain IDs:JA (auth: e)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7W1 Pfam ID:PF00333, PF03719

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsF
Chain IDs:KA (auth: f)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P02358 Pfam ID:PF01250

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsG
Chain IDs:LA (auth: g)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P02359 Pfam ID:PF00177

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsH
Chain IDs:MA (auth: h)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7W7 Pfam ID:PF00410

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsI
Chain IDs:NA (auth: i)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7X3 Pfam ID:PF00380

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsJ
Chain IDs:OA (auth: j)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7R5 Pfam ID:PF00338

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsK
Chain IDs:PA (auth: k)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7R9 Pfam ID:PF00411

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsL
Chain IDs:QA (auth: l)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7S3 Pfam ID:PF00164

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsM
Chain IDs:RA (auth: m)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7S9 Pfam ID:PF00416

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsN
Chain IDs:SA (auth: n)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0AG59 Pfam ID:PF00253

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsO
Chain IDs:TA (auth: o)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0ADZ4 Pfam ID:PF00312

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsP
Chain IDs:UA (auth: p)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7T3 Pfam ID:PF00886

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsQ
Chain IDs:VA (auth: q)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0AG63 Pfam ID:PF00366

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsR
Chain IDs:WA (auth: r)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7T7 Pfam ID:PF01084

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsS
Chain IDs:XA (auth: s)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7U3 Pfam ID:PF00203

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsT
Chain IDs:YA (auth: t)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7U7 Pfam ID:PF01649

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S21
Gene (Uniprot):rpsU
Chain IDs:ZA (auth: u)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P68679 Pfam ID:PF01165

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosome hibernation promotin
Gene (Uniprot):hpf
Chain IDs:AB (auth: v)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0AFX0 Pfam ID:PF02482

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosome modulation factor
Gene (Uniprot):rmf
Chain IDs:BB (auth: y)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0AFW2 Pfam ID:PF04957

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribonuclease I
Gene (Uniprot):rna
Mutagens:H78F/H156F
Chain IDs:CB (auth: z)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P21338 Pfam ID:PF00445 EC:4.6.1.18

Modified Residue

Compound ID	Chain ID	Parent Comp ID	Details
2MG	FA	G	modified residue
4D4	R	ARG	modified residue
4OC	FA	C	modified residue
5MC	FA	C	modified residue
D2T	QA	ASP	modified residue
G7M	FA	G	modified residue
MA6	FA	A	modified residue
MEQ	J	GLN	modified residue
PSU	FA	U	modified residue
UR3	FA	U	modified residue