8URM image
Deposition Date 2023-10-26
Release Date 2025-07-09
Last Version Date 2025-07-09
Entry Detail
PDB ID:
8URM
Keywords:
RIBOSOME
Title:
E. coli 70S ribosome with unmodified tRNAPro(GGG) bound to slippery P-site CCC-C codon and tRNAVal(UAC) in the A site
Biological Source:
Source Organism:
Escherichia coli (Taxon ID: 562)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.00 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
8URM validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:13S ribosomal RNA
Chain IDs:A (auth: 1)
Chain Length:2904
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:16S ribosomal RNA
Chain IDs:B (auth: 2)
Chain Length:1540
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:5S ribosomal RNA
Chain IDs:C (auth: 3)
Chain Length:120
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:mRNA
Chain IDs:D (auth: 4)
Chain Length:18
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:tRNA ProL
Chain IDs:E (auth: 5)
Chain Length:77
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:tRNA Val
Chain IDs:F (auth: 6)
Chain Length:76
Number of Molecules:1
Biological Source:Escherichia coli
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Gene (Uniprot):rplB
Chain IDs:G (auth: B)
Chain Length:273
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P60422 Pfam ID:PF00181, PF03947
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L3
Gene (Uniprot):rplC
Chain IDs:H (auth: C)
Chain Length:209
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P60438 Pfam ID:PF00297
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4
Gene (Uniprot):rplD
Chain IDs:I (auth: D)
Chain Length:46
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:A1AGK6 Pfam ID:PF00573
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5
Chain IDs:J (auth: E)
Chain Length:179
Number of Molecules:1
Biological Source:Escherichia coli
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L6
Gene (Uniprot):rplF
Chain IDs:K (auth: F)
Chain Length:38
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:C3SR17 Pfam ID:PF00347
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L9
Gene (Uniprot):rplI
Chain IDs:L (auth: G)
Chain Length:241
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:C3SFP2 Pfam ID:PF01281, PF03948
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL13
Gene (Uniprot):rplM
Chain IDs:M (auth: J)
Chain Length:167
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0AA12 Pfam ID:PF00572
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Gene (Uniprot):rplN
Chain IDs:N (auth: K)
Chain Length:135
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:S1NW45 Pfam ID:PF00238
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15
Gene (Uniprot):rplO
Chain IDs:O (auth: L)
Chain Length:178
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:A0A037Y8L6 Pfam ID:PF00828
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16
Gene (Uniprot):rplP
Chain IDs:P (auth: M)
Chain Length:136
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0ADY7 Pfam ID:PF00252
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L17
Gene (Uniprot):rplQ
Chain IDs:Q (auth: N)
Chain Length:127
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:C3SR72 Pfam ID:PF01196
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL18
Gene (Uniprot):rplR
Chain IDs:R (auth: O)
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:A0A828U007 Pfam ID:PF00861
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL19
Gene (Uniprot):rplS
Chain IDs:S (auth: P)
Chain Length:115
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7K8 Pfam ID:PF01245
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L20
Gene (Uniprot):rplT
Chain IDs:T (auth: Q)
Chain Length:124
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:B7MAS6 Pfam ID:PF00453
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L21
Gene (Uniprot):rplU
Chain IDs:U (auth: R)
Chain Length:118
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:C3SSG2 Pfam ID:PF00829
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22
Gene (Uniprot):rplV
Chain IDs:V (auth: S)
Chain Length:110
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P61175 Pfam ID:PF00237
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L23
Gene (Uniprot):rplW
Chain IDs:W (auth: T)
Chain Length:100
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:C3SQV2 Pfam ID:PF00276
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24
Gene (Uniprot):rplX
Chain IDs:X (auth: U)
Chain Length:104
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:C3SQZ7 Pfam ID:PF00467, PF17136
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL25
Gene (Uniprot):rplY
Chain IDs:Y (auth: V)
Chain Length:84
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P68919 Pfam ID:PF01386
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL27
Gene (Uniprot):rpmA
Chain IDs:Z (auth: W)
Chain Length:75
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:C3SSG7 Pfam ID:PF01016
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L28
Gene (Uniprot):rpmB
Chain IDs:AA (auth: X)
Chain Length:92
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:A0A1X3JA73 Pfam ID:PF00830
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL29
Gene (Uniprot):rpmC
Chain IDs:BA (auth: Y)
Chain Length:63
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:C3SQY2 Pfam ID:PF00831
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L30
Gene (Uniprot):rpmD
Chain IDs:CA (auth: Z)
Chain Length:71
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:C3SR32 Pfam ID:PF00327
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L31
Gene (Uniprot):rpmE
Chain IDs:DA (auth: a)
Chain Length:70
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7M9 Pfam ID:PF01197
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32
Gene (Uniprot):rpmF
Chain IDs:EA (auth: b)
Chain Length:273
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:C3TE02 Pfam ID:PF01783
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L33
Gene (Uniprot):rpmG
Chain IDs:FA (auth: c)
Chain Length:209
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:C3SME7 Pfam ID:PF00471
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L34
Gene (Uniprot):rpmH
Chain IDs:GA (auth: d)
Chain Length:46
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:B7MGC4 Pfam ID:PF00468
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L35
Gene (Uniprot):rpmI
Chain IDs:HA (auth: e)
Chain Length:179
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7Q1 Pfam ID:PF01632
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L36
Gene (Uniprot):rpmJ
Chain IDs:IA (auth: f)
Chain Length:38
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:A0A0E2L017 Pfam ID:PF00444
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Gene (Uniprot):rpsB
Chain IDs:JA (auth: g)
Chain Length:241
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:C3TPN2 Pfam ID:PF00318
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S3
Gene (Uniprot):rpsC
Chain IDs:KA (auth: h)
Chain Length:233
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:B7MCS9 Pfam ID:PF07650, PF00189
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S4
Gene (Uniprot):rpsD
Chain IDs:LA (auth: i)
Chain Length:206
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7V8 Pfam ID:PF00163, PF01479
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S5
Gene (Uniprot):rpsE
Chain IDs:MA (auth: j)
Chain Length:167
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7W1 Pfam ID:PF00333, PF03719
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S6
Gene (Uniprot):rpsF
Chain IDs:NA (auth: k)
Chain Length:135
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P02358 Pfam ID:PF01250
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS7
Gene (Uniprot):rpsG
Chain IDs:OA (auth: l)
Chain Length:178
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:C4ZUJ6 Pfam ID:PF00177
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS8
Gene (Uniprot):rpsH
Chain IDs:PA (auth: m)
Chain Length:136
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:C3SR12 Pfam ID:PF00410
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS9
Gene (Uniprot):rpsI
Chain IDs:QA (auth: n)
Chain Length:127
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:C3SRY2 Pfam ID:PF00380
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS10
Gene (Uniprot):rpsJ
Chain IDs:RA (auth: o)
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:C3SQT7 Pfam ID:PF00338
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S11
Gene (Uniprot):rpsK
Chain IDs:SA (auth: p)
Chain Length:115
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:B7MCR3 Pfam ID:PF00411
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS12
Gene (Uniprot):rpsL
Chain IDs:TA (auth: q)
Chain Length:124
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:C3SQR7 Pfam ID:PF00164
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S13
Gene (Uniprot):rpsM
Chain IDs:UA (auth: r)
Chain Length:118
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:A0A7U9IV78 Pfam ID:PF00416
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS14
Gene (Uniprot):rpsN
Chain IDs:VA (auth: s)
Chain Length:110
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:A0A2X1PQW4 Pfam ID:PF00253
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS15
Gene (Uniprot):rpsO
Chain IDs:WA (auth: t)
Chain Length:100
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:C3SSQ7 Pfam ID:PF00312
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S16
Gene (Uniprot):rpsP
Chain IDs:XA (auth: u)
Chain Length:104
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:C3SYP2 Pfam ID:PF00886
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS17
Gene (Uniprot):rpsQ
Chain IDs:YA (auth: v)
Chain Length:84
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:C3SQY7 Pfam ID:PF00366
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S18
Gene (Uniprot):rpsR
Chain IDs:ZA (auth: w)
Chain Length:75
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:A0A0E2KXL3 Pfam ID:PF01084
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS19
Gene (Uniprot):rpsS
Chain IDs:AB (auth: x)
Chain Length:92
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:C3SQW2 Pfam ID:PF00203
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S20
Gene (Uniprot):rpsT
Chain IDs:BB (auth: y)
Chain Length:63
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:C3TRH7 Pfam ID:PF01649
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S21
Gene (Uniprot):rpsU
Chain IDs:CB (auth: z)
Chain Length:71
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:A0A0E2L2J1 Pfam ID:PF01165
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
0TD TA ASP modified residue
1MG A G modified residue
2MA A A modified residue
2MG A G modified residue
4OC B C modified residue
4SU F U modified residue
5MC A C modified residue
5MU A U modified residue
6MZ A A modified residue
7MG B G modified residue
G7M A G modified residue
MA6 B A modified residue
OMC A C modified residue
OMG A G modified residue
OMU A U modified residue
PSU A U modified residue
UR3 B U modified residue
Ligand Molecules
MG
Primary Citation
An RNA modification prevents extended codon-anticodon interactions from facilitating +1 frameshifting
Nat Commun ? ? ? (2025)
Primary Citation of related structures
8URM