ISDA: 8W2N

Deposition Date 2024-02-20

Release Date 2025-08-13

Last Version Date 2025-08-13

Entry Detail

PDB ID:

8W2N

Keywords:

RIBOSOME

Title:

E. coli 70S ribosome with unmodified Lys-tRNAPro(GGG) in the P/P conformation on a slippery CCC-C codon and Elongation Factor P bound (uL1 in the open conformation)

Biological Source:

Source Organism:

Escherichia coli (Taxon ID: 562)

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

3.20 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Polymer Type:polyribonucleotide
Molecule:23S 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 mRNA
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 (GGG)
Chain IDs:E (auth: 5)
Chain Length:77
Number of Molecules:1
Biological Source:Escherichia coli

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Elongation factor P
Gene (Uniprot):efp
Chain IDs:F (auth: 6)
Chain Length:188
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:C3SGD7 Pfam ID:PF08207, PF01132, PF09285

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Gene (Uniprot):rplB
Chain IDs:G (auth: B)
Chain Length:57
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: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

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4
Gene (Uniprot):rplD
Chain IDs:I (auth: D)
Chain Length:201
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:65
Number of Molecules:1
Biological Source:Escherichia coli

Structures with similar UniProt ID

Protein Blast

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

UniProt ID:C3SR17 Pfam ID:PF00347

Structures with similar UniProt ID

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

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13
Chain IDs:M (auth: J)
Chain Length:142
Number of Molecules:1
Biological Source:Escherichia coli

Structures with similar UniProt ID

Protein Blast

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

UniProt ID:S1NW45 Pfam ID:PF00238

Structures with similar UniProt ID

Protein Blast

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

UniProt ID:A0A037Y8L6 Pfam ID:PF00828

Structures with similar UniProt ID

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

Structures with similar UniProt ID

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

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18
Chain IDs:R (auth: O)
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19
Chain IDs:S (auth: P)
Chain Length:115
Number of Molecules:1
Biological Source:Escherichia coli

Structures with similar UniProt ID

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

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S 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

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22
Gene (Uniprot):rplV
Chain IDs:V (auth: S)
Chain Length:101
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P61175 Pfam ID:PF00237

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L23
Chain IDs:W (auth: T)
Chain Length:100
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24
Chain IDs:X (auth: U)
Chain Length:104
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L25
Chain IDs:Y (auth: V)
Chain Length:94
Number of Molecules:1
Biological Source:Escherichia coli

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
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

Structures with similar UniProt ID

Protein Blast

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

UniProt ID:A0A1X3JA73 Pfam ID:PF00830

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29
Chain IDs:BA (auth: Y)
Chain Length:63
Number of Molecules:1
Biological Source:Escherichia coli

Structures with similar UniProt ID

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

Structures with similar UniProt ID

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

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32
Chain IDs:EA (auth: b)
Chain Length:57
Number of Molecules:1
Biological Source:Escherichia coli

Structures with similar UniProt ID

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

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L34
Gene (Uniprot):rpmH
Chain IDs:GA (auth: d)
Chain Length:201
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:B7MGC4 Pfam ID:PF00468

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L35
Gene (Uniprot):rpmI
Chain IDs:HA (auth: e)
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:50S ribosomal protein L36
Gene (Uniprot):rpmJ
Chain IDs:IA (auth: f)
Chain Length:177
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:A0A0E2L017 Pfam ID:PF00444

Structures with similar UniProt ID

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

Structures with similar UniProt ID

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

Structures with similar UniProt ID

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

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S5
Gene (Uniprot):rpsE
Chain IDs:MA (auth: j)
Chain Length:142
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:30S ribosomal protein S6
Gene (Uniprot):rpsF
Chain IDs:NA (auth: k)
Chain Length:123
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:30S ribosomal protein S7
Gene (Uniprot):rpsG
Chain IDs:OA (auth: l)
Chain Length:144
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P02359 Pfam ID:PF00177

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S8
Chain IDs:PA (auth: m)
Chain Length:136
Number of Molecules:1
Biological Source:Escherichia coli

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S9
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

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S10
Chain IDs:RA (auth: o)
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli

Structures with similar UniProt ID

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

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S12
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

Structures with similar UniProt ID

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

Structures with similar UniProt ID

Protein Blast

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

UniProt ID:A0A2X1PQW4 Pfam ID:PF00253

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S15
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

Structures with similar UniProt ID

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

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S17
Gene (Uniprot):rpsQ
Chain IDs:YA (auth: v)
Chain Length:94
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:C3SQY7 Pfam ID:PF00366

Structures with similar UniProt ID

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

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S19
Chain IDs:AB (auth: x)
Chain Length:78
Number of Molecules:1
Biological Source:Escherichia coli

Structures with similar UniProt ID

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

Structures with similar UniProt ID

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
0TD	TA	ASP	modified residue
2MG	B	G	modified residue
4OC	B	C	modified residue
5MC	B	C	modified residue
G7M	B	G	modified residue
KEO	F	LYS	modified residue
MA6	B	A	modified residue
PSU	B	U	modified residue
UR3	B	U	modified residue