9Q3Q image
Deposition Date 2025-08-19
Release Date 2026-08-26
Last Version Date 2026-09-23
Entry Detail
PDB ID:
9Q3Q
Keywords:
RIBOSOME
Title:
Cryo-EM structure of translating Escherichia coli 70S ribosome bound to mRNA, P-site QKF-peptidyl-tRNAPhe, glycyl-tRNAGly in A/T conformation, EF-Tu-GDP, and bottromycin at 2.01A resolution
Biological Source:
Source Organism(s):
Escherichia coli (Taxon ID: 562)
Expression System(s):
Escherichia coli bl21(de3)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
2.01 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
9Q3Q validation report missing
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:YA (auth: 1)
Chain Length:63
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:C3SQY2
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L30
Gene (Uniprot):rpmD
Chain IDs:ZA (auth: 2)
Chain Length:59
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:C3SR32
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L31
Gene (Uniprot):rpmE
Chain IDs:AB (auth: 3)
Chain Length:70
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:50S ribosomal protein L32
Gene (Uniprot):rpmF
Chain IDs:BB (auth: 4)
Chain Length:57
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:C3TE02
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L33
Gene (Uniprot):rpmG
Chain IDs:CB (auth: 5)
Chain Length:55
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:C3SME7
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpmH
Chain IDs:DB (auth: 6)
Chain Length:46
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:50S ribosomal protein L35
Gene (Uniprot):rpmI
Chain IDs:EB (auth: 7)
Chain Length:65
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:Large ribosomal subunit prote
Gene (Uniprot):rpmJ
Chain IDs:FB (auth: 8)
Chain Length:38
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7Q6 Pfam ID:PF00444
Polymer Type:polyribonucleotide
Molecule:23S Ribosomal RNA
Chain IDs:AA (auth: A)
Chain Length:2904
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:5S Ribosomal RNA
Chain IDs:BA (auth: B)
Chain Length:120
Number of Molecules:1
Biological Source:Escherichia coli
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Gene (Uniprot):rplB
Chain IDs:CA (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
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L3
Gene (Uniprot):rplC
Chain IDs:DA (auth: D)
Chain Length:209
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:C3SQU2
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplD
Chain IDs:EA (auth: E)
Chain Length:201
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:FA (auth: F)
Chain Length:179
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:GA (auth: G)
Chain Length:177
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:HA (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
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L11
Gene (Uniprot):rplK
Chain IDs:IA (auth: J)
Chain Length:142
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7J7 Pfam ID:PF03946, PF00298
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplM
Chain IDs:JA (auth: L)
Chain Length:142
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:Large ribosomal subunit prote
Gene (Uniprot):rplN
Chain IDs:KA (auth: M)
Chain Length:123
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:50S ribosomal protein L15
Gene (Uniprot):rplO
Chain IDs:LA (auth: N)
Chain Length:144
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:S5NDE9
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplP
Chain IDs:MA (auth: O)
Chain Length:136
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:A7ZSK2 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:NA (auth: P)
Chain Length:127
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:OA (auth: Q)
Chain Length:117
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:PA (auth: R)
Chain Length:115
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7K8 Pfam ID:PF01245
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L20
Gene (Uniprot):rplT
Chain IDs:QA (auth: S)
Chain Length:118
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:B7MAS6 Pfam ID:PF00453
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplU
Chain IDs:RA (auth: T)
Chain Length:103
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:Large ribosomal subunit prote
Gene (Uniprot):rplV
Chain IDs:SA (auth: U)
Chain Length:110
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:50S ribosomal protein L23
Gene (Uniprot):rplW
Chain IDs:TA (auth: V)
Chain Length:100
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:C3SQV2
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24
Gene (Uniprot):rplX
Chain IDs:UA (auth: W)
Chain Length:104
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:C3SQZ7
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplY
Chain IDs:VA (auth: X)
Chain Length:94
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:50S ribosomal protein L27
Gene (Uniprot):rpmA
Chain IDs:WA (auth: Y)
Chain Length:85
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:50S ribosomal protein L28
Gene (Uniprot):rpmB
Chain IDs:XA (auth: Z)
Chain Length:78
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:A0A1X3JA73
Polymer Type:polyribonucleotide
Molecule:16S Ribosomal RNA
Chain IDs:A (auth: a)
Chain Length:1542
Number of Molecules:1
Biological Source:Escherichia coli
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Gene (Uniprot):rpsB
Chain IDs:B (auth: b)
Chain Length:241
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:J7QM75
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsC
Chain IDs:C (auth: c)
Chain Length:233
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:B7MCS9 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:D (auth: d)
Chain Length:206
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:E (auth: e)
Chain Length:167
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:30S ribosomal protein S6
Gene (Uniprot):rpsF
Chain IDs:F (auth: f)
Chain Length:131
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:C3SFQ7
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S7
Gene (Uniprot):rpsG
Chain IDs:G (auth: g)
Chain Length:156
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:H (auth: h)
Chain Length:130
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:C3SR12
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsI
Chain IDs:I (auth: i)
Chain Length:130
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:C3SRY2
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsJ
Chain IDs:J (auth: j)
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:C3SQT7
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsK
Chain IDs:K (auth: k)
Chain Length:129
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:A7ZSI6 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:L (auth: l)
Chain Length:124
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:A0A0F1AUC4
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsM
Chain IDs:M (auth: m)
Chain Length:118
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:A0A7U9IV78
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsN
Chain IDs:N (auth: n)
Chain Length:101
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:A0A2X1PQW4
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsO
Chain IDs:O (auth: o)
Chain Length:89
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:C3SSQ7
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsP
Chain IDs:P (auth: p)
Chain Length:82
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:C3SYP2
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsQ
Chain IDs:Q (auth: q)
Chain Length:84
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:C3SQY7
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsR
Chain IDs:R (auth: r)
Chain Length:75
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:A0A0E2KXL3
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsS
Chain IDs:S (auth: s)
Chain Length:92
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:C3SQW2
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsT
Chain IDs:T (auth: t)
Chain Length:87
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:C3TRH7
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsU
Chain IDs:U (auth: u)
Chain Length:71
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:A0A0E2L2J1
Polymer Type:polyribonucleotide
Molecule:dapG mRNA
Chain IDs:V (auth: v)
Chain Length:45
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:A/T-site glycine tRNA
Chain IDs:W (auth: w)
Chain Length:76
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:P-site phenylalanine tRNA
Chain IDs:X (auth: x)
Chain Length:76
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:QKF peptide
Chain IDs:Y (auth: y)
Chain Length:3
Number of Molecules:1
Biological Source:Escherichia coli
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Elongation factor Tu 2
Gene (Uniprot):tuf2
Chain IDs:Z (auth: z)
Chain Length:394
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:A8A779 EC:3.6.5.3
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
2MG A G modified residue
4D4 MA ARG modified residue
4OC A C modified residue
4SU X U modified residue
5MC A C modified residue
5MU X U modified residue
D2T L ASP modified residue
G7M A, X G modified residue
MA6 A A modified residue
MEQ DA GLN modified residue
MIA X A modified residue
MS6 MA MET modified residue
PSU A, X U modified residue
UR3 A U modified residue
Ligand Molecules
GDP
K
MG
MQH
ZN
Primary Citation
Sequence-specific trapping of EF-Tu/glycyl-tRNA complex on the ribosome by bottromycin
To Be Published ? ? ? (?)
Primary Citation of related structures
9Q3Q
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