9NLS image
Deposition Date 2025-03-03
Release Date 2025-04-02
Last Version Date 2026-04-15
Entry Detail
PDB ID:
9NLS
Keywords:
RIBOSOME
Title:
E. coli initiation complex with EQ2-YbiT in Intermediate/PtIM(b) conformation
Biological Source:
Source Organism(s):
Escherichia coli (Taxon ID: 562)
Expression System(s):
Escherichia coli
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.30 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
9NLS 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):rplA
Chain IDs:A (auth: 1)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7L0 Pfam ID:PF00687
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplM
Chain IDs:B (auth: 13)
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
Chain IDs:C (auth: 14)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0ADY3
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplO
Chain IDs:D (auth: 15)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P02413 Pfam ID:PF00828
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16
Gene (Uniprot):rplP
Chain IDs:E (auth: 16)
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:F (auth: 17)
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:G (auth: 18)
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:50S ribosomal protein L19
Chain IDs:H (auth: 19)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7K6
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Gene (Uniprot):rplB
Chain IDs:I (auth: 2)
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:Large ribosomal subunit prote
Chain IDs:J (auth: 20)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7L3
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:K (auth: 21)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0AG48
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:L (auth: 22)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P61175
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:M (auth: 23)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0ADZ0
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:N (auth: 24)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P60624
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplY
Chain IDs:O (auth: 25)
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:P (auth: 27)
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:50S ribosomal protein L28
Chain IDs:Q (auth: 28)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7M2
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:R (auth: 29)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7M6
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L3
Gene (Uniprot):rplC
Chain IDs:S (auth: 3)
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 L30
Gene (Uniprot):rpmD
Chain IDs:T (auth: 30)
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:U (auth: 31)
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:50S ribosomal protein L32
Chain IDs:V (auth: 32)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7N4
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpmG
Chain IDs:W (auth: 33)
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
Chain IDs:X (auth: 34)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7P5
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:Y (auth: 35)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7Q1
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L36
Chain IDs:Z (auth: 36)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7Q6
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplD
Chain IDs:AA (auth: 4)
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:50S ribosomal protein L5
Chain IDs:BA (auth: 5)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P62399
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Chain IDs:CA (auth: 6)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0AG55
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplI
Chain IDs:DA (auth: 9)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7R1 Pfam ID:PF01281, PF03948
Polymer Type:polyribonucleotide
Molecule:mRNA
Chain IDs:EA (auth: M)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:23S ribosomal RNA
Chain IDs:FA (auth: R1)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:5S ribosomal RNA
Chain IDs:GA (auth: R2)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:16S ribosomal RNA
Chain IDs:HA (auth: R3)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:tRNA
Chain IDs:IA (auth: T)
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:Probable ATP-binding protein
Gene (Uniprot):ybiT
Chain IDs:JA (auth: Y)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A9U3 Pfam ID:PF12848, PF00005
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsB
Chain IDs:KA (auth: sb)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7V0 Pfam ID:PF00318
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Chain IDs:LA (auth: sc)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7V3
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S4
Chain IDs:MA (auth: sd)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7V8
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsE
Chain IDs:NA (auth: se)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7W1 Pfam ID:PF03719, PF00333
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S6, non
Gene (Uniprot):rpsF
Chain IDs:OA (auth: sf)
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:30S ribosomal protein S7
Gene (Uniprot):rpsG
Chain IDs:PA (auth: sg)
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:30S ribosomal protein S8
Chain IDs:QA (auth: sh)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7W7
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Chain IDs:RA (auth: si)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7X3
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S10
Chain IDs:SA (auth: sj)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7R5
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Chain IDs:TA (auth: sk)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7R9
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Chain IDs:UA (auth: sl)
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:30S ribosomal protein S13
Chain IDs:VA (auth: sm)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7S9
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Chain IDs:WA (auth: sn)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0AG59
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsO
Chain IDs:XA (auth: so)
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
Chain IDs:YA (auth: sp)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7T3
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsQ
Chain IDs:ZA (auth: sq)
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:30S ribosomal protein S18
Chain IDs:AB (auth: sr)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7T7
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S19
Chain IDs:BB (auth: ss)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7U3
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S20
Chain IDs:CB (auth: st)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7U7
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsU
Chain IDs:DB (auth: su)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P68679 Pfam ID:PF01165
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
4OC IA C modified residue
5MU IA U modified residue
H2U IA U modified residue
PSU IA U modified residue
Ligand Molecules
ATP
FME
MG
NA
ZN
Primary Citation
Cryo-EM studies of the four E. coli paralogs establish ABCF proteins as master plumbers of the peptidyl-transferase center of the ribosome
Biorxiv ? ? ? (2023)
DOI: 10.1101/2023.06.15.543498
Primary Citation of related structures
9NLS
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