9NL7 image
Deposition Date 2025-03-02
Release Date 2025-04-02
Last Version Date 2025-04-02
Entry Detail
PDB ID:
9NL7
Keywords:
RIBOSOME
Title:
E. coli initiation complex with EQ2-YbiT in Non-hydrolytic 2/PtIM(b) conformation
Biological Source:
Source Organism:
Escherichia coli (Taxon ID: 562)
Host Organism:
Escherichia coli
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.30 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
9NL7 validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL1
Gene (Uniprot):rplA
Chain IDs:A (auth: 1)
Chain Length:220
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7L0 Pfam ID:PF00687
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL13
Gene (Uniprot):rplM
Chain IDs:B (auth: 13)
Chain Length:142
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0AA10 Pfam ID:PF00572
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Chain IDs:C (auth: 14)
Chain Length:122
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0ADY3
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL15
Gene (Uniprot):rplO
Chain IDs:D (auth: 15)
Chain Length:144
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P02413 Pfam ID:PF00828
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16
Gene (Uniprot):rplP
Chain IDs:E (auth: 16)
Chain Length:136
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0ADY7 Pfam ID:PF00252
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL17
Gene (Uniprot):rplQ
Chain IDs:F (auth: 17)
Chain Length:120
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0AG44 Pfam ID:PF01196
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL18
Gene (Uniprot):rplR
Chain IDs:G (auth: 18)
Chain Length:116
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0C018 Pfam ID:PF00861
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19
Chain IDs:H (auth: 19)
Chain Length:114
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7K6
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Gene (Uniprot):rplB
Chain IDs:I (auth: 2)
Chain Length:271
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P60422 Pfam ID:PF00181, PF03947
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL20
Chain IDs:J (auth: 20)
Chain Length:117
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7L3
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL21
Chain IDs:K (auth: 21)
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0AG48
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL22
Chain IDs:L (auth: 22)
Chain Length:110
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P61175
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL23
Chain IDs:M (auth: 23)
Chain Length:93
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0ADZ0
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL24
Chain IDs:N (auth: 24)
Chain Length:102
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P60624
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL25
Gene (Uniprot):rplY
Chain IDs:O (auth: 25)
Chain Length:94
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P68919 Pfam ID:PF01386
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Chain IDs:P (auth: 27)
Chain Length:75
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7L8
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L28
Chain IDs:Q (auth: 28)
Chain Length:77
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7M2
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL29
Chain IDs:R (auth: 29)
Chain Length:63
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7M6
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L3
Gene (Uniprot):rplC
Chain IDs:S (auth: 3)
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 L30
Gene (Uniprot):rpmD
Chain IDs:T (auth: 30)
Chain Length:58
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0AG51 Pfam ID:PF00327
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL31
Gene (Uniprot):rpmE
Chain IDs:U (auth: 31)
Chain Length:66
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
Chain IDs:V (auth: 32)
Chain Length:56
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7N4
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL33
Gene (Uniprot):rpmG
Chain IDs:W (auth: 33)
Chain Length:50
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7N9 Pfam ID:PF00471
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L34
Chain IDs:X (auth: 34)
Chain Length:46
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7P5
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL35
Chain IDs:Y (auth: 35)
Chain Length:64
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7Q1
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L36
Chain IDs:Z (auth: 36)
Chain Length:38
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7Q6
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL4
Gene (Uniprot):rplD
Chain IDs:AA (auth: 4)
Chain Length:201
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P60723 Pfam ID:PF00573
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5
Chain IDs:BA (auth: 5)
Chain Length:177
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P62399
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL6
Chain IDs:CA (auth: 6)
Chain Length:176
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0AG55
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL9
Gene (Uniprot):rplI
Chain IDs:DA (auth: 9)
Chain Length:149
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:9
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:23S ribosomal RNA
Chain IDs:FA (auth: R1)
Chain Length:2903
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:5S ribosomal RNA
Chain IDs:GA (auth: R2)
Chain Length:119
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:16S ribosomal RNA
Chain IDs:HA (auth: R3)
Chain Length:1539
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:tRNA
Chain IDs:IA (auth: T)
Chain Length:77
Number of Molecules:1
Biological Source:Escherichia coli
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Probable ATP-binding protein YbiT
Gene (Uniprot):ybiT
Chain IDs:JA (auth: Y)
Chain Length:530
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A9U3 Pfam ID:PF00005, PF12848
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS2
Gene (Uniprot):rpsB
Chain IDs:KA (auth: sb)
Chain Length:218
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7V0 Pfam ID:PF00318
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS3
Chain IDs:LA (auth: sc)
Chain Length:206
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7V3
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S4
Chain IDs:MA (auth: sd)
Chain Length:205
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7V8
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS5
Gene (Uniprot):rpsE
Chain IDs:NA (auth: se)
Chain Length:157
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, non-modified isoform
Gene (Uniprot):rpsF
Chain IDs:OA (auth: sf)
Chain Length:100
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P02358 Pfam ID:PF01250
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S7
Gene (Uniprot):rpsG
Chain IDs:PA (auth: sg)
Chain Length:151
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P02359 Pfam ID:PF00177
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S8
Chain IDs:QA (auth: sh)
Chain Length:129
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7W7
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS9
Chain IDs:RA (auth: si)
Chain Length:127
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7X3
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S10
Chain IDs:SA (auth: sj)
Chain Length:98
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7R5
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS11
Chain IDs:TA (auth: sk)
Chain Length:116
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7R9
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS12
Chain IDs:UA (auth: sl)
Chain Length:123
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7S3
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S13
Chain IDs:VA (auth: sm)
Chain Length:114
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7S9
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS14
Chain IDs:WA (auth: sn)
Chain Length:100
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0AG59
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS15
Gene (Uniprot):rpsO
Chain IDs:XA (auth: so)
Chain Length:88
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0ADZ4 Pfam ID:PF00312
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein bS16
Chain IDs:YA (auth: sp)
Chain Length:82
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7T3
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS17
Gene (Uniprot):rpsQ
Chain IDs:ZA (auth: sq)
Chain Length:80
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0AG63 Pfam ID:PF00366
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S18
Chain IDs:AB (auth: sr)
Chain Length:65
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7T7
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS19
Gene (Uniprot):rpsS
Chain IDs:BB (auth: ss)
Chain Length:80
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7U3 Pfam ID:PF00203
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S20
Chain IDs:CB (auth: st)
Chain Length:85
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7U7
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein bS21
Gene (Uniprot):rpsU
Chain IDs:DB (auth: su)
Chain Length:70
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
Primary Citation
E. coli initiation complex with EQ2-YbiT in Non-hydrolytic 2/PtIM(b) conformation
To Be Published ? ? ? (?)
Primary Citation of related structures
9NL7