9Q87 image
Entry Detail
PDB ID:
9Q87
EMDB ID:
EMD-15793
Keywords:
RIBOSOME
Title:
Principles of ion binding to RNA inferred from the analysis of a 1.55 Angstrom resolution bacterial ribosome structure - Part I: Mg2+
Biological Source:
Source Organism:
Escherichia coli B
PDB Version:
Deposition Date:
2025-02-23
Release Date:
2025-05-14
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
1.55 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
9Q87 validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein bL33
Chain IDs:X (auth: 0)
Chain Length:55
Number of Molecules:1
Biological Source:Escherichia coli B
UniProt ID:C3SME7 Pfam ID:PF00471
Protein Blast
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein bL34
Chain IDs:Y (auth: 1)
Chain Length:46
Number of Molecules:1
Biological Source:Escherichia coli B
UniProt ID:C3SLL2 Pfam ID:PF00468
Protein Blast
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein bL35
Chain IDs:Z (auth: 2)
Chain Length:65
Number of Molecules:1
Biological Source:Escherichia coli B
UniProt ID:C3T7Q2 Pfam ID:PF01632
Protein Blast
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein bL36
Chain IDs:AA (auth: 3)
Chain Length:38
Number of Molecules:1
Biological Source:Escherichia coli B
UniProt ID:A0A2X1PTA3 Pfam ID:PF00444
Protein Blast
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein uL11
Chain IDs:BA (auth: 5)
Chain Length:141
Number of Molecules:1
Biological Source:Escherichia coli B
UniProt ID:C3SIC7 Pfam ID:PF03946, PF00298
Polymer Type:polyribonucleotide
Description:A-site tRNA
Chain IDs:CA (auth: 6)
Chain Length:2
Number of Molecules:1
Biological Source:Escherichia coli B
Polymer Type:polyribonucleotide
Description:16S rRNA
Chain IDs:A
Chain Length:2908
Number of Molecules:1
Biological Source:Escherichia coli B
Protein Blast
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS2
Chain IDs:B
Chain Length:233
Number of Molecules:1
Biological Source:Escherichia coli B
UniProt ID:C3TPN2 Pfam ID:PF00318
Protein Blast
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS3
Chain IDs:C
Chain Length:273
Number of Molecules:1
Biological Source:Escherichia coli B
UniProt ID:C3SQX2 Pfam ID:PF07650, PF00189
Protein Blast
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS4
Chain IDs:D
Chain Length:206
Number of Molecules:1
Biological Source:Escherichia coli B
UniProt ID:C3SR62 Pfam ID:PF00163, PF01479
Protein Blast
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS5
Chain IDs:E
Chain Length:201
Number of Molecules:1
Biological Source:Escherichia coli B
UniProt ID:C3SR27 Pfam ID:PF00333, PF03719
Protein Blast
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein bS6, fully modified isoform
Chain IDs:F
Chain Length:135
Number of Molecules:1
Biological Source:Escherichia coli B
UniProt ID:P02358 Pfam ID:PF01250
Protein Blast
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS7
Chain IDs:G
Chain Length:177
Number of Molecules:1
Biological Source:Escherichia coli B
UniProt ID:P02359 Pfam ID:PF00177
Protein Blast
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS8
Chain IDs:H
Chain Length:130
Number of Molecules:1
Biological Source:Escherichia coli B
UniProt ID:C3SR12 Pfam ID:PF00410
Protein Blast
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS9
Chain IDs:I
Chain Length:130
Number of Molecules:1
Biological Source:Escherichia coli B
UniProt ID:C3SRY2 Pfam ID:PF00380
Protein Blast
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS10
Chain IDs:J
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli B
UniProt ID:C3SQT7 Pfam ID:PF00338
Protein Blast
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS11
Chain IDs:K
Chain Length:144
Number of Molecules:1
Biological Source:Escherichia coli B
UniProt ID:C3SR57 Pfam ID:PF00411
Protein Blast
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS12
Chain IDs:L
Chain Length:124
Number of Molecules:1
Biological Source:Escherichia coli B
UniProt ID:C3SQR7 Pfam ID:PF00164
Protein Blast
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS13
Chain IDs:M
Chain Length:127
Number of Molecules:1
Biological Source:Escherichia coli B
UniProt ID:C3SR52 Pfam ID:PF00416
Protein Blast
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS14
Chain IDs:N
Chain Length:101
Number of Molecules:1
Biological Source:Escherichia coli B
UniProt ID:A0A2X1PQW4 Pfam ID:PF00253
Protein Blast
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS15
Chain IDs:O
Chain Length:89
Number of Molecules:1
Biological Source:Escherichia coli B
UniProt ID:C3SSQ7 Pfam ID:PF00312
Protein Blast
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein bS16
Chain IDs:P
Chain Length:118
Number of Molecules:1
Biological Source:Escherichia coli B
UniProt ID:C3SYP2 Pfam ID:PF00886
Protein Blast
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS17
Chain IDs:Q
Chain Length:84
Number of Molecules:1
Biological Source:Escherichia coli B
UniProt ID:C3SQY7 Pfam ID:PF00366
Protein Blast
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein bS18
Chain IDs:R
Chain Length:75
Number of Molecules:1
Biological Source:Escherichia coli B
UniProt ID:P0A7T7 Pfam ID:PF01084
Protein Blast
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS19
Chain IDs:S
Chain Length:92
Number of Molecules:1
Biological Source:Escherichia coli B
UniProt ID:C3SQW2 Pfam ID:PF00203
Protein Blast
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein bS20
Chain IDs:T
Chain Length:87
Number of Molecules:1
Biological Source:Escherichia coli B
UniProt ID:C3TRH7 Pfam ID:PF01649
Protein Blast
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein bS21
Chain IDs:U
Chain Length:94
Number of Molecules:1
Biological Source:Escherichia coli B
UniProt ID:P68679 Pfam ID:PF01165
Polymer Type:polyribonucleotide
Description:mRNA
Chain IDs:V (auth: X)
Chain Length:6
Number of Molecules:1
Biological Source:Escherichia coli B
Polymer Type:polyribonucleotide
Description:P-site tRNA
Chain IDs:W (auth: Z)
Chain Length:77
Number of Molecules:1
Biological Source:Escherichia coli B
Polymer Type:polyribonucleotide
Description:23S rRNA
Chain IDs:DA (auth: a)
Chain Length:2908
Number of Molecules:1
Biological Source:Escherichia coli B
Polymer Type:polyribonucleotide
Description:5S rRNA
Chain IDs:EA (auth: b)
Chain Length:233
Number of Molecules:1
Biological Source:Escherichia coli B
Protein Blast
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein uL2
Chain IDs:FA (auth: c)
Chain Length:273
Number of Molecules:1
Biological Source:Escherichia coli B
UniProt ID:C3SQV7 Pfam ID:PF00181, PF03947
Protein Blast
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein uL3
Chain IDs:GA (auth: d)
Chain Length:206
Number of Molecules:1
Biological Source:Escherichia coli B
UniProt ID:C3SQU2 Pfam ID:PF00297
Protein Blast
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein uL4
Chain IDs:HA (auth: e)
Chain Length:201
Number of Molecules:1
Biological Source:Escherichia coli B
UniProt ID:C3SQU7 Pfam ID:PF00573
Protein Blast
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein uL5
Chain IDs:IA (auth: f)
Chain Length:135
Number of Molecules:1
Biological Source:Escherichia coli B
UniProt ID:C3SR02 Pfam ID:PF00281, PF00673
Protein Blast
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein uL6
Chain IDs:JA (auth: g)
Chain Length:177
Number of Molecules:1
Biological Source:Escherichia coli B
UniProt ID:C3SR17 Pfam ID:PF00347
Protein Blast
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein bL9
Chain IDs:KA (auth: h)
Chain Length:130
Number of Molecules:1
Biological Source:Escherichia coli B
UniProt ID:C3SFP2 Pfam ID:PF01281, PF03948
Protein Blast
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein uL13
Chain IDs:LA (auth: i)
Chain Length:130
Number of Molecules:1
Biological Source:Escherichia coli B
UniProt ID:C3SRX7 Pfam ID:PF00572
Protein Blast
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein uL14
Chain IDs:MA (auth: j)
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli B
UniProt ID:C3SQZ2 Pfam ID:PF00238
Protein Blast
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein uL15
Chain IDs:NA (auth: k)
Chain Length:144
Number of Molecules:1
Biological Source:Escherichia coli B
UniProt ID:A0A037Y8L6 Pfam ID:PF00828
Protein Blast
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein uL16
Chain IDs:OA (auth: l)
Chain Length:124
Number of Molecules:1
Biological Source:Escherichia coli B
UniProt ID:C3SQX7 Pfam ID:PF00252
Protein Blast
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein bL17
Chain IDs:PA (auth: m)
Chain Length:127
Number of Molecules:1
Biological Source:Escherichia coli B
UniProt ID:C3SR72 Pfam ID:PF01196
Protein Blast
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein uL18
Chain IDs:QA (auth: n)
Chain Length:101
Number of Molecules:1
Biological Source:Escherichia coli B
UniProt ID:C3SR22 Pfam ID:PF00861
Protein Blast
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein bL19
Chain IDs:RA (auth: o)
Chain Length:89
Number of Molecules:1
Biological Source:Escherichia coli B
UniProt ID:C3SYQ7 Pfam ID:PF01245
Protein Blast
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein bL20
Chain IDs:SA (auth: p)
Chain Length:118
Number of Molecules:1
Biological Source:Escherichia coli B
UniProt ID:C3T7Q7 Pfam ID:PF00453
Protein Blast
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein bL21
Chain IDs:TA (auth: q)
Chain Length:84
Number of Molecules:1
Biological Source:Escherichia coli B
UniProt ID:C3SSG2 Pfam ID:PF00829
Protein Blast
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein uL22
Chain IDs:UA (auth: r)
Chain Length:75
Number of Molecules:1
Biological Source:Escherichia coli B
UniProt ID:C3SQW7 Pfam ID:PF00237
Protein Blast
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein uL23
Chain IDs:VA (auth: s)
Chain Length:92
Number of Molecules:1
Biological Source:Escherichia coli B
UniProt ID:C3SQV2 Pfam ID:PF00276
Protein Blast
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein uL24
Chain IDs:WA (auth: t)
Chain Length:87
Number of Molecules:1
Biological Source:Escherichia coli B
UniProt ID:C3SQZ7 Pfam ID:PF00467, PF17136
Protein Blast
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein bL25
Chain IDs:XA (auth: u)
Chain Length:94
Number of Molecules:1
Biological Source:Escherichia coli B
UniProt ID:C3T3H7 Pfam ID:PF01386
Protein Blast
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein bL27
Chain IDs:YA (auth: v)
Chain Length:85
Number of Molecules:1
Biological Source:Escherichia coli B
UniProt ID:C3SSG7 Pfam ID:PF01016
Protein Blast
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein bL28
Chain IDs:ZA (auth: w)
Chain Length:78
Number of Molecules:1
Biological Source:Escherichia coli B
UniProt ID:C3SME2 Pfam ID:PF00830
Protein Blast
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein uL29
Chain IDs:AB (auth: x)
Chain Length:6
Number of Molecules:1
Biological Source:Escherichia coli B
UniProt ID:C3SQY2 Pfam ID:PF00831
Protein Blast
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein uL30
Chain IDs:BB (auth: y)
Chain Length:59
Number of Molecules:1
Biological Source:Escherichia coli B
UniProt ID:C3SR32 Pfam ID:PF00327
Protein Blast
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein bL32
Chain IDs:CB (auth: z)
Chain Length:77
Number of Molecules:1
Biological Source:Escherichia coli B
UniProt ID:C3TE02 Pfam ID:PF01783
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
2MG A G modified residue
4D4 OA ARG modified residue
4OC A C modified residue
4SU W U modified residue
5MC A C modified residue
5MU W U modified residue
D2T L ASP modified residue
G7M A G modified residue
H2U W U modified residue
MA6 A A modified residue
MEQ GA GLN modified residue
OMC W C modified residue
PSU A U modified residue
UR3 A U modified residue
Ligand Molecules
K
MG
ZN
Primary Citation
Principles of ion binding to RNA inferred from the analysis of a 1.55 Angs. resolution bacterial ribosome structure - Part I: Mg2+.
Nucleic Acids Res ? ? ? (2024)
DOI: 10.1093/nar/gkae1235
Primary Citation of related structures
8B0X