9FY3 image
Deposition Date 2024-07-02
Release Date 2026-01-14
Last Version Date 2026-01-14
Entry Detail
PDB ID:
9FY3
Keywords:
RIBOSOME
Title:
Structure of CliM-stalled Bacillus subtilis 70S ribosome with tRNA-Tyr in the A-site
Biological Source:
Source Organism(s):
Clostridioides difficile 630 (Taxon ID: 272563)
Bacillus subtilis subsp. subtilis str. 168 (Taxon ID: 224308)
Expression System(s):
Bacillus subtilis subsp. subtilis str. 168
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
2.80 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
9FY3 validation report
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL32
Gene (Uniprot):rpmF
Chain IDs:A (auth: 0)
Chain Length:59
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:O34687 Pfam ID:PF01783
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L33 1
Gene (Uniprot):rpmGA
Chain IDs:B (auth: 1)
Chain Length:49
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P56849 Pfam ID:PF00471
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L34
Gene (Uniprot):rpmH
Chain IDs:C (auth: 2)
Chain Length:44
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P05647 Pfam ID:PF00468
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L35
Gene (Uniprot):rpmI
Chain IDs:D (auth: 3)
Chain Length:66
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P55874 Pfam ID:PF01632
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L36
Gene (Uniprot):rpmJ
Chain IDs:E (auth: 4)
Chain Length:37
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P20278 Pfam ID:PF00444
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Nascent Chain CliM
Gene (Uniprot):KRM00_002591, SAMEA1402366_02051, SAMEA1402399_03315, SAMEA3375112_02550
Chain IDs:F (auth: 5)
Chain Length:38
Number of Molecules:1
Biological Source:Clostridioides difficile 630
UniProt ID:A0A9Q7T0I1
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L31
Gene (Uniprot):rpmE
Chain IDs:G (auth: 6)
Chain Length:66
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:Q03223 Pfam ID:PF01197
Polymer Type:polyribonucleotide
Molecule:mRNA
Chain IDs:WA (auth: 7)
Chain Length:9
Number of Molecules:1
Biological Source:Clostridioides difficile 630
Polymer Type:polyribonucleotide
Molecule:A-site tRNA-Tyr
Chain IDs:XA (auth: 9)
Chain Length:85
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
Polymer Type:polyribonucleotide
Molecule:23S rRNA
Chain IDs:TA (auth: A)
Chain Length:2928
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
Polymer Type:polyribonucleotide
Molecule:5S rRNA
Chain IDs:H (auth: B)
Chain Length:112
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL2
Gene (Uniprot):rplB
Chain IDs:I (auth: C)
Chain Length:277
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P42919 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:J (auth: D)
Chain Length:209
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P42920 Pfam ID:PF00297
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4
Gene (Uniprot):rplD
Chain IDs:K (auth: E)
Chain Length:207
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P42921 Pfam ID:PF00573
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5
Gene (Uniprot):rplE
Chain IDs:L (auth: F)
Chain Length:95
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P12877 Pfam ID:PF00281, PF00673
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL6
Gene (Uniprot):rplF
Chain IDs:M (auth: G)
Chain Length:179
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P46898 Pfam ID:PF00347
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13
Gene (Uniprot):rplM
Chain IDs:N (auth: J)
Chain Length:145
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P70974 Pfam ID:PF00572
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Gene (Uniprot):rplN
Chain IDs:O (auth: K)
Chain Length:131
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P12875 Pfam ID:PF00238
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15
Gene (Uniprot):rplO
Chain IDs:P (auth: L)
Chain Length:146
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P19946 Pfam ID:PF00828
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16
Gene (Uniprot):rplP
Chain IDs:Q (auth: M)
Chain Length:121
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P14577 Pfam ID:PF00252
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L17
Gene (Uniprot):rplQ
Chain IDs:R (auth: N)
Chain Length:61
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P20277 Pfam ID:PF01196
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18
Gene (Uniprot):rplR
Chain IDs:S (auth: O)
Chain Length:120
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P46899 Pfam ID:PF00861
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19
Gene (Uniprot):rplS
Chain IDs:T (auth: P)
Chain Length:115
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:O31742 Pfam ID:PF01245
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL20
Gene (Uniprot):rplT
Chain IDs:U (auth: Q)
Chain Length:119
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P55873 Pfam ID:PF00453
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L21
Gene (Uniprot):rplU
Chain IDs:V (auth: R)
Chain Length:79
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P26908 Pfam ID:PF00829
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22
Gene (Uniprot):rplV
Chain IDs:W (auth: S)
Chain Length:113
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P42060 Pfam ID:PF00237
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL23
Gene (Uniprot):rplW
Chain IDs:X (auth: T)
Chain Length:88
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P42924 Pfam ID:PF00276
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24
Gene (Uniprot):rplX
Chain IDs:Y (auth: U)
Chain Length:103
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P0CI78 Pfam ID:PF00467, PF17136
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL27
Gene (Uniprot):rpmA
Chain IDs:ZA (auth: W)
Chain Length:94
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P05657 Pfam ID:PF01016
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL28
Gene (Uniprot):rpmB
Chain IDs:Z (auth: X)
Chain Length:62
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P37807 Pfam ID:PF00830
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29
Gene (Uniprot):rpmC
Chain IDs:AA (auth: Y)
Chain Length:66
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P12873 Pfam ID:PF00831
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL30
Gene (Uniprot):rpmD
Chain IDs:BA (auth: Z)
Chain Length:59
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P19947 Pfam ID:PF00327
Polymer Type:polyribonucleotide
Molecule:16S rRNA
Chain IDs:YA (auth: a)
Chain Length:2928
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Gene (Uniprot):rpsB
Chain IDs:UA (auth: b)
Chain Length:112
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P21464 Pfam ID:PF00318
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS3
Gene (Uniprot):rpsC
Chain IDs:CA (auth: c)
Chain Length:277
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P21465 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:AB (auth: d)
Chain Length:209
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P21466 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:DA (auth: e)
Chain Length:207
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P21467 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:EA (auth: f)
Chain Length:95
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P21468 Pfam ID:PF01250
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS7
Gene (Uniprot):rpsG
Chain IDs:FA (auth: g)
Chain Length:179
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P21469 Pfam ID:PF00177
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S8
Gene (Uniprot):rpsH
Chain IDs:GA (auth: h)
Chain Length:132
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P12879 Pfam ID:PF00410
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS9
Gene (Uniprot):rpsI
Chain IDs:HA (auth: i)
Chain Length:130
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P21470 Pfam ID:PF00380
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S10
Gene (Uniprot):rpsJ
Chain IDs:IA (auth: j)
Chain Length:145
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P21471 Pfam ID:PF00338
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S11
Gene (Uniprot):rpsK
Chain IDs:JA (auth: k)
Chain Length:131
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P04969 Pfam ID:PF00411
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS12
Gene (Uniprot):rpsL
Chain IDs:KA (auth: l)
Chain Length:146
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P21472 Pfam ID:PF00164
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS13
Gene (Uniprot):rpsM
Chain IDs:LA (auth: m)
Chain Length:121
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P20282 Pfam ID:PF00416
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S14
Gene (Uniprot):rpsN1
Chain IDs:MA (auth: n)
Chain Length:61
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P12878 Pfam ID:PF00253
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S15
Gene (Uniprot):rpsO
Chain IDs:NA (auth: o)
Chain Length:120
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P21473 Pfam ID:PF00312
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S16
Gene (Uniprot):rpsP
Chain IDs:OA (auth: p)
Chain Length:115
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P21474 Pfam ID:PF00886
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S17
Gene (Uniprot):rpsQ
Chain IDs:PA (auth: q)
Chain Length:119
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P12874 Pfam ID:PF00366
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S18
Gene (Uniprot):rpsR
Chain IDs:QA (auth: r)
Chain Length:79
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P21475 Pfam ID:PF01084
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S19
Gene (Uniprot):rpsS
Chain IDs:VA (auth: s)
Chain Length:113
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P21476 Pfam ID:PF00203
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S20
Gene (Uniprot):rpsT
Chain IDs:RA (auth: t)
Chain Length:88
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
UniProt ID:P21477 Pfam ID:PF01649
Polymer Type:polyribonucleotide
Molecule:P-site tRNA-Phe
Chain IDs:SA (auth: v)
Chain Length:76
Number of Molecules:1
Biological Source:Bacillus subtilis subsp. subtilis str. 168
Ligand Molecules
ZN
Primary Citation
The arrest peptide CliM employs extensive compaction and induces ribosomal stalling by secondary structure formation
To Be Published ? ? ? (?)
Primary Citation of related structures
9FY3
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