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Cryo- EM structure of Mycobacterium smegmatis 30S ribosomal subunit (body 2) of 70S ribosome, bS1 and RafH.

Electron Microscopy
3.5Å resolution
PDB entry 8wi9 coloured by chain, front view.
PDB entry 8wi9 coloured by chain, side view.
PDB entry 8wi9 coloured by chain, top view.
Source organism: Mycolicibacterium smegmatis MC2 155
Assembly composition:
hetero 24-mer (preferred)
Entry contents: 23 distinct polypeptide molecules
1 distinct RNA molecule

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Assemblies

Assembly 1 (preferred)
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Multimeric state: hetero 24-mer
Accessible surface area: 298250.72 Å2
Buried surface area: 96488.88 Å2
Dissociation area: 1,438.3 Å2
Dissociation energy (ΔGdiss): -2.83 kcal/mol
Dissociation entropy (TΔSdiss): 13.61 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-279087

Macromolecules

Small ribosomal subunit protein bS1
Chain: b
Length: 479 amino acids
Theoretical weight: 53.38 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QYY6 (Residues: 1-479; Coverage: 100%)
Gene names: LJ00_19040, MSMEG_3833, MSMEI_3743, rpsA
Pfam: S1 RNA binding domain
Small ribosomal subunit protein bS1 in PDB entry 8wi9, assembly 1, front view.
Small ribosomal subunit protein bS1 in PDB entry 8wi9, assembly 1, side view.
Small ribosomal subunit protein bS1 in PDB entry 8wi9, assembly 1, top view.
PDBe-KB: UniProt Coverage View: A0QYY6  
147950100150200250300350400450
 
200400
UniProt
A0QYY6
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Ribosomal protein mS38 C-terminal domain-containing protein
Chain: v
Length: 33 amino acids
Theoretical weight: 4.16 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QR10 (Residues: 1-33; Coverage: 100%)
Gene name: MSMEG_0945
Pfam: Mitochondrial mRNA-processing protein COX24, C-terminal
Ribosomal protein mS38 C-terminal domain-containing protein in PDB entry 8wi9, assembly 1, front view.
Ribosomal protein mS38 C-terminal domain-containing protein in PDB entry 8wi9, assembly 1, side view.
Ribosomal protein mS38 C-terminal domain-containing protein in PDB entry 8wi9, assembly 1, top view.
PDBe-KB: UniProt Coverage View: A0QR10  
13351015202530
 
102030MGSVIKKRRKRMSKKKHRKLLRRTRVQRRKLGK
UniProt
A0QR10
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Small ribosomal subunit protein uS3
Chain: d
Length: 275 amino acids
Theoretical weight: 30.19 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QSD7 (Residues: 1-275; Coverage: 100%)
Gene names: MSMEG_1442, MSMEI_1406, rpsC
Pfam:
Small ribosomal subunit protein uS3 in PDB entry 8wi9, assembly 1, front view.
Small ribosomal subunit protein uS3 in PDB entry 8wi9, assembly 1, side view.
Small ribosomal subunit protein uS3 in PDB entry 8wi9, assembly 1, top view.
PDBe-KB: UniProt Coverage View: A0QSD7  
127520406080100120140160180200220240260
 
100200
UniProt
A0QSD7
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Small ribosomal subunit protein uS4
Chain: e
Length: 201 amino acids
Theoretical weight: 23.42 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QSL7 (Residues: 1-201; Coverage: 100%)
Gene names: MSMEG_1523, MSMEI_1487, rpsD
Pfam:
Small ribosomal subunit protein uS4 in PDB entry 8wi9, assembly 1, front view.
Small ribosomal subunit protein uS4 in PDB entry 8wi9, assembly 1, side view.
Small ribosomal subunit protein uS4 in PDB entry 8wi9, assembly 1, top view.
PDBe-KB: UniProt Coverage View: A0QSL7  
120120406080100120140160180200
 
50100150200
UniProt
A0QSL7
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Small ribosomal subunit protein uS5
Chain: f
Length: 214 amino acids
Theoretical weight: 21.95 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QSG6 (Residues: 1-214; Coverage: 100%)
Gene names: MSMEG_1472, MSMEI_1436, rpsE
Pfam:
Small ribosomal subunit protein uS5 in PDB entry 8wi9, assembly 1, front view.
Small ribosomal subunit protein uS5 in PDB entry 8wi9, assembly 1, side view.
Small ribosomal subunit protein uS5 in PDB entry 8wi9, assembly 1, top view.
PDBe-KB: UniProt Coverage View: A0QSG6  
121420406080100120140160180200
 
100200
UniProt
A0QSG6
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Small ribosomal subunit protein bS6
Chain: g
Length: 96 amino acids
Theoretical weight: 10.99 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0R7F9 (Residues: 1-90; Coverage: 100%)
Gene names: MSMEG_6897, MSMEI_6713, rpsF
Pfam: Ribosomal protein S6
Small ribosomal subunit protein bS6 in PDB entry 8wi9, assembly 1, front view.
Small ribosomal subunit protein bS6 in PDB entry 8wi9, assembly 1, side view.
Small ribosomal subunit protein bS6 in PDB entry 8wi9, assembly 1, top view.
PDBe-KB: UniProt Coverage View: A0R7F9  
196102030405060708090
 
50MRPYEIMVILDPTLDERTVAPSLETFLNVIRKDGGTVDKVDIWGRRRLAYEIAKHAEGIYAVIDVKAEPATVSELDRQLNLNESVLRTKVLRTDKH
UniProt
A0R7F9
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Small ribosomal subunit protein uS7
Chain: h
Length: 156 amino acids
Theoretical weight: 17.66 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QS97 (Residues: 1-156; Coverage: 100%)
Gene names: MSMEG_1399, MSMEI_1361, rpsG
Pfam: Ribosomal protein S7p/S5e
Small ribosomal subunit protein uS7 in PDB entry 8wi9, assembly 1, front view.
Small ribosomal subunit protein uS7 in PDB entry 8wi9, assembly 1, side view.
Small ribosomal subunit protein uS7 in PDB entry 8wi9, assembly 1, top view.
PDBe-KB: UniProt Coverage View: A0QS97  
115620406080100120140
 
50100150
UniProt
A0QS97
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Small ribosomal subunit protein uS8
Chain: i
Length: 132 amino acids
Theoretical weight: 14.49 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QSG3 (Residues: 1-132; Coverage: 100%)
Gene names: MSMEG_1469, MSMEI_1433, rpsH
Pfam: Ribosomal protein S8
Small ribosomal subunit protein uS8 in PDB entry 8wi9, assembly 1, front view.
Small ribosomal subunit protein uS8 in PDB entry 8wi9, assembly 1, side view.
Small ribosomal subunit protein uS8 in PDB entry 8wi9, assembly 1, top view.
PDBe-KB: UniProt Coverage View: A0QSG3  
1132102030405060708090100110120130
 
50100
UniProt
A0QSG3
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Small ribosomal subunit protein uS9
Chain: j
Length: 150 amino acids
Theoretical weight: 16.79 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QSP9 (Residues: 1-150; Coverage: 100%)
Gene names: MSMEG_1557, MSMEI_1520, rpsI
Pfam: Ribosomal protein S9/S16
Small ribosomal subunit protein uS9 in PDB entry 8wi9, assembly 1, front view.
Small ribosomal subunit protein uS9 in PDB entry 8wi9, assembly 1, side view.
Small ribosomal subunit protein uS9 in PDB entry 8wi9, assembly 1, top view.
PDBe-KB: UniProt Coverage View: A0QSP9  
115020406080100120140
 
50100150
UniProt
A0QSP9
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Small ribosomal subunit protein uS10
Chain: k
Length: 101 amino acids
Theoretical weight: 11.45 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QSD0 (Residues: 1-101; Coverage: 100%)
Gene names: MSMEG_1435, MSMEI_1399, rpsJ
Pfam: Ribosomal protein S10p/S20e
Small ribosomal subunit protein uS10 in PDB entry 8wi9, assembly 1, front view.
Small ribosomal subunit protein uS10 in PDB entry 8wi9, assembly 1, side view.
Small ribosomal subunit protein uS10 in PDB entry 8wi9, assembly 1, top view.
PDBe-KB: UniProt Coverage View: A0QSD0  
1101102030405060708090100
 
50100MAGQKIRIRLKAYDHEAIDASARKIVETVTRTGASVVGPVPLPTEKNVYCVIRSPHKYKDSREHFEMRTHKRLIDILDPTPKTVDALMRIDLPASVDVNIQ
UniProt
A0QSD0
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Small ribosomal subunit protein uS11
Chain: l
Length: 138 amino acids
Theoretical weight: 14.67 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QSL6 (Residues: 1-138; Coverage: 100%)
Gene names: MSMEG_1522, MSMEI_1486, rpsK
Pfam: Ribosomal protein S11
Small ribosomal subunit protein uS11 in PDB entry 8wi9, assembly 1, front view.
Small ribosomal subunit protein uS11 in PDB entry 8wi9, assembly 1, side view.
Small ribosomal subunit protein uS11 in PDB entry 8wi9, assembly 1, top view.
PDBe-KB: UniProt Coverage View: A0QSL6  
1138102030405060708090100110120130
 
50100
UniProt
A0QSL6
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Small ribosomal subunit protein uS12
Chain: m
Length: 124 amino acids
Theoretical weight: 13.9 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QS96 (Residues: 1-124; Coverage: 100%)
Gene names: MSMEG_1398, MSMEI_1360, rpsL
Pfam: Ribosomal protein S12/S23
Small ribosomal subunit protein uS12 in PDB entry 8wi9, assembly 1, front view.
Small ribosomal subunit protein uS12 in PDB entry 8wi9, assembly 1, side view.
Small ribosomal subunit protein uS12 in PDB entry 8wi9, assembly 1, top view.
PDBe-KB: UniProt Coverage View: A0QS96  
1124102030405060708090100110120
 
50100
UniProt
A0QS96
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Small ribosomal subunit protein uS13
Chain: n
Length: 124 amino acids
Theoretical weight: 14.25 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QSL5 (Residues: 1-124; Coverage: 100%)
Gene names: MSMEG_1521, MSMEI_1485, rpsM
Pfam: Ribosomal protein S13/S18
Small ribosomal subunit protein uS13 in PDB entry 8wi9, assembly 1, front view.
Small ribosomal subunit protein uS13 in PDB entry 8wi9, assembly 1, side view.
Small ribosomal subunit protein uS13 in PDB entry 8wi9, assembly 1, top view.
PDBe-KB: UniProt Coverage View: A0QSL5  
1124102030405060708090100110120
 
50100
UniProt
A0QSL5
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Small ribosomal subunit protein uS14B
Chain: o
Length: 61 amino acids
Theoretical weight: 6.98 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QSG2 (Residues: 1-61; Coverage: 100%)
Gene names: MSMEG_1468, MSMEI_1432, rpsN, rpsZ
Pfam: Ribosomal protein S14p/S29e
Small ribosomal subunit protein uS14B in PDB entry 8wi9, assembly 1, front view.
Small ribosomal subunit protein uS14B in PDB entry 8wi9, assembly 1, side view.
Small ribosomal subunit protein uS14B in PDB entry 8wi9, assembly 1, top view.
PDBe-KB: UniProt Coverage View: A0QSG2  
16151015202530354045505560
 
204060MAKKALVHKANKKPKFAVRAYTRCNKCGRPHSVYRKFGLCRICLREMAHAGELPGVQKSSW
UniProt
A0QSG2
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Small ribosomal subunit protein uS15
Chain: p
Length: 89 amino acids
Theoretical weight: 10.37 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QVQ3 (Residues: 1-89; Coverage: 100%)
Gene names: MSMEG_2654, MSMEI_2591, rpsO
Pfam: Ribosomal protein S15
Small ribosomal subunit protein uS15 in PDB entry 8wi9, assembly 1, front view.
Small ribosomal subunit protein uS15 in PDB entry 8wi9, assembly 1, side view.
Small ribosomal subunit protein uS15 in PDB entry 8wi9, assembly 1, top view.
PDBe-KB: UniProt Coverage View: A0QVQ3  
1891020304050607080
 
20406080MALTAEQKKEILGQYGLHDTDTGSPEAQVALLTKRIQDLTEHLKVHKHDHHSRRGLLLLVGRRRRLLKYVAQVDVARYRSLIERLGLRR
UniProt
A0QVQ3
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Small ribosomal subunit protein bS16
Chain: q
Length: 156 amino acids
Theoretical weight: 16.8 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QV37 (Residues: 1-156; Coverage: 100%)
Gene names: MSMEG_2435, MSMEI_2374, rpsP
Pfam: Ribosomal protein S16
Small ribosomal subunit protein bS16 in PDB entry 8wi9, assembly 1, front view.
Small ribosomal subunit protein bS16 in PDB entry 8wi9, assembly 1, side view.
Small ribosomal subunit protein bS16 in PDB entry 8wi9, assembly 1, top view.
PDBe-KB: UniProt Coverage View: A0QV37  
115620406080100120140
 
50100150
UniProt
A0QV37
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Small ribosomal subunit protein uS17
Chain: r
Length: 98 amino acids
Theoretical weight: 11.13 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QSE0 (Residues: 1-98; Coverage: 100%)
Gene names: MSMEG_1445, MSMEI_1409, rpsQ
Pfam: Ribosomal protein S17
Small ribosomal subunit protein uS17 in PDB entry 8wi9, assembly 1, front view.
Small ribosomal subunit protein uS17 in PDB entry 8wi9, assembly 1, side view.
Small ribosomal subunit protein uS17 in PDB entry 8wi9, assembly 1, top view.
PDBe-KB: UniProt Coverage View: A0QSE0  
198102030405060708090
 
50MADQKGPKYTPAAEKPRGRRKTAIGYVVSDKMQKTIVVELEDRKSHPLYGKIIRTTKKVKAHDENGEAGIGDRVSLMETRPLSATKRWRLVEILEKAK
UniProt
A0QSE0
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Small ribosomal subunit protein bS18B
Chain: s
Length: 84 amino acids
Theoretical weight: 9.52 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0R7F7 (Residues: 1-84; Coverage: 100%)
Gene names: MSMEG_6895, MSMEI_6711, rpsR1, rpsR2
Pfam: Ribosomal protein S18
Small ribosomal subunit protein bS18B in PDB entry 8wi9, assembly 1, front view.
Small ribosomal subunit protein bS18B in PDB entry 8wi9, assembly 1, side view.
Small ribosomal subunit protein bS18B in PDB entry 8wi9, assembly 1, top view.
PDBe-KB: UniProt Coverage View: A0R7F7  
1841020304050607080
 
20406080MAKSNKRRPAPEKPVKTRKCVFCSKKGQTIDYKDTALLRTYISERGKIRARRVTGNCVQHQRDIAVAVKNAREVALLPFGSSTR
UniProt
A0R7F7
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Small ribosomal subunit protein uS19
Chain: t
Length: 93 amino acids
Theoretical weight: 10.8 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QSD5 (Residues: 1-93; Coverage: 100%)
Gene names: MSMEG_1440, MSMEI_1404, rpsS
Pfam: Ribosomal protein S19
Small ribosomal subunit protein uS19 in PDB entry 8wi9, assembly 1, front view.
Small ribosomal subunit protein uS19 in PDB entry 8wi9, assembly 1, side view.
Small ribosomal subunit protein uS19 in PDB entry 8wi9, assembly 1, top view.
PDBe-KB: UniProt Coverage View: A0QSD5  
193102030405060708090
 
20406080MPRSLKKGPFVDDHLLKKVDVQNEKNTKQVIKTWSRRSTIIPDFIGHTFAVHDGRKHVPVFVTEAMVGHKLGEFAPTRTFKGHIKDDRKSKRR
UniProt
A0QSD5
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Small ribosomal subunit protein bS20
Chain: u
Length: 86 amino acids
Theoretical weight: 9.56 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0R102 (Residues: 1-86; Coverage: 100%)
Gene names: MSMEG_4571, MSMEI_4459, rpsT
Pfam: Ribosomal protein S20
Small ribosomal subunit protein bS20 in PDB entry 8wi9, assembly 1, front view.
Small ribosomal subunit protein bS20 in PDB entry 8wi9, assembly 1, side view.
Small ribosomal subunit protein bS20 in PDB entry 8wi9, assembly 1, top view.
PDBe-KB: UniProt Coverage View: A0R102  
1861020304050607080
 
20406080MANIKSQIKRIRTNERRRLRNQSVKSSLRTAIRGFREAVDAGDKDKASELLHATSRKLDKAASKGVIHPNQAANKKSALALALNKL
UniProt
A0R102
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Small ribosomal subunit protein uS2
Chain: c
Length: 277 amino acids
Theoretical weight: 30.15 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QVB8 (Residues: 1-277; Coverage: 100%)
Gene names: MSMEG_2519, MSMEI_2460, rpsB
Pfam: Ribosomal protein S2
Small ribosomal subunit protein uS2 in PDB entry 8wi9, assembly 1, front view.
Small ribosomal subunit protein uS2 in PDB entry 8wi9, assembly 1, side view.
Small ribosomal subunit protein uS2 in PDB entry 8wi9, assembly 1, top view.
PDBe-KB: UniProt Coverage View: A0QVB8  
127720406080100120140160180200220240260
 
100200
UniProt
A0QVB8
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Large ribosomal subunit protein bL31
Chain: x
Length: 11 amino acids
Theoretical weight: 1.34 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0R215 (Residues: 56-66; Coverage: 15%)
Gene names: MSMEG_4951, MSMEI_4823, rpmE
Large ribosomal subunit protein bL31 in PDB entry 8wi9, assembly 1, front view.
Large ribosomal subunit protein bL31 in PDB entry 8wi9, assembly 1, side view.
Large ribosomal subunit protein bL31 in PDB entry 8wi9, assembly 1, top view.
PDBe-KB: UniProt Coverage View: A0R215  
1111234567891011
 
510GRVARFEKRYG
UniProt
A0R215
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Sigma 54 modulation/S30EA ribosomal protein C-terminal domain-containing protein
Chain: w
Length: 264 amino acids
Theoretical weight: 29.9 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A0QZ86 (Residues: 1-258; Coverage: 100%)
Gene name: MSMEG_3935
Pfam:
Sigma 54 modulation/S30EA ribosomal protein C-terminal domain-containing protein in PDB entry 8wi9, assembly 1, front view.
Sigma 54 modulation/S30EA ribosomal protein C-terminal domain-containing protein in PDB entry 8wi9, assembly 1, side view.
Sigma 54 modulation/S30EA ribosomal protein C-terminal domain-containing protein in PDB entry 8wi9, assembly 1, top view.
PDBe-KB: UniProt Coverage View: A0QZ86  
126420406080100120140160180200220240260
 
100200
UniProt
A0QZ86
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RNA chain a
Name: 16S ribosomal RNA
Representative chains: a
Length: 1528 nucleotides
Theoretical weight: 495.37 KDa
16S ribosomal RNA in PDB entry 8wi9, assembly 1, front view.
16S ribosomal RNA in PDB entry 8wi9, assembly 1, side view.
16S ribosomal RNA in PDB entry 8wi9, assembly 1, top view.
115282004006008001,0001,2001,400
 
50010001500
Chains
Chain A (auth a)
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