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Assembly intermediate of human mitochondrial ribosome small subunit without mS37 in complex with RBFA and METTL15 conformation b

Electron Microscopy
3.06Å resolution
PDB entry 7pny coloured by chain, front view.
PDB entry 7pny coloured by chain, side view.
PDB entry 7pny coloured by chain, top view.
Source organism: Homo sapiens
Assembly composition:
hetero 32-mer (preferred)
Entry contents: 31 distinct polypeptide molecules
1 distinct RNA molecule

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Assemblies

Assembly 1 (preferred)
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Multimeric state: hetero 32-mer
Accessible surface area: 374873.41 Å2
Buried surface area: 218327.18 Å2
Dissociation area: 1,591.94 Å2
Dissociation energy (ΔGdiss): 15.31 kcal/mol
Dissociation entropy (TΔSdiss): 15.01 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-215624

Macromolecules

Small ribosomal subunit protein uS2m
Chain: B
Length: 296 amino acids
Theoretical weight: 33.3 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9Y399 (Residues: 1-296; Coverage: 100%)
Gene names: CGI-91, MRPS2
Pfam: Ribosomal protein S2
InterPro:
Small ribosomal subunit protein uS2m in PDB entry 7pny, assembly 1, front view.
Small ribosomal subunit protein uS2m in PDB entry 7pny, assembly 1, side view.
Small ribosomal subunit protein uS2m in PDB entry 7pny, assembly 1, top view.
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Small ribosomal subunit protein uS3m
Chain: C
Length: 167 amino acids
Theoretical weight: 19.05 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q96EL2 (Residues: 1-167; Coverage: 100%)
Gene names: HSPC335, MRPS24
Pfam: Mitochondrial ribosome subunit S24
InterPro: Small ribosomal subunit protein uS3m, metazoan
Small ribosomal subunit protein uS3m in PDB entry 7pny, assembly 1, front view.
Small ribosomal subunit protein uS3m in PDB entry 7pny, assembly 1, side view.
Small ribosomal subunit protein uS3m in PDB entry 7pny, assembly 1, top view.
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Small ribosomal subunit protein uS5m
Chain: D
Length: 430 amino acids
Theoretical weight: 48.09 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P82675 (Residues: 1-430; Coverage: 100%)
Gene name: MRPS5
Pfam:
InterPro:
Small ribosomal subunit protein uS5m in PDB entry 7pny, assembly 1, front view.
Small ribosomal subunit protein uS5m in PDB entry 7pny, assembly 1, side view.
Small ribosomal subunit protein uS5m in PDB entry 7pny, assembly 1, top view.
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Small ribosomal subunit protein bS6m
Chain: E
Length: 125 amino acids
Theoretical weight: 14.25 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P82932 (Residues: 1-125; Coverage: 100%)
Gene names: C21orf101, MRPS6, RPMS6
Pfam: Ribosomal protein S6
InterPro:
Small ribosomal subunit protein bS6m in PDB entry 7pny, assembly 1, front view.
Small ribosomal subunit protein bS6m in PDB entry 7pny, assembly 1, side view.
Small ribosomal subunit protein bS6m in PDB entry 7pny, assembly 1, top view.
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Small ribosomal subunit protein uS7m
Chain: F
Length: 242 amino acids
Theoretical weight: 28.19 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9Y2R9 (Residues: 1-242; Coverage: 100%)
Gene name: MRPS7
Pfam: Ribosomal protein S7p/S5e
InterPro:
Small ribosomal subunit protein uS7m in PDB entry 7pny, assembly 1, front view.
Small ribosomal subunit protein uS7m in PDB entry 7pny, assembly 1, side view.
Small ribosomal subunit protein uS7m in PDB entry 7pny, assembly 1, top view.
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Small ribosomal subunit protein uS9m
Chain: G
Length: 396 amino acids
Theoretical weight: 45.91 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P82933 (Residues: 1-396; Coverage: 100%)
Gene names: MRPS9, RPMS9
Pfam: Ribosomal protein S9/S16
InterPro:
Small ribosomal subunit protein uS9m in PDB entry 7pny, assembly 1, front view.
Small ribosomal subunit protein uS9m in PDB entry 7pny, assembly 1, side view.
Small ribosomal subunit protein uS9m in PDB entry 7pny, assembly 1, top view.
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Small ribosomal subunit protein uS10m
Chain: H
Length: 201 amino acids
Theoretical weight: 23.03 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P82664 (Residues: 1-201; Coverage: 100%)
Gene names: MRPS10, MSTP040
Pfam: Ribosomal protein S10p/S20e
InterPro:
Small ribosomal subunit protein uS10m in PDB entry 7pny, assembly 1, front view.
Small ribosomal subunit protein uS10m in PDB entry 7pny, assembly 1, side view.
Small ribosomal subunit protein uS10m in PDB entry 7pny, assembly 1, top view.
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Small ribosomal subunit protein uS11m
Chain: I
Length: 194 amino acids
Theoretical weight: 20.66 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P82912 (Residues: 1-194; Coverage: 100%)
Gene names: HCC2, MRPS11, RPMS11
Pfam: Ribosomal protein S11
InterPro:
Small ribosomal subunit protein uS11m in PDB entry 7pny, assembly 1, front view.
Small ribosomal subunit protein uS11m in PDB entry 7pny, assembly 1, side view.
Small ribosomal subunit protein uS11m in PDB entry 7pny, assembly 1, top view.
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Small ribosomal subunit protein uS12m
Chain: J
Length: 138 amino acids
Theoretical weight: 15.2 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O15235 (Residues: 1-138; Coverage: 100%)
Gene names: MRPS12, RPMS12, RPSM12
Pfam: Ribosomal protein S12/S23
InterPro:
Small ribosomal subunit protein uS12m in PDB entry 7pny, assembly 1, front view.
Small ribosomal subunit protein uS12m in PDB entry 7pny, assembly 1, side view.
Small ribosomal subunit protein uS12m in PDB entry 7pny, assembly 1, top view.
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Small ribosomal subunit protein uS14m
Chain: K
Length: 128 amino acids
Theoretical weight: 15.17 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O60783 (Residues: 1-128; Coverage: 100%)
Gene name: MRPS14
Pfam: Ribosomal protein S14p/S29e
InterPro: Small ribosomal subunit protein uS14
Small ribosomal subunit protein uS14m in PDB entry 7pny, assembly 1, front view.
Small ribosomal subunit protein uS14m in PDB entry 7pny, assembly 1, side view.
Small ribosomal subunit protein uS14m in PDB entry 7pny, assembly 1, top view.
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Small ribosomal subunit protein uS15m
Chain: L
Length: 257 amino acids
Theoretical weight: 29.9 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P82914 (Residues: 1-257; Coverage: 100%)
Gene names: DC37, MRPS15, RPMS15
Pfam: Ribosomal protein S15
InterPro:
Small ribosomal subunit protein uS15m in PDB entry 7pny, assembly 1, front view.
Small ribosomal subunit protein uS15m in PDB entry 7pny, assembly 1, side view.
Small ribosomal subunit protein uS15m in PDB entry 7pny, assembly 1, top view.
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Small ribosomal subunit protein bS16m
Chain: M
Length: 137 amino acids
Theoretical weight: 15.37 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9Y3D3 (Residues: 1-137; Coverage: 100%)
Gene names: CGI-132, MRPS16, RPMS16
Pfam: Ribosomal protein S16
InterPro:
Small ribosomal subunit protein bS16m in PDB entry 7pny, assembly 1, front view.
Small ribosomal subunit protein bS16m in PDB entry 7pny, assembly 1, side view.
Small ribosomal subunit protein bS16m in PDB entry 7pny, assembly 1, top view.
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Small ribosomal subunit protein uS17m
Chain: N
Length: 130 amino acids
Theoretical weight: 14.53 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9Y2R5 (Residues: 1-130; Coverage: 100%)
Gene names: HSPC011, MRPS17, RPMS17
Pfam: Ribosomal protein S17
InterPro:
Small ribosomal subunit protein uS17m in PDB entry 7pny, assembly 1, front view.
Small ribosomal subunit protein uS17m in PDB entry 7pny, assembly 1, side view.
Small ribosomal subunit protein uS17m in PDB entry 7pny, assembly 1, top view.
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Small ribosomal subunit protein mS40
Chain: O
Length: 258 amino acids
Theoretical weight: 29.44 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9Y676 (Residues: 1-258; Coverage: 100%)
Gene names: C6orf14, HSPC183, MRPS18B, PTD017
Pfam: Ribosomal protein S18
InterPro:
Small ribosomal subunit protein mS40 in PDB entry 7pny, assembly 1, front view.
Small ribosomal subunit protein mS40 in PDB entry 7pny, assembly 1, side view.
Small ribosomal subunit protein mS40 in PDB entry 7pny, assembly 1, top view.
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Small ribosomal subunit protein bS18m
Chain: P
Length: 142 amino acids
Theoretical weight: 15.88 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9Y3D5 (Residues: 1-142; Coverage: 100%)
Gene names: CGI-134, MRPS18C
Pfam: Ribosomal protein S18
InterPro:
Small ribosomal subunit protein bS18m in PDB entry 7pny, assembly 1, front view.
Small ribosomal subunit protein bS18m in PDB entry 7pny, assembly 1, side view.
Small ribosomal subunit protein bS18m in PDB entry 7pny, assembly 1, top view.
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Small ribosomal subunit protein bS21m
Chain: Q
Length: 86 amino acids
Theoretical weight: 10.68 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P82921 (Residues: 2-87; Coverage: 99%)
Gene names: MDS016, MRPS21, RPMS21
Pfam: Ribosomal protein S21
InterPro:
Small ribosomal subunit protein bS21m in PDB entry 7pny, assembly 1, front view.
Small ribosomal subunit protein bS21m in PDB entry 7pny, assembly 1, side view.
Small ribosomal subunit protein bS21m in PDB entry 7pny, assembly 1, top view.
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Small ribosomal subunit protein mS22
Chain: R
Length: 360 amino acids
Theoretical weight: 41.34 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P82650 (Residues: 1-360; Coverage: 100%)
Gene names: C3orf5, GK002, MRPS22, RPMS22
Pfam: Mitochondrial 28S ribosomal protein S22
InterPro: Small ribosomal subunit protein mS22
Small ribosomal subunit protein mS22 in PDB entry 7pny, assembly 1, front view.
Small ribosomal subunit protein mS22 in PDB entry 7pny, assembly 1, side view.
Small ribosomal subunit protein mS22 in PDB entry 7pny, assembly 1, top view.
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Small ribosomal subunit protein mS23
Chain: S
Length: 190 amino acids
Theoretical weight: 21.81 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9Y3D9 (Residues: 1-190; Coverage: 100%)
Gene names: CGI-138, HSPC329, MRPS23
Pfam: Mitochondrial ribosomal protein S23
InterPro:
Small ribosomal subunit protein mS23 in PDB entry 7pny, assembly 1, front view.
Small ribosomal subunit protein mS23 in PDB entry 7pny, assembly 1, side view.
Small ribosomal subunit protein mS23 in PDB entry 7pny, assembly 1, top view.
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Small ribosomal subunit protein mS25
Chain: T
Length: 173 amino acids
Theoretical weight: 20.15 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P82663 (Residues: 1-173; Coverage: 100%)
Gene names: MRPS25, RPMS25
Pfam: Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain
InterPro:
Small ribosomal subunit protein mS25 in PDB entry 7pny, assembly 1, front view.
Small ribosomal subunit protein mS25 in PDB entry 7pny, assembly 1, side view.
Small ribosomal subunit protein mS25 in PDB entry 7pny, assembly 1, top view.
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Small ribosomal subunit protein mS26
Chain: U
Length: 205 amino acids
Theoretical weight: 24.26 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9BYN8 (Residues: 1-205; Coverage: 100%)
Gene names: C20orf193, MRPS26, RPMS13
Pfam: Mitochondrial ribosome subunit S26
InterPro: Small ribosomal subunit protein mS26
Small ribosomal subunit protein mS26 in PDB entry 7pny, assembly 1, front view.
Small ribosomal subunit protein mS26 in PDB entry 7pny, assembly 1, side view.
Small ribosomal subunit protein mS26 in PDB entry 7pny, assembly 1, top view.
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Small ribosomal subunit protein mS27
Chain: V
Length: 414 amino acids
Theoretical weight: 47.67 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q92552 (Residues: 1-414; Coverage: 100%)
Gene names: KIAA0264, MRPS27
Pfam: Mitochondrial 28S ribosomal protein S27
InterPro:
Small ribosomal subunit protein mS27 in PDB entry 7pny, assembly 1, front view.
Small ribosomal subunit protein mS27 in PDB entry 7pny, assembly 1, side view.
Small ribosomal subunit protein mS27 in PDB entry 7pny, assembly 1, top view.
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Small ribosomal subunit protein bS1m
Chain: W
Length: 187 amino acids
Theoretical weight: 20.88 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9Y2Q9 (Residues: 1-187; Coverage: 100%)
Gene names: HSPC007, MRPS28, MRPS35
Pfam: Mitochondrial ribosomal protein MRP-S35
InterPro: Small ribosomal subunit protein bS1m
Small ribosomal subunit protein bS1m in PDB entry 7pny, assembly 1, front view.
Small ribosomal subunit protein bS1m in PDB entry 7pny, assembly 1, side view.
Small ribosomal subunit protein bS1m in PDB entry 7pny, assembly 1, top view.
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Small ribosomal subunit protein mS29
Chain: X
Length: 398 amino acids
Theoretical weight: 45.63 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P51398 (Residues: 1-398; Coverage: 100%)
Gene names: DAP3, MRPS29
Pfam: Mitochondrial ribosomal death-associated protein 3
InterPro:
Small ribosomal subunit protein mS29 in PDB entry 7pny, assembly 1, front view.
Small ribosomal subunit protein mS29 in PDB entry 7pny, assembly 1, side view.
Small ribosomal subunit protein mS29 in PDB entry 7pny, assembly 1, top view.
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Small ribosomal subunit protein mS31
Chain: Y
Length: 395 amino acids
Theoretical weight: 45.39 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q92665 (Residues: 1-395; Coverage: 100%)
Gene names: IMOGN38, MRPS31
Pfam: Mitochondrial 28S ribosomal protein S31
InterPro: Mitochondrial 28S ribosomal protein S31
Small ribosomal subunit protein mS31 in PDB entry 7pny, assembly 1, front view.
Small ribosomal subunit protein mS31 in PDB entry 7pny, assembly 1, side view.
Small ribosomal subunit protein mS31 in PDB entry 7pny, assembly 1, top view.
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Small ribosomal subunit protein mS33
Chain: Z
Length: 106 amino acids
Theoretical weight: 12.66 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9Y291 (Residues: 1-106; Coverage: 100%)
Gene names: CGI-139, MRPS33, PTD003
Pfam: Mitochondrial ribosomal subunit S27
InterPro: Small ribosomal subunit protein mS33
Small ribosomal subunit protein mS33 in PDB entry 7pny, assembly 1, front view.
Small ribosomal subunit protein mS33 in PDB entry 7pny, assembly 1, side view.
Small ribosomal subunit protein mS33 in PDB entry 7pny, assembly 1, top view.
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Small ribosomal subunit protein mS34
Chain: 0
Length: 218 amino acids
Theoretical weight: 25.7 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P82930 (Residues: 1-218; Coverage: 100%)
Gene name: MRPS34
Pfam: Mitochondrial 28S ribosomal protein S34
InterPro: Small ribosomal subunit protein mS34
Small ribosomal subunit protein mS34 in PDB entry 7pny, assembly 1, front view.
Small ribosomal subunit protein mS34 in PDB entry 7pny, assembly 1, side view.
Small ribosomal subunit protein mS34 in PDB entry 7pny, assembly 1, top view.
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Small ribosomal subunit protein mS35
Chain: 1
Length: 323 amino acids
Theoretical weight: 36.9 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P82673 (Residues: 1-323; Coverage: 100%)
Gene names: HDCMD11P, MDS023, MRPS28, MRPS35, PSEC0213
Pfam: Mitochondrial ribosomal subunit protein
InterPro:
Small ribosomal subunit protein mS35 in PDB entry 7pny, assembly 1, front view.
Small ribosomal subunit protein mS35 in PDB entry 7pny, assembly 1, side view.
Small ribosomal subunit protein mS35 in PDB entry 7pny, assembly 1, top view.
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Small ribosomal subunit protein mS38
Chain: 3
Length: 199 amino acids
Theoretical weight: 22.4 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9NWT8 (Residues: 1-199; Coverage: 100%)
Gene names: AIP, AKIP, AURKAIP1, MRPS38
Pfam: Mitochondrial mRNA-processing protein COX24, C-terminal
InterPro: Ribosomal protein mS38, C-terminal
Small ribosomal subunit protein mS38 in PDB entry 7pny, assembly 1, front view.
Small ribosomal subunit protein mS38 in PDB entry 7pny, assembly 1, side view.
Small ribosomal subunit protein mS38 in PDB entry 7pny, assembly 1, top view.
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Small ribosomal subunit protein mS39
Chain: 4
Length: 689 amino acids
Theoretical weight: 78.65 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q96EY7 (Residues: 1-689; Coverage: 100%)
Gene names: MRPS39, PTCD3, TRG15
Pfam:
InterPro:
Small ribosomal subunit protein mS39 in PDB entry 7pny, assembly 1, front view.
Small ribosomal subunit protein mS39 in PDB entry 7pny, assembly 1, side view.
Small ribosomal subunit protein mS39 in PDB entry 7pny, assembly 1, top view.
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Putative ribosome-binding factor A, mitochondrial
Chain: a
Length: 343 amino acids
Theoretical weight: 38.42 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q8N0V3 (Residues: 1-343; Coverage: 100%)
Gene names: C18orf22, RBFA
Pfam: Ribosome-binding factor A
InterPro:
Putative ribosome-binding factor A, mitochondrial in PDB entry 7pny, assembly 1, front view.
Putative ribosome-binding factor A, mitochondrial in PDB entry 7pny, assembly 1, side view.
Putative ribosome-binding factor A, mitochondrial in PDB entry 7pny, assembly 1, top view.
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12S rRNA N4-methylcytidine (m4C) methyltransferase
Chain: b
Length: 407 amino acids
Theoretical weight: 46.18 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: A6NJ78 (Residues: 1-407; Coverage: 100%)
Gene names: METT5D1, METTL15
Pfam: MraW methylase family
InterPro:
12S rRNA N4-methylcytidine (m4C) methyltransferase in PDB entry 7pny, assembly 1, front view.
12S rRNA N4-methylcytidine (m4C) methyltransferase in PDB entry 7pny, assembly 1, side view.
12S rRNA N4-methylcytidine (m4C) methyltransferase in PDB entry 7pny, assembly 1, top view.
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RNA chain A
Name: 12S mitochondrial rRNA
Representative chains: A
Length: 955 nucleotides
Theoretical weight: 306.55 KDa
Rfam: Bacterial small subunit ribosomal RNA
12S mitochondrial rRNA in PDB entry 7pny, assembly 1, front view.
12S mitochondrial rRNA in PDB entry 7pny, assembly 1, side view.
12S mitochondrial rRNA in PDB entry 7pny, assembly 1, top view.
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