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Human TOP3B-TDRD3 core complex in DNA rejoining state with ssDNA 5'-GACAGATATT-3

Electron Microscopy
3.01Å resolution
PDB entry 9cak coloured by chain, front view.
PDB entry 9cak coloured by chain, side view.
PDB entry 9cak coloured by chain, top view.
Source organism: Homo sapiens
Assembly composition:
hetero tetramer (preferred)
Entry contents: 2 distinct polypeptide molecules
2 distinct DNA molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: Tudor domain-containing protein 3 and DNA topoisomerase 3-beta-1 and DNA
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Multimeric state: hetero tetramer
Accessible surface area: 37264.92 Å2
Buried surface area: 4900.56 Å2
Dissociation area: 1,301.03 Å2
Dissociation energy (ΔGdiss): -0.4 kcal/mol
Dissociation entropy (TΔSdiss): 19.36 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-284810

Macromolecules

DNA topoisomerase 3-beta-1
Chain: A
Length: 612 amino acids
Theoretical weight: 69.12 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: O95985 (Residues: 1-611; Coverage: 71%)
Gene names: TOP3B, TOP3B1
Pfam:
DNA topoisomerase 3-beta-1 in PDB entry 9cak, assembly 1, front view.
DNA topoisomerase 3-beta-1 in PDB entry 9cak, assembly 1, side view.
DNA topoisomerase 3-beta-1 in PDB entry 9cak, assembly 1, top view.
PDBe-KB: UniProt Coverage View: O95985  
161250100150200250300350400450500550600
 
200400600VMKTVLMVAEMPSLAQSIAKILSRGSLSSHKGLNGACSVHEYTGTFAGQPVRFKMTSVCGHVMTLDFLGKYNKWDKVDPAELFSQAPTEKKEANPKLNMVKFLQVEGRGCDYIVLWLDCDKEGENICFEVLDAVLPVMNKAHGGEKTVFRARFSSITDTDICNAMACLGEPDHNEALSVDARQELDLRIGCAFTRFQTKYFQGKYGDLDSSLISFGPCQTPTLGFCVERHDKIQSFKPETYWVLQAKVNTDKDRSLLLDWDRVRVFDREIAQMFLNMTKLEKEAQVEATSRKEKAKQRPLALNTVEMLRVASSSLGMGPQHAMQTAERLYTQGYIS*PRTETTHYPENFDLKGSLRQQANHPYWADTVKRLLAEGINRPRKGHDAGDHPPITPMKSATEAELGGDAWRLYEYITRHFIATVSHDCKYLQSTISFRIGPELFTCSGKTVLSPGFTEVMPWQSVPLEESLPTCQRGDAFPVGEVKMLEKQTNPPDYLTEAELITLMEKHGIGTDASIPVHINNICQRNYVTVESGRRLKPTNLGIVLVHGYYKIDAELVLPTIRSAVEKQLNLIAQGKADYRQVLGHTLDVFKRKFHYFVDSIAGMDELMEVSF
UniProt
O95985
Chains
Ligand binding sites
Interaction interfaces
Sequence conservation
Variants
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Tudor domain-containing protein 3
Chain: B
Length: 161 amino acids
Theoretical weight: 17.43 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q9H7E2 (Residues: 1-68; Coverage: 10%)
  • Best match: Q9H7E2-3 (Residues: 1-161)
Gene name: TDRD3
Pfam: RMI1, N-terminal OB-fold domain
Tudor domain-containing protein 3 in PDB entry 9cak, assembly 1, front view.
Tudor domain-containing protein 3 in PDB entry 9cak, assembly 1, side view.
Tudor domain-containing protein 3 in PDB entry 9cak, assembly 1, top view.
PDBe-KB: UniProt Coverage View: Q9H7E2  
116120406080100120140160
 
50100150MAQVAGAALSQAGWYLSDEGIEACTSSPDKVNVNDIILIALNTDLRTIGKKFLPSDINSGKVEKLEGPCVLQIQKIRNVAAPKDNEESQAAPRMLRLQMTDGHISCTAVEFSYMSKISLNTPPGTKVKLSGIVDIKNGFLLLNDSNTTVLGGEVEHLIEKW
UniProt
Q9H7E2
Chains
Interaction interfaces
Sequence conservation
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DNA chain D
Name: DNA (5'-D(P*GP*AP*CP*AP*GP*AP*T)-3')
Representative chains: D
Length: 7 nucleotides
Theoretical weight: 2.15 KDa
DNA (5'-D(P*GP*AP*CP*AP*GP*AP*T)-3') in PDB entry 9cak, assembly 1, front view.
DNA (5'-D(P*GP*AP*CP*AP*GP*AP*T)-3') in PDB entry 9cak, assembly 1, side view.
DNA (5'-D(P*GP*AP*CP*AP*GP*AP*T)-3') in PDB entry 9cak, assembly 1, top view.
171.01.52.02.53.03.54.04.55.05.56.06.57.0
 
2468GACAGAT
Chains
Chain C (auth D)
Ligand binding sites
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DNA chain E
Name: DNA (5'-D(*AP*TP*T)-3')
Representative chains: E
Length: 3 nucleotides
Theoretical weight: 877 Da
DNA (5'-D(*AP*TP*T)-3') in PDB entry 9cak, assembly 1, front view.
DNA (5'-D(*AP*TP*T)-3') in PDB entry 9cak, assembly 1, side view.
DNA (5'-D(*AP*TP*T)-3') in PDB entry 9cak, assembly 1, top view.
131.01.21.41.61.82.02.22.42.62.83.0
 
1234ATT
Chains
Chain D (auth E)
Interaction interfaces
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