1EJ9: Human topoisomerase I DNA complex

Crystal structure of human topoisomerase I DNA complex. Determined by X-ray diffraction at 2.6 Å resolution. Released 3 Aug 2000.

Method
X-ray diffraction
Resolution
2.6 Å
Organism
Homo sapiens
Chains
3
Atoms
5,215
Mol. weight
80.67 kDa
Released
3 Aug 2000

Explore 1EJ9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1EJ9 contains 29 α-helices and 21 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 29 helices, 21 β-strands

ElementResiduesLengthSheet
α-helix205-2073
α-helix209-2113
β-strand220-22121
β-strand22612
α-helix227-2359
β-strand241-24223
β-strand245-24623
α-helix248-2503
α-helix251-26111
α-helix268-2703
α-helix272-28413
α-helix288-2936
β-strand300-30123
α-helix303-31816
α-helix321-33818
β-strand340-34341
β-strand346-34941
β-strand35014
β-strand35412
α-helix355-3584
β-strand359-36025
α-helix3721
β-strand373-37425
α-helix376-3783
α-helix379-3813
β-strand383-38536
α-helix391-3966
β-strand403-40536
β-strand414-41856
β-strand423-42756
β-strand42914
α-helix434-45118
α-helix454-46411
α-helix470-48516
α-helix491-4944
β-strand50817
α-helix509-5113
β-strand512-51878
β-strand521-530108
α-helix532-5343
β-strand536-54278
α-helix545-55410
β-strand56317
α-helix570-58011
α-helix586-60520
α-helix612-63019
α-helix717-7226
α-helix726-73510
α-helix740-7423
α-helix746-75712

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
DNA (5'-d(*c*ap*ap*ap*ap*ap*gp*ap*cp*tp*cp*ap*gp*ap*ap*ap*ap*ap*tp*tp*tp*tp*t)-3')CDNA23
DNA (5'-d(*c*ap*ap*ap*ap*ap*tp*tp*tp*tp*tp*cp*tp*gp*ap*gp*tp*cp*tp*tp*tp*tp*t)-3')DDNA23
DNA topoisomerase IAprotein563Homo sapiensP11387 (AlphaFold model)
Sequence of entity 1 (C), FASTA
>1EJ9_1 DNA (5'-D(*C*AP*AP*AP*AP*AP*GP*AP*CP*TP*CP*AP*GP*AP*AP*AP*AP*AP*TP*TP*TP*TP*T)-3') (chains C)
CAAAAAGACTCAGAAAAATTTTT
Sequence of entity 2 (D), FASTA
>1EJ9_2 DNA (5'-D(*C*AP*AP*AP*AP*AP*TP*TP*TP*TP*TP*CP*TP*GP*AP*GP*TP*CP*TP*TP*TP*TP*T)-3') (chains D)
CAAAAATTTTTCTGAGTCTTTTT
Sequence of entity 3 (A), FASTA
>1EJ9_3 DNA TOPOISOMERASE I (chains A)
WKWWEEERYPEGIKWKFLEHKGPVFAPPYEPLPENVKFYYDGKVMKLSPKAEEVATFFAK
MLDHEYTTKEIFRKNFFKDWRKEMTNEEKNIITNLSKCDFTQMSQYFKAQTEARKQMSKE
EKLKIKEENEKLLKEYGFCIMDNHKERIANFKIEPPGLFRGRGNHPKMGMLKRRIMPEDI
IINCSKDAKVPSPPPGHKWKEVRHDNKVTWLVSWTENIQGSIKYIMLNPSSRIKGEKDWQ
KYETARRLKKCVDKIRNQYREDWKSKEMKVRQRAVALYFIDKLALRAGNEKEEGETADTV
GCCSLRVEHINLHPELDGQEYVVEFDFLGKDSIRYYNKVPVEKRVFKNLQLFMENKQPED
DLFDRLNTGILNKHLQDLMEGLTAKVFRTYNASITLQQQLKELTAPDENIPAKILSYNRA
NRAVAILCNHQIAPPKTFEKSMMNLQTKIDAKKEQLADARRDLKSAKADAKVMKDAKTKK
VVESKKKAVQRLEEQLMKLEVQATDREENKQIALGTSKLNFLDPRITVAWCKKWGVPIEK
IYNKTQREKFAWAIDMADEDYEF

Primary citation

Novel insights into catalytic mechanism from a crystal structure of human topoisomerase I in complex with DNA. Redinbo, M.R., Champoux, J.J., Hol, W.G. Biochemistry (2000) 39:6832-6840. DOI 10.1021/bi992690t · PubMed

Other PDB entries of the same protein (UniProt P11387 (AlphaFold model), which also has an AlphaFold model), best resolution first:

Browse structure collections

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