DNA polymerase 3D structures: Difference between revisions

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*DNA polymerase iota
*DNA polymerase iota


**[[3q8r]], [[3q8s]], [[3h4b]], [[3h4d]], [[3gv5]], [[3gv7]], [[3gv8]], [[3epg]], [[3epi]], [[2fll]], [[2fln]], [[2flp]], [[2dpi]], [[2dpj]], [[2alz]], [[1zet]], [[1t3n]], [[4ebc]], [[4ebd]], [[4ebe]], [[4fs1]], [[4fs2]], [[4eyh]], [[4eyi]], [[3g6v]], [[3g6x]], [[3g6y]], [[5ulx]], [[5ulw]], [[5kt7]], [[5kt6]], [[5kt5]], [[5kt4]], [[5kt3]], [[5kt2]] - hDpo + DNA + nucleotide<br />
**[[3q8r]], [[3q8s]], [[3h4b]], [[3h4d]], [[3gv5]], [[3gv7]], [[3gv8]], [[3epg]], [[3epi]], [[2fll]], [[2fln]], [[2flp]], [[2dpi]], [[2dpj]], [[2alz]], [[1zet]], [[1t3n]], [[4ebc]], [[4ebd]], [[4ebe]], [[4fs1]], [[4fs2]], [[4eyh]], [[4eyi]], [[3g6v]], [[3g6x]], [[3g6y]], [[5ulx]], [[5ulw]], [[5kt7]], [[5kt6]], [[5kt5]], [[5kt4]], [[5kt3]], [[5kt2]] - hDpo iota + DNA + nucleotide<br />
**[[3ngd]], [[3osn]], [[3h40]] - hDpo catalytic fragment + DNA <br />
**[[3ngd]], [[3osn]], [[3h40]] - hDpo iota catalytic fragment + DNA <br />
**[[2ktf]] - hDpo + ubiquitin<br />
**[[2ktf]] - hDpo iota + ubiquitin<br />
**[[2l0f]], [[2l0g]] - hDpo + ubiquitin – NMR<br />
**[[2l0f]], [[2l0g]] - hDpo iota + ubiquitin – NMR<br />
**[[2khu]] - hDpo ubiquitin binding motif – NMR<br />
**[[2khu]] - hDpo iota ubiquitin binding motif – NMR<br />
**[[2khw]] - hDpo ubiquitin binding motif + ubiquitin – NMR<br />
**[[2khw]] - hDpo iota ubiquitin binding motif + ubiquitin – NMR<br />
**[[2kwu]], [[2kwv]] - mDpo C-terminal + ubiquitin - NMR<br />
**[[2kwu]], [[2kwv]] - mDpo iota C-terminal + ubiquitin - NMR<br />
**[[3ai4]] - mDpo /yEGFP<br />
**[[3ai4]] - mDpo iota/yEGFP<br />


*DNA polymerase kappa
*DNA polymerase kappa


**[[1t94]] - hDpo <br />
**[[1t94]] - hDpo kappa<br />
**[[3in5]], [[5w2c]], [[5w2a]], [[5t14]] - hDpo + DNA<br />
**[[3in5]], [[5w2c]], [[5w2a]], [[5t14]] - hDpo kappa + DNA<br />
**[[2w7o]], [[2w7p]], [[2oh2]], [[3pzp]], [[4u6p]], [[6cst]], [[6bs1]], [[6brx]], [[5w2a]], [[5w2c]] - hDpo + DNA + nucleotide<br />
**[[2w7o]], [[2w7p]], [[2oh2]], [[3pzp]], [[4u6p]], [[6cst]], [[6bs1]], [[6brx]], [[5w2a]], [[5w2c]] - hDpo kappa + DNA + nucleotide<br />
**[[7nv0]], [[7nv1]] - hDpo + PCNA + DNA + nucleotide<br />
**[[7nv0]], [[7nv1]] - hDpo kappa + PCNA + DNA + nucleotide<br />
**[[4u7c]], [[4y6p]] - hDpo + DNA + benzopyrene derivative<br />
**[[4u7c]], [[4y6p]] - hDpo kappa + DNA + benzopyrene derivative<br />
**[[2lsi]] - hDpo peptide + hRev1<br />
**[[2lsi]] - hDpo kappa peptide + hRev1<br />
**[[2lsk]] - mDpo + DNA repair protein Rev1<br />
**[[2lsk]] - mDpo lappa + DNA repair protein Rev1<br />


*DNA polymerase lambda
*DNA polymerase lambda
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*DNA polymerase mu or DNA-directed DNA/RNA polymerase
*DNA polymerase mu or DNA-directed DNA/RNA polymerase


**[[2htf]], [[2dun]] - hDpo BRCT domain residues 24-143 – NMR<br />
**[[2htf]], [[2dun]] - hDpo mu BRCT domain residues 24-143 – NMR<br />
**[[4lzd]] - hDpo residues 132-494 <br />
**[[4lzd]] - hDpo mu residues 132-494 <br />
**[[4lzg]], [[5tyz]], [[5tyy]], [[5tyx]], [[5tyw]], [[5tyv]], [[5tyu]], [[5tyg]], [[5tyf]], [[5tye]], [[5tyd]], [[5tyc]], [[5tyb]], [[5txz]], [[5txx]], [[5tws]], [[5twr]], [[5twq]], [[5twp]], [[5zlc]] - hDpo residues 132-494 + DNA <br />
**[[4lzg]], [[5tyz]], [[5tyy]], [[5tyx]], [[5tyw]], [[5tyv]], [[5tyu]], [[5tyg]], [[5tyf]], [[5tye]], [[5tyd]], [[5tyc]], [[5tyb]], [[5txz]], [[5txx]], [[5tws]], [[5twr]], [[5twq]], [[5twp]], [[5zlc]] - hDpo mu residues 132-494 + DNA <br />
**[[4yd2]], [[4ycx]] - hDpo residues 132-494 (mutant) + DNA <br />
**[[4yd2]], [[4ycx]] - hDpo mu residues 132-494 (mutant) + DNA <br />
**[[6ak5]] - hDpo residues 132-397+411-494 + nucleotide derivative<br />
**[[6ak5]] - hDpo mu residues 132-397+411-494 + nucleotide derivative<br />
**[[6ipn]], [[6ipm]], [[6ipl]], [[6ipk]], [[6ipj]], [[6ipi]], [[6iph]], [[6aec]], [[6aeh]], [[6ak6]] - hDpo residues 132-397+411-494 (mutant) + nucleotide derivative<br />
**[[6ipn]], [[6ipm]], [[6ipl]], [[6ipk]], [[6ipj]], [[6ipi]], [[6iph]], [[6aec]], [[6aeh]], [[6ak6]] - hDpo mu residues 132-397+411-494 (mutant) + nucleotide derivative<br />
**[[6vez]], [[6vf0]], [[6vf1]], [[6vf2]], [[6vf3]], [[6vf4]], [[6vf5]], [[6vf6]], [[6vf7]], [[6vf8]], [[6vf9]], [[6vfa]], [[6vfb]], [[6vfc]], [[7co6]], [[7co8]], [[7co9]], [[7coa]], [[7cob]], [[7cod]], [[7kss]], [[7kst]], [[7ksu]], [[7ksv]], [[7ksw]], [[7ksx]], [[7ksy]], [[7ksz]], [[7kt0]], [[7kt1]], [[7kt2]], [[7kt3]], [[7kt4]], [[7kt5]], [[7kt6]], [[7kt7]], [[7kt9]], [[7kta]], [[7ktb]], [[7ktc]], [[7ktd]], [[7kte]], [[7ktf]], [[7ktg]], [[7kth]], [[7kti]], [[7ktj]], [[7ktk]], [[7ktl]], [[7ktm]], [[7ktn]] - hDpo + DNA + nucleotide derivative<br />
**[[6vez]], [[6vf0]], [[6vf1]], [[6vf2]], [[6vf3]], [[6vf4]], [[6vf5]], [[6vf6]], [[6vf7]], [[6vf8]], [[6vf9]], [[6vfa]], [[6vfb]], [[6vfc]], [[7co6]], [[7co8]], [[7co9]], [[7coa]], [[7cob]], [[7cod]], [[7kss]], [[7kst]], [[7ksu]], [[7ksv]], [[7ksw]], [[7ksx]], [[7ksy]], [[7ksz]], [[7kt0]], [[7kt1]], [[7kt2]], [[7kt3]], [[7kt4]], [[7kt5]], [[7kt6]], [[7kt7]], [[7kt9]], [[7kta]], [[7ktb]], [[7ktc]], [[7ktd]], [[7kte]], [[7ktf]], [[7ktg]], [[7kth]], [[7kti]], [[7ktj]], [[7ktk]], [[7ktl]], [[7ktm]], [[7ktn]] - hDpo mu + DNA + nucleotide derivative<br />
**[[4m04]], [[4m0a]], [[4yd1]], [[6ipg]], [[6ipf]], [[6ipe]], [[6ipd]], [[5vz7]], [[5vz8]], [[5vz9]], [[5vza]], [[5vzb]], [[5vzc]], [[5vzd]], [[5vze]], [[5vzf]], [[5vzg]], [[5vzh]], [[5vzi]], [[6ak8]], [[6ak9]], [[6akh]], [[6p1m]], [[6p1n]], [[6p1o]], [[6p1p]], [[6p1q]], [[6p1r]], [[6p1s]], [[6p1t]], [[6p1u]], [[6p1v]], [[6p1w]], [[7coc]] - hDpo residues 132-494+411-494 (mutant) + DNA + nucleotide derivative<br />
**[[4m04]], [[4m0a]], [[4yd1]], [[6ipg]], [[6ipf]], [[6ipe]], [[6ipd]], [[5vz7]], [[5vz8]], [[5vz9]], [[5vza]], [[5vzb]], [[5vzc]], [[5vzd]], [[5vze]], [[5vzf]], [[5vzg]], [[5vzh]], [[5vzi]], [[6ak8]], [[6ak9]], [[6akh]], [[6p1m]], [[6p1n]], [[6p1o]], [[6p1p]], [[6p1q]], [[6p1r]], [[6p1s]], [[6p1t]], [[6p1u]], [[6p1v]], [[6p1w]], [[7coc]] - hDpo mu residues 132-494+411-494 (mutant) + DNA + nucleotide derivative<br />
**[[2ihm]] - mDpo catalytic domain + DNA <br />
**[[2ihm]] - mDpo malpha catalytic domain + DNA <br />


*DNA polymerase nu
*DNA polymerase nu
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*DNA polymerase from yeast
*DNA polymerase from yeast


**[[3oiq]] - yDpo + cell division control protein 13 <br />
**[[3oiq]] - yDpo alpha + cell division control protein 13 <br />
**[[3flo]], [[3lgb]] - yDpo  subunits A,B<br />
**[[3flo]], [[3lgb]] - yDpo alpha subunits A,B<br />
**[[8foc]], [[8fod]], [[8foe]] - yDpo  subunits A,B + primase small+large subunits – Cryo EM<br />
**[[8foc]], [[8fod]], [[8foe]] - yDpo alpha subunits A,B + primase small+large subunits – Cryo EM<br />
**[[8fok]] - yDpo  subunits A,B + primase small+large subunits + DNA – Cryo EM<br />
**[[8fok]] - yDpo alpha subunits A,B + primase small+large subunits + DNA – Cryo EM<br />
**[[4b08]], [[4fvm]] - yDpo  subunit A<br />
**[[4b08]], [[4fvm]] - yDpo alpha subunit A<br />
**[[4fxd]], [[4fyd]] - yDpo  subunit A + RNA + DNA<br />
**[[4fxd]], [[4fyd]] - yDpo alpha subunit A + RNA + DNA<br />
**[[5oki]] - yDpo  subunit A + DCC1 + chromosome fidelity protein<br />
**[[5oki]] - yDpo alpha subunit A + DCC1 + chromosome fidelity protein<br />
**[[9c51]], [[9c52]], [[9c53]] – yDpo gamma catalytic+small+3 subunits + DNA + nucleotide – Cryo EM<br />
**[[9c51]], [[9c52]], [[9c53]] – yDpo gamma catalytic+small+3 subunits + DNA + nucleotide – Cryo EM<br />
**[[9d2i]] – yDpo gamma catalytic subunit + DNA + nucleotide – Cryo EM<br />
**[[9d2i]] – yDpo gamma catalytic subunit + DNA + nucleotide – Cryo EM<br />
**[[3iay]] - yDpo catalytic subunit + DNA<br />
**[[3iay]] - yDpo delta catalytic subunit + DNA<br />
**[[6p1h]] - yDpo catalytic+small+3 subunits + DNA + nucleotide – Cryo EM<br />
**[[6p1h]] - yDpo delta catalytic+small+3 subunits + DNA + nucleotide – Cryo EM<br />
**[[6wjv]] - yDpo II – Cryo EM<br />
**[[6wjv]] - yDpo II epsilon – Cryo EM<br />
**[[6hv8]] - yDpo II subunit A+B – Cryo EM<br />
**[[6hv8]] - yDpo II epsilon subunit A+B – Cryo EM<br />
**[[8xgc]] - yDpo II in replication origin complex – Cryo EM<br />
**[[8xgc]] - yDpo II epsilon in replication origin complex – Cryo EM<br />
**[[3oha]], [[3ohb]], [[3mfh]] - yDpo (mutant) + DNA<br />
**[[3oha]], [[3ohb]], [[3mfh]] - yDpo epsilon (mutant) + DNA<br />
**[[6i8a]], [[6qib]], [[7r3x]], [[7r3y]] - yDpo II subunit A + DNA + nucleotide <br />
**[[6i8a]], [[6qib]], [[7r3x]], [[7r3y]] - yDpo II epsilon subunit A + DNA + nucleotide <br />
**[[6g0a]], [[6fwk]], [[3mfi]], [[4m8o]] - yDpo II subunit A (mutant) + DNA + nucleotide derivative<br />
**[[6g0a]], [[6fwk]], [[3mfi]], [[4m8o]] - yDpo II epsilon subunit A (mutant) + DNA + nucleotide derivative<br />
**[[6s1c]], [[6s2e]], [[6s2f]] - yDpo II subunit A (mutant) + DCC1 + chromosome transmission fidelity proteins<br />
**[[6s1c]], [[6s2e]], [[6s2f]] - yDpo II epsilon subunit A (mutant) + DCC1 + chromosome transmission fidelity proteins<br />
**[[6hv9]] - yDpo II subunit A+B + CMG + DNA + nucleotide – Cryo EM<br />
**[[6hv9]] - yDpo II epsilon subunit A+B + CMG + DNA + nucleotide – Cryo EM<br />
**[[2r8j]], [[2r8k]], [[4ptf]] - yDpo catalytic domain + DNA + nucleotide <br />
**[[2r8j]], [[2r8k]], [[4ptf]] - yDpo epsilon catalytic domain + DNA + nucleotide <br />
**[[6h1v]], [[8b67]], [[8b6k]], [[8b77]], [[8b79]] - yDpo catalytic domain (mutant) + DNA + nucleotide <br />
**[[6h1v]], [[8b67]], [[8b6k]], [[8b77]], [[8b79]] - yDpo epsilon catalytic domain (mutant) + DNA + nucleotide <br />
**[[2xgp]], [[2xgq]], [[2wtf]] - yDpo + DNA<br />
**[[2xgp]], [[2xgq]], [[2wtf]] - yDpo epsilon + DNA<br />
**[[9b8r]] - yDpo + DNA – Cryo EM<br />
**[[9b8r]] - yDpo epsilon + DNA – Cryo EM<br />
**[[7lxd]] - yDpo   catalytic+processivity subunits + hDpo delta subunits 3+small – Cryo EM<br />
**[[7lxd]] - yDpo  zeta catalytic+processivity subunits + hDpo delta subunits 3+small – Cryo EM<br />
**[[7s0t]] - yDpo   catalytic+processivity subunits + hDpo delta subunits 3+small + DNA – Cryo EM<br />
**[[7s0t]] - yDpo  zeta catalytic+processivity subunits + hDpo delta subunits 3+small + DNA – Cryo EM<br />
**[[8tlq]] - yDpo   catalytic+processivity subunits + hDpo delta subunit 3 + DNA + dCTP – Cryo EM<br />
**[[8tlq]] - yDpo  zeta catalytic+processivity subunits + hDpo delta subunit 3 + DNA + dCTP – Cryo EM<br />
**[[5y27]], [[5y26]] - Dpo subunit D + transcription factor – fission yeast<br />
**[[5y27]], [[5y26]] - Dpo epsilon subunit D + transcription factor – fission yeast<br />
**[[1jih]], [[5vtp]] – yDpo catalytic domain<br />
**[[1jih]], [[5vtp]] – yDpo nu catalytic domain<br />
**[[8b9b]], [[8kg6]], [[8kg8]], [[8kg9]], [[8w7m]], [[8w7s]] - yDpo III in replisome complex – Cryo EM<br />
**[[8b9b]], [[8kg6]], [[8kg8]], [[8kg9]], [[8w7m]], [[8w7s]] - yDpo III in replisome complex – Cryo EM<br />


Revision as of 07:48, 27 April 2025

3D Structures of DNA polymerase

Updated on 27-April-2025

6ctq, 6ctp, 6cto, 6ctn, 6ctm, 6ctl, 6ctk, 6ctj, 6cti, 6crh, 6crc, 6crb, 6cr9, 6cr8, 6cr7, 6cr6, 6cr5, 6cr4, 6cr3, 6cpq, 6cly, 6bem, 6bel, 6ph6, 6u2o, 6u6b, 6uok, 6uol, 6uom, 6w2m, 7k96 - hDpo beta + DNA + nucleotide analog

catalytic+2+3+4 + PCNA + DNA + nucleotide analog – Cryo EM

Terminal deoxynucleotidyl transferase binary complex

    • 4iqt, 4iqu, 4iqv, 4iqw – mTdT catalytic domain + inhibitor
    • 4i2i – mTdT catalytic domain + Mg + Zn + adenosine-pentaphosphate
    • 4i2j – mTdT catalytic domain + CTP + Zn
    • 1kej – mTdT catalytic domain + ATP derivative + Co
    • 4i2d – mTdT catalytic domain + ATP derivative + Mg
    • 4i29 – mTdT catalytic domain + AMP derivative + Mn
    • 4i2b – mTdT catalytic domain + AMPCPP + Mg
    • 4i2c – mTdT catalytic domain + AMPCPP + Mn
    • 4i2a – mTdT catalytic domain + UMP derivative + Mg
  • Terminal deoxynucleotidyl transferase ternary complex with DNA
    • 4i2e – mTdT catalytic domain + AMPCPP + Co + DNA
    • 4i2h – mTdT catalytic domain + AMPCPP + Zn + Mg + DNA
    • 4i27 – mTdT catalytic domain + TTP derivative + TMP + Mg + DNA
    • 1kdh – mTdT catalytic domain + UMP derivative + Mg + DNA
    • 4i28, 4i2f – mTdT catalytic domain + Mg + Zn + DNA
    • 4i2g – mTdT catalytic domain + Mg + Co + DNA

Proteopedia Page Contributors and Editors (what is this?)

Michal Harel, Jaime Prilusky, Joel L. Sussman

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