DNA polymerase 3D structures: Difference between revisions

Revision as of 07:14, 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  + DNA + nucleotide analog

- 4f5o, 4f5p, 4f5q, 4f5r, 6dic, 6btf, 6bte, 6nkr, 6nks, 6nkt, 6nku, 6nkv, 6nkw, 6nkx, 6nky, 6nkz, 6nl0, 6pkz - hDpo  (mutant) + DNA + nucleotide analog
- 3ogu, 4jwm, 4jwn, 4m9g, 4m9h, 4m9j, 4m9l, 4m9n, 4r63, 4r64, 4r65, 4r66 - hDpo  (mutant) + DNA
- 5hhi, 5hhh - hDpo  + DNA + azanide derivative
- 2v6z - hDpo  N-terminal (mutant)]] - NMR
- 3k75, 3lqc - hDpo  + DNA repair protein XRCC1
- 9dwg, 9dwh, 9dwi, 9dwk, 9dwm - hDpo  in nucleosome complex – Cryo EM
- 1rpl, 2bpc, 1bpe, 1bpb, 1bpd, 3uxn - rDpo  – rat
- 2van, 1jn3, 3uxo, 3v7l- rDpo  (mutant)
- 1dk2, 1dk3, 1bno, 1bnp - rDpo  N-terminal – NMR
- 1nom - rDpo  C-terminal
- 1huo, 1huz, 3v7j - rDpo  + DNA
- 3uxp, 3v72, 3v7k - rDpo  (mutant) + DNA
- 1bpe - rDpo  + nucleotide
- 2bpf, 2bpg - rDpo  + DNA + nucleotide
- 8e10 - mDpo 
- 8e11 - mDpo  (mutant)
- 3au2 – TtDpo β + GTP – Thermus thermophilus
- 3b0x, 3b0y – TtDpo β (mutant) + GTP
- 3au6, 3auo – TtDpo β + GTP + DNA
- 4p4m, 4p4o, 4p4p - Dpo  + DNA + nucleotide – Leishmania infantum
DNA polymerase beta-like protein
- 5hrb, 5hrd, 5hre, 7cpw - AsfvDpo + DNA – African swine fever virus
- 5hr9, 5hrg - AsfvDpo (mutant) + DNA
- 1jaj - AsfvDpo - NMR
- 5hrf, 5hri, 5hrl - AsfvDpo + DNA + nucleotide
- 5hrh, 5hrk - AsfvDpo (mutant) + DNA + nucleotide
DNA polymerase gamma
- 3ikm - hDpo 1+2
- 8v5d - hDpo1 – Cryo EM
- 3ikl, 2g4c - hDpo 2
- 2jw5 - hDpo  BRCT domain
- 1xsl - hDpo  catalytic domain
- 1nzp - hDpo  lyase domain - NMR
- 3pmn, 3pnc, 3mda, 2gws, 2bcq, 2bcr, 2bcs, 2bcu, 2bcv, 1xsp, 1rzt - hDpo  + DNA
- 8g5i, 8g5j, 8g5l, 8g5m, 8g5n, 8g5o, 8g5s, 8t7e, 8udl, 8v54, 8v5r - hDpo  + DNA – Cryo EM
- 8v55 - hDpo (mutant) + DNA – Cryo EM
- 3mgh, 3c5f, 3c5g, 2pfn - hDpo  (mutant) + DNA
- 8g5p - hDpo  + DNA + RNA – Cryo EM
- 3pml, 3mdc, 1xsn, 8udk - hDpo  + DNA + nucleotide
- 5c53, 5c52, 5c51 - hDpo  + DNA + nucleotide + pyrimidine derivative
- 4ztz, 4ztu - hDpo  + DNA + nucleotide
- 8d33, 8d37, 8d3r, 8d42, 9ggf - hDpo  + DNA + nucleotide – Cryo EM
- 9ggb, 9ggc, 9ggd, 9gge - hDpo  (mutant) + DNA + nucleotide – Cryo EM
- 4k4g, 4k4h, 4k4i - hDpo  + DNA + nucleotide analog
- 3mgi, 3hw8, 3hwt, 3hx0, 2pfo, 2pfp, 2pfq - hDpo  (mutant) + DNA + nucleotide
- 8f69 - mDpo 2 + DNA - mouse
DNA polymerase delta
- 3e0j - hDpo 2+3
- 3upq, 3uq0, 3uq2 - hDpo δ (mutant) + DNA
- 4fo6 - hDpo δ (mutant) + DNA + nucleotide analog
- 9ekb - hDpo δ subunits catalytic+2+3+4 – Cryo EM
- 6s1m, 6s1n, 6s1o, 6tny - hDpo δ subunits

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

- 6tnz - hDpo δ subunits catalytic+2+3+4 + PCNA + FLAP endonuclease +DNA + nucleotide analog – Cryo EM
- 7kc0 - hDpo δ + PCNA + POL31 + POL32 +DNA + nucleotide analog – Cryo EM
DNA polymerase epsilon
- 5vbn - hDpo subunits A+2
- 9f6i, 9f6j, 9f6l - hDpo subunit A + DNA – Cryo EM
- 9b8s, 9f6e, 9f6f - hDpo subunit A + DNA + PCNA – Cryo EM
- 9b8t - hDpo subunit A + DNA + PCNA + nucleotide – Cryo EM
DNA polymerase zeta
- 3abd, 3abe - hDpo  catalytic subunit Rev3 + mitotic spindle assembly checkpoint protein Rev7
- 6ekm, 6bi7, 6bcd, 6bc8 - hDpo  catalytic subunit + MAD2B
- 3vu7, 4gk0, 6ws0 - hDpo  catalytic subunit + DNA repair protein Rev1 + MAD2B
- 6ws5 - hDpo  catalytic subunit + DNA repair protein Rev1 + MAD2B + inhibitor
- 4fjo, 4gk5 - hDpo  + hDpo  catalytic subunit + DNA repair protein Rev1 + MAD2B
- 6v8p - hDpo  catalytic subunit + hDpo d subunits 3+small – Cryo EM
- 6v93 - hDpo  catalytic+processivity subunits + hDpo delta subunits 3+small + DNA + dCTP – Cryo EM
DNA polymerase eta or DNA polymerase theta; domains: helicase 1-894; polymerase 1819-2590
- 2i5o - hDpo  ubiquitin-binding zinc finger – NMR
- 3wup - hDpo  ubiquitin-binding zinc finger
- 5a9j – hDpo helicase domain
- 9asj, 9ask, 9asl, 9bh6, 9bh7 - hDpo  - Cryo EM
- 9bp9, 9bpa - hDpo  + inhibitor - Cryo EM
- 8ski, 8w0a, 9bh8, 9bh9, 9bha, 9c5q - hDpo  helicase domain + DNA - Cryo EM
- 3tq1, 4j9k, 4j9l, 4j9m, 4j9n, 4j9o, 4j9p, 4j9q, 4j9r, 4j9s, 6mp3, 8eve, 8evf - hDpo  + DNA
- 3jaa, 3mr2, 3mr3, 3mr5, 3mr6, 3si8, 4dl2, 4dl3, 4dl4, 4dl5, 4dl6, 4dl7, 4eey, 4ecq, 4ecr, 4ecs, 4ect, 4ecu, 4ecv, 4ecw, 4ecx, 4ecy, 4ecz, 4ed0, 4ed1, 4ed2, 4ed3, 4ed6, 4ed7, 4ed8, 4o3n, 4o3o, 4o3p, 4o3q, 4o3r, 4o3s, 4q8e, 4q8f, 4rnm, 4rnn, 4rno, 4x0p, 4x0q, 5l9x, 5l1l, 5l1k, 5l1j, 5l1i, 5kg7, 5kg6, 5kg5, 5kg4, 5kg3, 5kg2, 5kg1, 5kg0, 5kfz, 5kfy, 5kfx, 5kfw, 5kfv, 5kfu, 5kft, 5kfs, 5kfr, 5kfq, 5kfp, 5kfo, 5kfn, 5kfm, 5kfl, 5kfk, 5kfj, 5kfi, 5kfh, 5kfg, 5kff, 5kfe, 5kfd, 5kfc, 5kfb, 5kfa, 5jum, 5f9n, 5f9l, 5ewg, 5ewf, 5ewe, 5dqi, 5dqh, 5dqg, 5dlg, 5dlf, 5dgb, 5dga, 5dg9, 5dg8, 5dg7, 4yr3, 4yr2, 4yr0, 4yqw, 4yp3, 4ru9, 6mxo, 6m7v, 6m7u, 6m7t, 6m7p, 6m7o, 6d0z, 6d0m, 6mq8, 6pl7, 6pl8, 6plc, 6ui2, 6uqi, 6v5k, 6w5x, 6wk6, 7l69, 7lcd, 7m7l, 7m7m, 7m7n, 7m7o, 7m7p, 7m7q, 7m7r, 7m7s, 7m7t, 7m7u, 7m7y, 7m7z, 7m80, 7m81, 7m82, 7m83, 7m84, 7m85, 7m86, 7m87, 7m88, 7m89, 7m8a, 7m8b, 7m8c, 7m8d, 7u72, 7u73, 7u74, 7u75, 7u76, 7u77, 7u78, 7u79, 7u7a, 7u7b, 7u7c, 7u7d, 7u7e, 7u7g, 7u7f, 7u7i, 7u7j, 7u7k, 7u7l, 7u7r, 7u7s, 7u7t, 7u7u, 7u7v, 7u7w, 7u7x, 7u7y, 7u7z, 7u80, 7u81, 7u82, 7u83, 7u84, 8e85, 8e86, 8e87, 8e88, 8e89, 8e8a, 8e8c, 8e8d, 8e8e, 8e8f, 8e8g, 8e8h, 8e8j, 8e8k, 8fn3, 8fog, 8foh, 8foj, 8g8h, 8g8j, 8gbf, 8gkr, 8gml, 8ujt, 8ujv, 8ujx, 8uk4, 8v7a, 8v7b, 8v7c, 8v7d, 8v7e, 8v7f, 8v7g, 8v7h, 8v7j, 8v7k, 8v7i, 9chw, 9ci9, 9cih, 9ciq - hDpo  + DNA + nucleotide
- 9au5, 9au8, 9au9 - hDpo  + DNA + nucleotide – Cryo EM
- 6pz3, 6q02 - hDpo  (mutant) + DNA + nucleotide
- 6xbu, 7zus – hDpo polymerase domain + nucleotide + DNA
- 5a9f, 5aga - hDpo  + nucleotide
- 7zx0, 7zx1, 8e23, 8e24 , 8gd7– hDpo polymerase domain + inhibitor + DNA
- 8ef9, 8efc, 8efk – Dpo polymerase domain + nucleotide + DNA – Lates calcarifer
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
- 3ngd, 3osn, 3h40 - hDpo  catalytic fragment + DNA
- 2ktf - hDpo  + ubiquitin
- 2l0f, 2l0g - hDpo + ubiquitin – NMR
- 2khu - hDpo ubiquitin binding motif – NMR
- 2khw - hDpo ubiquitin binding motif + ubiquitin – NMR
- 2kwu, 2kwv - mDpo  C-terminal + ubiquitin - NMR
- 3ai4 - mDpo /yEGFP
DNA polymerase kappa
- 1t94 - hDpo 
- 3in5, 5w2c, 5w2a, 5t14 - hDpo  + DNA
- 2w7o, 2w7p, 2oh2, 3pzp, 4u6p, 6cst, 6bs1, 6brx, 5w2a, 5w2c - hDpo  + DNA + nucleotide
- 7nv0, 7nv1 - hDpo  + PCNA + DNA + nucleotide
- 4u7c, 4y6p - hDpo  + DNA + benzopyrene derivative
- 2lsi - hDpo  peptide + hRev1
- 2lsk - mDpo  + DNA repair protein Rev1
DNA polymerase lambda
- 5cb1 – hDpo
- 5iio, 5iin, 5iim, 5iil, 5iik, 5iij, 5iii, 5ddm – hDpo + DNA
- 5cp2, 8u0o – hDpo (mutant) + DNA
- 5dkw, 5ca7, 4xus, 4xrh, 4xq8, 4xa5, 4x5v, 7m07, 7m08, 7m09, 7m0a, 7m0b, 7m0c, 7m0d, 7m0e – hDpo + DNA + nucleotide
- 5cwr, 5cr0, 5cj7, 5chg, 7m43, 7m44, 7m45, 7m46, 7m47, 7m48, 7m49, 7m4a, 7m4b, 7m4c, 7m4d, 7m4e, 7m4f, 7m4h, 7m4i, 7m4j, 7m4k, 7m4l, 8u0p – hDpo (mutant) + DNA + nucleotide
- 5ddy – hDpo + nucleotide
DNA polymerase mu or DNA-directed DNA/RNA polymerase
- 2htf, 2dun - hDpo  BRCT domain residues 24-143 – NMR
- 4lzd - hDpo  residues 132-494
- 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
- 4yd2, 4ycx - hDpo  residues 132-494 (mutant) + DNA
- 6ak5 - hDpo  residues 132-397+411-494 + nucleotide derivative
- 6ipn, 6ipm, 6ipl, 6ipk, 6ipj, 6ipi, 6iph, 6aec, 6aeh, 6ak6 - hDpo  residues 132-397+411-494 (mutant) + nucleotide derivative
- 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
- 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
- 2ihm - mDpo  catalytic domain + DNA
DNA polymerase nu
- 4xvi, 4xvk, 4xvl, 4xvm – hDpo nu catalytic domain + DNA
DNA polymerase chi or repair DNA polymerase chi
- 2m2t – AsfvDpo X – African swine fever virus – NMR
- 2m2u, 2m2v – AsfvDpo X + nucleotide – NMR
- 2m2w – AsfvDpo X + nucleotide + DNA – NMR
- 5xma, 5xm9, 5xm8, 8e9a – AsfvDpo X + DNA
- 8ild, 8ile, 8ilf, 8ilg, 8ilh, 8ili – AsfvDpo X + DNA + nucleotide – Cryo EM
- 2w9m – DrDpo X
DNA polymerase from yeast
- 3oiq - yDpo  + cell division control protein 13
- 3flo, 3lgb - yDpo  subunits A,B
- 8foc, 8fod, 8foe - yDpo  subunits A,B + primase small+large subunits – Cryo EM
- 8fok - yDpo  subunits A,B + primase small+large subunits + DNA – Cryo EM
- 4b08, 4fvm - yDpo  subunit A
- 4fxd, 4fyd - yDpo  subunit A + RNA + DNA
- 5oki - yDpo  subunit A + DCC1 + chromosome fidelity protein
- 9c51, 9c52, 9c53 – yDpo gamma catalytic+small+3 subunits + DNA + nucleotide – Cryo EM
- 9d2i – yDpo gamma catalytic subunit + DNA + nucleotide – Cryo EM
- 3iay - yDpo  catalytic subunit + DNA
- 6p1h - yDpo  catalytic+small+3 subunits + DNA + nucleotide – Cryo EM
- 6wjv - yDpo II  – Cryo EM
- 6hv8 - yDpo II  subunit A+B – Cryo EM
- 8xgc - yDpo II  in replication origin complex – Cryo EM
- 3oha, 3ohb, 3mfh - yDpo  (mutant) + DNA
- 6i8a, 6qib, 7r3x, 7r3y - yDpo II  subunit A + DNA + nucleotide
- 6g0a, 6fwk, 3mfi, 4m8o - yDpo II  subunit A (mutant) + DNA + nucleotide derivative
- 6s1c, 6s2e, 6s2f - yDpo II  subunit A (mutant) + DCC1 + chromosome transmission fidelity proteins
- 6hv9 - yDpo II  subunit A+B + CMG + DNA + nucleotide – Cryo EM
- 2r8j, 2r8k, 4ptf - yDpo  catalytic domain + DNA + nucleotide
- 6h1v, 8b67, 8b6k, 8b77, 8b79 - yDpo  catalytic domain (mutant) + DNA + nucleotide
- 2xgp, 2xgq, 2wtf - yDpo  + DNA
- 9b8r - yDpo  + DNA – Cryo EM
- 7lxd - yDpo  catalytic+processivity subunits + hDpo delta subunits 3+small – Cryo EM
- 7s0t - yDpo  catalytic+processivity subunits + hDpo delta subunits 3+small + DNA – Cryo EM
- 8tlq - yDpo  catalytic+processivity subunits + hDpo delta subunit 3 + DNA + dCTP – Cryo EM
- 5y27, 5y26 - Dpo subunit D + transcription factor – fission yeast
- 1jih, 5vtp – yDpo  catalytic domain
- 8b9b, 8kg6, 8kg8, 8kg9, 8w7m, 8w7s - yDpo III in replisome complex – Cryo EM
Terminal deoxynucleotidyl transferase
- 2coe – TdT BRCT domain – NMR
- 1jms – mTdT catalytic domain + Mg

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

@@ Line 138: / Line 138: @@
 *DNA polymerase III subunit gamma
-**[[5c51]], [[5c52]], [[5c53]] - hDpo III  subunit + DNA + nucleotide<br />
+**[[5c51]], [[5c52]], [[5c53]] - hDpo III gamma subunit + DNA + nucleotide<br />
-**[[1njf]], [[1njg]] - EcDpo III subunit  N-terminal domains 1-2<br />
+**[[1njf]], [[1njg]] - EcDpo III subunit gamma N-terminal domains 1-2<br />
-**[[2gno]] - TmDpo III  subunit<br />
+**[[2gno]] - TmDpo III gamma subunit<br />
-**[[1xxh]], [[1jr3]] - EcDpo III subunit ’ <br />
+**[[1xxh]], [[1jr3]] - EcDpo III subunits gamma, delta, delta’ <br />
-**[[1xxi]] - EcDpo III subunit ’ + nucleotide<br />
+**[[1xxi]] - EcDpo III subunits gamma, delta, delta’ + nucleotide<br />
 *DNA polymerase III subunit delta
-**[[1jqj]], [[1jql]] - EcDpo III subunit (mutant) <br />
+**[[1jqj]], [[1jql]] - EcDpo III subunits beta, delta (mutant) <br />
-**[[1a5t]] - EcDpo III subunit ’ <br />
+**[[1a5t]] - EcDpo III subunit delta’ <br />
-**[[1xxh]], [[1jr3]] - EcDpo III subunit ’ <br />
+**[[1xxh]], [[1jr3]] - EcDpo III subunits gamma, delta, delta’ <br />
-**[[1xxi]] - EcDpo III subunit ’ + nucleotide<br />
+**[[1xxi]] - EcDpo III subunits gamm. delta, delta’ + nucleotide<br />
-**[[3glh]] - EcDpo III subunit ’<br />
+**[[3glh]] - EcDpo III subunits delta, delta’, tau<br />
-**[[3glf]] - EcDpo III subunit ’ DNA<br />
+**[[3glf]] - EcDpo III subunits delta, delta’, tau + DNA<br />
-**[[3gli]] - EcDpo III subunit ’ DNA<br />
+**[[3glg]] - EcDpo III subunits delta, delta’, tau (mutant) +  DNA<br />
-**[[3glg]] - EcDpo III subunit ’mutant DNA<br />
+**[[3gli]] - EcDpo III subunits delta, delta’, tau, xi + DNA<br />
 *DNA polymerase III subunit epsilon

DNA polymerase 3D structures: Difference between revisions

Revision as of 07:14, 27 April 2025

3D Structures of DNA polymerase

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