DNA polymerase 3D structures

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3D Structures of DNA polymerase

Updated on 06-February-2023 {{#tree:id=OrganizedByTopic|openlevels=0|

  • DNA polymerase I
  • DNA polymerase I klenow fragment or Taq polymerase
  • DNA polymerase II
    • 3maq, 3k57, 3k58, 3k59, 3k5l, 3k5m - EcDpo II (mutant) + DNA + nucleotide
    • 3k5n - EcDpo II (mutant) + DNA
    • 3k5o, 1q8i - EcDpo II (mutant)
    • 3o59, 5bkh - PhDpo II large subunit - Pyrococcus horikoshii<br />
    • 2kxe - PhDpo II small subunit
    • 1qqc – DeDpo II – Desulfurococcus
    • 5ijl - PaDpo II large subunit
    • 5ihe - PaDpo II small subunit
    • 6hmf - PaDpo II small subunit (mutant)
    • 6hms - PaDpo II small+large subunits + DNA – Cryo EM
    • 6knb, 6knc - TkPol II small+large subunits + PCNA + DNA - Thermococcus kodakarensis – Cryo EM
    • 7rsr, 7rss, 7rsu, 7tqw - TkPol + purine derivative + DNA
    • 7om3, 7omb, 7omg - TkPol + DNA + nucleotide
    • 7e15 - TkPol II small subunit + GINS51 + ssDNA-specific exonuclease
  • DNA polymerase III subunit alpha
    • 2hnh, 2hqa - EcDpo III subunit alpha catalytic fragment
    • 4jom - EcDpo III alpha subunit catalytic fragment (mutant)
    • 5m1s, 5fkw, 5fkv, 5fku - EcDpo III alpha (mutant) beta, epsilon subunits + DNA – Cryo EM
    • 1ok7 - EcDpo III residues 1-366 + EcDpo IV C-terminal
    • 2hpi, 2hpm - TaDpo III alpha subunit
    • 3e0d - TaDpo III alpha subunit + DNA
    • 3f2b, 3f2c, 3f2d, 4iqj – GkDpo III alpha subunit + DNA + nucleotide
    • 1zd7, 1zde, 3nzm, 5ol5, 5ol1 - SyDpo III alpha subunit – Synechocystis
    • 4gig - SyDpo III alpha subunit (mutant)
    • 2keq, 4kl5, 4kl6 - NpDpo III alpha subunit – Nostoc punctiforme
    • 4lx3, 4qfq - NpDpo III alpha subunit + nucleic acid binding tRNA/helicase
    • 5lew - MtPol III alpha subunit – Mycobacterrium tuberculosis
    • 7pu7 - MtDpo III alpha subunit + DNA
  • DNA polymerase III subunit beta or sliding clamp
    • 1mmi, 2pol, 4k3s, 4pnv, 4pnw - EcDpo III subunit beta
    • 2xur, 3f1v, 3pwe - EcDpo III subunit beta (mutant)
    • 3d1e - EcDpo III subunit beta + EcDpo II C-terminal
    • 1unn - EcDpo III subunit beta + EcDpo IV little finger
    • 2avt - Dpo III beta subunit – Streptococcus pyogenes
    • 2awa - Dpo III beta subunit – Streptococcus pneumoniae
    • 4trt – DrDpo III beta subunit – Deinococcus radiodurans
    • 2p1j – TmDpo III exonuclease domain – Thermotoga maritima
    • 1vpk - TmDpo III beta subunit
    • 3t0p - Dpo III beta subunit – Eubacterium rectale
    • 6ap4 - Dpo III beta subunit – Acinetobacter baumannii
    • 6amq - Dpo III beta subunit – Enterobacter cloacae
    • 5wyp, 5wce, 6izo, 6jir - Dpo III beta subunit – Caulobacter crescentus
    • 5w7z - RcDpo III beta subunit – Rickettsia conorii
    • 6man - Dpo III beta subunit – Rickettsia bellii
    • 6d46 - RtDpo III beta subunit – Rickettsia typhi
    • 6dlk - RrDpo III beta subunit – Rickettsia rickettsii
    • 6d47 - MmDpo III beta subunit – Mycobacterium marinum
    • 1jqj, 1jql - EcDpo III subunit beta,delta(mutant)
    • 4tr6 - Pol III beta subunit – Bacillus subtilis
    • 3p16, 3rb9, 4tr7 - MtPol III beta subunit
    • 4tr8, 6ams - PsaPol III beta subunit – Pseudomonas aeruginosa
    • 6pth - PsaPol III beta subunit + griselimycin
    • 4s3i, 4rki - HpPol III beta subunit – Helicobacter pylori
    • 6aig - Dpo III beta subunit – Aeropyrum pernix
    • 6deg - BbDpo III beta subunit – Bartonella birtlesii
    • 7rzm - Dpo III beta subunit – Stenotrophomonas maltophilia
    • 8dt6 - Dpo III beta subunit – Elizabethkingia anophelis
  • DNA polymerase III subunit beta or sliding clamp complex
  • DNA polymerase III subunit gamma
    • 5c51, 5c52, 5c53 - hDpo III gamma subunit + DNA + nucleotide
    • 1njf, 1njg - EcDpo III subunit gamma N-terminal domains 1-2
    • 2gno - TmDpo III gamma subunit
    • 1xxh, 1jr3 - EcDpo III subunit gamma, delta,delta’
    • 1xxi - EcDpo III subunit gamma, delta,delta’ + nucleotide
  • DNA polymerase III subunit delta
    • 1jqj, 1jql - EcDpo III subunit beta,delta(mutant)
    • 1a5t - EcDpo III subunit delta’
    • 1xxh, 1jr3 - EcDpo III subunit gamma, delta,delta’
    • 1xxi - EcDpo III subunit gamma, delta,delta’ + nucleotide
    • 3glh - EcDpo III subunit delta,delta’,tau
    • 3glf - EcDpo III subunitdelta,delta’,tau + DNA
    • 3gli - EcDpo III subunit delta,delta’,tau, zeta + DNA
    • 3glg - EcDpo III subunit delta,delta’,tau(mutant) + DNA
  • DNA polymerase III subunit epsilon
    • 2gui – EcDpo III subunit epsilon N-terminal
    • 1j53, 1j54 - EcDpo III subunit epsilon N-terminal exonuclease domain
    • 2ido - EcDpo III subunit epsilon+ HOT protein
    • 4gx8 - EcDpo III ε subunit/ EcDpo III α subunit
    • 4gx9 - EcDpo III ε subunit/ EcDpo III α subunit (mutant)
    • 2xy8 - EcDpo III subunit epsilon, theta
  • DNA polymerase III subunit tau
    • 2aya - EcDpo III subunit tau
    • 3glh - EcDpo III subunit delta, delta', tau
    • 3glf - EcDpo III subunit delta, delta', tau DNA
    • 3glg - EcDpo III subunit delta, delta', tau (mutant) + DNA
  • DNA polymerase III subunit xi
    • 3gli - EcDpo III subunit delta, delta', tau, xi + DNA
  • DNA polymerase III subunit theta
  • DNA polymerase III subunit chi+phi
    • 1em8 - EcDpo III subunit chi, phi
    • 3sxu - EcDpo III subunit chi, phi + peptide
  • DNA polymerase IV
  • DNA polymerase V
    • 8gmt - EcPol V subumit umud + RecA + DNA + nucleotide – Cryo EM
  • DNA polymerase from enterobacteria phage T7
  • DNA polymerase
  • DNA polymerase alpha
    • 4e2i – hDpo α subunit β + large T antigen – human
    • 4y97 - hDpo α catalytic+B subunits
    • 5iud - hDpo α catalytic subunit + DNA
    • 6as7 - hDpo α catalytic subunit (mutant) + DNA
    • 4bpx - hDpo α catalytic subunit + DNA primase small subunit
    • 5exr - hDpo α catalytic+B subunits + DNA primase small+large subunits
    • 7opl - hDpo α catalytic+B subunits + DNA primase small+large subunits + Nsp1 – Cryo EM
    • 7u5c, 8d08 - hDpo α catalytic+B subunits + DNA primase small+large subunits + CST + DNA – Cryo EM
    • 4q5v - hDpo α catalytic subunit + DNA + RNA + aphidicolin
    • 4qcl, 7n2m - hDpo α catalytic subunit + DNA + RNA + nucleotide
    • 2keb - hDpo alphaB - NMR
    • 1n5g, 1k0p, 1k18 - hDpo alpha zinc finger domain – NMR
    • 7uy7, 7uy8l - Dpo α B subunit + DNA primase small+large subunits – Tetrahymena thermophile - Cryo EM
  • DNA polymerase beta

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

  • DNA polymerase beta-like protein
  • DNA polymerase gamma
  • DNA polymerase delta
    • 3e0j - hDpo delta2+delta3
    • 3upq, 3uq0, 3uq2 - hDpo δ (mutant) + DNA
    • 4fo6 - hDpo δ (mutant) + DNA + nucleotide analog
    • 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 epsilon subunits A+2
  • DNA polymerase zeta
    • 3abd, 3abe - hDpo zeta catalytic subunit Rev3 + mitotic spindle assembly checkpoint protein Rev7
    • 6ekm, 6bi7, 6bcd, 6bc8 - hDpo zeta catalytic subunit + MAD2B
    • 3vu7, 4gk0, 6ws0 - hDpo zeta catalytic subunit + DNA repair protein Rev1 + MAD2B
    • 6ws5 - hDpo zeta catalytic subunit + DNA repair protein Rev1 + MAD2B + inhibitor
    • 4fjo, 4gk5 - hDpo kappa + hDpo zeta catalytic subunit + DNA repair protein Rev1 + MAD2B
    • 6v8p - hDpo zeta catalytic subunit + hDpo d subunits 3+small – Cryo EM
    • 6v93 - hDpo zeta catalytic+processivity subunits + hDpo d subunits 3+small + DNA + dCTP – Cryo EM
  • DNA polymerase eta
  • DNA polymerase iota
  • DNA polymerase kappa
  • DNA polymerase lambda
  • DNA polymerase mu or DNA-directed DNA/RNA polymerase
  • DNA polymerase nu
  • 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 – AsfvDpo X + DNA
    • 2w9m – DrDpo X
  • DNA polymerase theta
    • 5a9j – hDpo helicase domain 1-894
    • 5a9f, 5aga – hDpo helicase domain + nucleotide
    • 4x0p, 4x0q – hDpo helicase domain + nucleotide + DNA
    • 6xbu, 7zus – hDpo polymerase domain 1819-2590 + nucleotide + DNA
    • 7zx0, 7zx1, 8e23, 8e24 – hDpo polymerase domain + inhibitor + DNA
    • 8ef9, 8efc, 8efk – Dpo polymerase domain + nucleotide + DNA – Lates calcarifer
  • DNA polymerase from yeast
    • 3oiq - yDpo alpha + cell division control protein 13
    • 3flo, 3lgb - yDpo alpha subunits A,B
    • 4b08, 4fvm - yDpo alpha subunit A
    • 4fxd, 4fyd - yDpo alpha subunit A + RNA + DNA
    • 5oki - yDpo alpha subunit A + DCC1 + chromosome fidelity protein
    • 3iay - yDpo delta catalytic subunit + DNA
    • 6p1h - yDpo delta catalytic+small+3 subunits + DNA + nucleotide – Cryo EM
    • 6wjv - yDpo II epsilon – Cryo EM
    • 6hv8 - yDpo II epsilon subunit A+B – Cryo EM
    • 3oha, 3ohb, 3mfh - yDpo epsilon (mutant) + DNA
    • 6i8a, 6qib, 7r3x, 7r3y - yDpo II epsilon subunit A + DNA + nucleotide 
    • 6g0a, 6fwk, 3mfi, 4m8o - yDpo II epsilon subunit A (mutant) + DNA + nucleotide derivative
    • 6s1c, 6s2e, 6s2f - yDpo II epsilon subunit A (mutant) + DCC1 + chromosome transmission fidelity proteins
    • 6hv9 - yDpo II epsilon subunit A+B + CMG + DNA + nucleotide – Cryo EM
    • 2r8j, 2r8k, 4ptf - yDpo epsilon catalytic domain + DNA + nucleotide 
    • 6h1v - yDpo epsilon catalytic domain (mutant) + DNA + nucleotide 
    • 2xgp, 2xgq, 2wtf - yDpo epsilon + DNA
    • 7lxd - yDpo eta catalytic+processivity subunits + hDpo d subunits 3+small – Cryo EM
    • 7s0t - yDpo eta catalytic+processivity subunits + hDpo d subunits 3+small + DNA – Cryo EM
    • 5y27, 5y26 - Dpo epsilon subunit D + transcription factor – fission yeast
    • 1jih, 5vtp – yDpo catalytic domain
  • DNA polymerase Rev1; Domains – BRCT 44-133; catalytic 330-833; UBM2 998-1040; C-terminal 1158-1251
    • 3gqc – hRev1 catalytic domain + DNA + nucleotide
    • 2ebw – hRev1 BRCT domain – NMR
    • 6axd – hRev1 UBM2 domain – NMR
    • 6asr – hRev1 UBM2 domain + ubiquitin
    • 5vzm – hRev1 UBM2 domain + ubiquitin - NMR
    • 2lsg, 2lsy – hRev1 C-terminal domain – NMR
    • 2n1g – hRev1 C-terminal domain + Dpo d subunit 3 – NMR
    • 2lsi – hRev1 C-terminal domain + hDpo kappa peptide
    • 2lsk – hRev1 C-terminal domain + hDpo kappa peptide
    • 4ext – hRev1 C-terminal domain + hDpo eta catalytic subunit peptide + MAD2B
    • 4gk5 – hRev1 C-terminal domain + hDpo kappa peptide + hDpo eta catalytic subunit peptide + MAD2B
    • 2lsj – mRev1 C-terminal domain + mDpo kappa peptide
    • 4fjo – mRev1 C-terminal domain + mDpo kappa peptide + MAD2B
    • 4id3, 5umv – yRev1 BRCT domain
    • 2m2i, 5vx7 – yRev1 BRCT domain – NMR
    • 6x70, 6x72, 6x73, 6x74, 6x76 – yRev1 catalytic domain + DNA
    • 3bjy, 2aq4, 3osp, 5wm1, 5wm8, 5wmb, 6x6z, 6x71, 6x75, 6x77 – yRev1 catalytic domain + DNA + nucleotide
  • 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

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Michal Harel, Joel L. Sussman

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