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Helicase 3D structures

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Line 21: Line 21:
**[[4n8o]], [[5n8o]] - EcHel I + DNA<br />
**[[4n8o]], [[5n8o]] - EcHel I + DNA<br />
**[[2a0i]] - EcHel I (mutant) + DNA<BR />
**[[2a0i]] - EcHel I (mutant) + DNA<BR />
 +
**[[6fws]], [[6fwr]] – EcHel I + DNA + ADP <br />
**[[1e0j]], [[1e0k]] – Hel 4D domain – Phage T7
**[[1e0j]], [[1e0k]] – Hel 4D domain – Phage T7
Line 27: Line 28:
**[[1q2z]], [[1rw2]] – hHel II KU86 C terminal – human - NMR<BR />
**[[1q2z]], [[1rw2]] – hHel II KU86 C terminal – human - NMR<BR />
**[[5y58]] – yHel II + DNA – yeast<br />
**[[5y58]] – yHel II + DNA – yeast<br />
 +
**[[6yhz]] – yHel II C terminal - NMR<br />
 +
**[[7egs]] – yHel II C terminal + RNA polymerase<br />
**[[5y59]] – yHel II subunit 2 + Sir4P peptide<br />
**[[5y59]] – yHel II subunit 2 + Sir4P peptide<br />
**[[3lfu]] – EcHel II <BR />
**[[3lfu]] – EcHel II <BR />
Line 35: Line 38:
**[[6ppr]], [[6ppu]] – MsHel + DNA – Cryo EM<br />
**[[6ppr]], [[6ppu]] – MsHel + DNA – Cryo EM<br />
**[[6yi2]] – EcHel 645-720 - NMR<br />
**[[6yi2]] – EcHel 645-720 - NMR<br />
 +
**[[7egt]] – TtHel II + UvrB – ''Thermus thermophilus''<br />
*ATP-dependent helicase ATRX
*ATP-dependent helicase ATRX
Line 53: Line 57:
**[[5gn1]] – yFun C-terminal<br />
**[[5gn1]] – yFun C-terminal<br />
-
*ATP-dependent helicase Rho
+
*ATP-dependent helicase Rho or transcription termination factor Rho
**[[3l0o]] – TmRho – ''Thermotoga maritima''<BR />
**[[3l0o]] – TmRho – ''Thermotoga maritima''<BR />
-
**[[3ice]] – EcRho + ADP + BeF3 + RNA<BR />
+
**[[6wa8]] – EcRho + ATP<br />
-
**[[2ht1]] - EcRho + RNA<BR />
+
**[[3ice]], [[8e5l]] – EcRho + ADP + BeF3 + RNA<BR />
-
**[[1a8v]], [[1a62]] – EcRho RNA-binding domain<br />
+
**[[2ht1]], [[5jjl]] - EcRho + RNA<BR />
 +
**[[8e6w]] - EcRho + RNA – Cryo EM<br />
 +
**[[1a8v]], [[1a62]] – EcRho RNA-binding domain 1-118<br />
**[[1a63]] - EcRho RNA-binding domain – NMR<br />
**[[1a63]] - EcRho RNA-binding domain – NMR<br />
**[[2a8v]] – EcRho RNA-binding domain + RNA<br />
**[[2a8v]] – EcRho RNA-binding domain + RNA<br />
 +
**[[5jjk]] – EcRho (mutant) + RNA<br />
**[[1pv4]] – EcRho + DNA<br />
**[[1pv4]] – EcRho + DNA<br />
**[[1pvo]] – EcRho + ssRNA + ANPPNP<br />
**[[1pvo]] – EcRho + ssRNA + ANPPNP<br />
-
**[[1xpr]], [[1xpu]], [[1xpo]] - EcRho + ssRNA + antibiotic
+
**[[1xpr]], [[1xpu]], [[1xpo]] - EcRho + ssRNA + antibiotic<br />
 +
**[[6duq]] – EcRho + NusG + Ru12<br />
 +
**[[7x2r]] – EcRho in transcription termination complex<br />
 +
**[[6xas]], [[6xav]], [[6z9p]], [[6z9s]], [[6z9t]], [[6z9q]], [[6z9r]], [[7adc]], [[7adb]], [[7add]], [[7ade]], [[8e3h]], [[8e5p]], [[8e70]] – EcRho in transcription termination complex – Cryo EM<br />
 +
**[[7oqh]] – MtRho in transcription termination complex – Cryo EM<br />
*ATP-dependent helicase MFD see [[Transcription-repair coupling factor]]
*ATP-dependent helicase MFD see [[Transcription-repair coupling factor]]
Line 69: Line 80:
*ATP-dependent helicase HEPA
*ATP-dependent helicase HEPA
-
**[[6bog]] – EcHEPA
+
**[[6bog]] – EcHEPA<br />
 +
**[[4s20]], [[7mkn]], [[7mkq]] – EcHEPA in RNA polymerase complex – Cryo EM<br />
 +
**[[7m8e]] – EcHEPA in elongation complex – Cryo EM<br />
*ATP-dependent helicase E1
*ATP-dependent helicase E1
-
**[[2v9p]] – PvE1 helicase domain – Bovine papillomavirus<br />
+
**[[2v9p]], [[5a9k]] – bPvE1 helicase domain – Bovine papillomavirus<br />
-
**[[2gxa]] – PvE1 + DNA + Mg-ADP<br />
+
**[[2gxa]] – bPvE1 + DNA + Mg-ADP<br />
-
**[[1tue]] – PvE1 + E2 – human papillomavirus
+
**[[7apd]] – bPvE1 in replication fork complex – Cryo EM<br />
 +
**[[1tue]] – hPvE1 + E2 – human papillomavirus
*ATP-dependent helicase CHD
*ATP-dependent helicase CHD
Line 82: Line 96:
**[[4b4c]] – hCHD1 DNA-binding domain<br />
**[[4b4c]] – hCHD1 DNA-binding domain<br />
**[[2b2t]], [[2b2u]], [[2b2v]], [[2b2w]] – hCHD1 (mutant) + histone H3 tail<br />
**[[2b2t]], [[2b2u]], [[2b2v]], [[2b2w]] – hCHD1 (mutant) + histone H3 tail<br />
-
**[[4nw2]] – hCHD1 + NS1 peptide<br />
+
**[[4nw2]], [[4o42]] – hCHD1 + NS1 peptide<br />
-
**[[2ee1]] – hCHD4 chromodomain – NMR<br />
+
**[[2n5n]] – hCHD1 N-terminal – NMR<br />
-
**[[2l5u]] – hCHD4 PHD1 domain – NMR<br />
+
**[[2ee1]] – hCHD4 chromodomain 2 618-674 – NMR<br />
-
**[[2l75]] – hCHD4 PHD2 domain + histone H3 peptide– NMR<br />
+
**[[4o9i]] – hCHD4 chromodomain 1+2 499-677 <br />
 +
**[[2l5u]] – hCHD4 PHD1 domain 365-420 – NMR<br />
 +
**[[6q3m]] – hCHD4 PHD2+chromodomain 1,2 <br />
 +
**[[2l75]] – hCHD4 PHD2 domain 446-501 + histone H3 peptide – NMR<br />
 +
**[[6ryr]], [[6ryu]] – hCHD4 in nucleosome – Cryo EM<br />
 +
**[[6guu]] – hCHD5 PHD2 domain <br />
**[[2epb]] – hCHD6 chromodomain – NMR<br />
**[[2epb]] – hCHD6 chromodomain – NMR<br />
**[[2ckc]], [[2v0e]], [[2v0f]] – hCHD7 BRK domain - NMR <br />
**[[2ckc]], [[2v0e]], [[2v0f]] – hCHD7 BRK domain - NMR <br />
Line 91: Line 110:
**[[2cka]] – hCHD8 <br />
**[[2cka]] – hCHD8 <br />
**[[2h1e]], [[2xb0]], [[3mwy]] – yCHD1 chromodomain<BR />
**[[2h1e]], [[2xb0]], [[3mwy]] – yCHD1 chromodomain<BR />
-
**[[2dy7]] - yCHD1 chromodomain 1 – NMR<BR />
+
**[[2dy7]] - yCHD1 chromodomain 1 1006-1274 – NMR<BR />
**[[2dy8]] - yCHD1 chromodomain 2 – NMR<BR />
**[[2dy8]] - yCHD1 chromodomain 2 – NMR<BR />
**[[3ted]] - yCHD1 chromodomain 1 + DNA<br />
**[[3ted]] - yCHD1 chromodomain 1 + DNA<br />
 +
**[[5j70]] - yCHD1 chromodomain 1 + DNA<br />
 +
**[[5o9g]], [[6g0l]], [[7nkx]], [[7tn2]] - yCHD1 in nucleosome – Cryo EM<br />
 +
 +
*ATP-dependent helicase Sth1
 +
 +
**[[6kmb]], [[6mr4]], [[6uy1]] – ySth1 bromodomain 1248-1359 <br />
 +
**[[6lqz]] – ySth1 1183-1240 + TFIID subunit 14 - NMR<br />
 +
**[[6kmj]], [[7f3s]] – ySth1 bromodomain + hisone H3<br />
 +
**[[6vz4]], [[6vzg]] – ySth1 + ARP7 + ARP9 + RTT102 – Cryo EM<br />
 +
**[[6k15]], [[6v8o]], [[6v92]] – ySth1 in RSC core – Cryo EM<br />
 +
**[[6kw3]], [[6kw4]], [[6kw5]], [[6tda]] – ySth1 in RSC + nucleosome – Cryo EM<br />
 +
 +
*ATP-dependent helicase GTF2F2 or general transcription factor IIF subunit 2
 +
 +
**[[7nvr]], [[7nvt]], [[7nvu]], [[7nvy]], [[7nvz]], [[7nw0]] – hGTF2F2 in RNA polymerase II core – Cryo EM<br />
 +
**[[5iy6]], [[5iy7]], [[5iy8]], [[5iy9]], [[5iya]], [[5iyb]], [[5iyc]], [[5iyd]], [[6o9l]], [[7edx]], [[7eg7]], [[7eg8]], [[7eg9]], [[7ega]], [[7egb]], [[7egc]] – hGTF2F2 in core-PIC – Cryo EM<br />
 +
 +
*ATP-dependent DNA helicase
 +
 +
**[[7a8r]] – bADDH + ADP - bovine<br />
 +
**[[8add]] – ADDH - zebrafish<br />
*ATP-dependent DNA helicase PIF1
*ATP-dependent DNA helicase PIF1
Line 103: Line 143:
**[[6s3e]], [[7ada]] – ToPIF residues 64-507 – ''Thermus oshimai''<br />
**[[6s3e]], [[7ada]] – ToPIF residues 64-507 – ''Thermus oshimai''<br />
**[[6xzt]] – ToPIF (mutant)<br />
**[[6xzt]] – ToPIF (mutant)<br />
-
**[[6s3p]], [[7bil]] – ToPIF + DNA<br />
+
**[[6s3p]], [[7bil]], [[7oar]] – ToPIF + DNA<br />
**[[6s3h]], [[6s3i]], [[6s3m]], [[6s3n]], [[6s3o]] – ToPIF + DNA + ADP<br />
**[[6s3h]], [[6s3i]], [[6s3m]], [[6s3n]], [[6s3o]] – ToPIF + DNA + ADP<br />
-
**[[6l3g]] – PIF + DNA + ADP - ''Bacterioides''<br />
+
**[[5ftd]] – BaPIF - ''Bacterioides''<br />
 +
**[[5fte]], [[6l3g]] – BaPIF + DNA + ADP<br />
 +
**[[5ftb]] – BaPIF + AMPPNP<br />
 +
**[[5ftc]], [[5ftf]] – BaPIF + ADP<br />
**[[7otj]] – PIF + DNA + ADP – ''Candida albicans''<br />
**[[7otj]] – PIF + DNA + ADP – ''Candida albicans''<br />
Line 124: Line 167:
**[[5e7i]] - hDDX3X residues 133-584<br />
**[[5e7i]] - hDDX3X residues 133-584<br />
**[[2jgn]] – hDDX3X helicase domain residues 408-579<BR />
**[[2jgn]] – hDDX3X helicase domain residues 408-579<BR />
 +
**[[4a4d]] – hDDX5 N-terminal<br />
 +
**[[4ct5]] – hDDX6 95-469<br />
 +
**[[6uv0]] – hDDX17 core domain <br />
**[[3ly5]] – hDDX18 dead domain<BR />
**[[3ly5]] – hDDX18 dead domain<BR />
**[[6l5l]], [[6l5o]] – hDDX21 residues 120-495 (mutant)<br />
**[[6l5l]], [[6l5o]] – hDDX21 residues 120-495 (mutant)<br />
-
**[[6l5m]] – hDDX21 + AMP<br />
 
-
**[[6l5n]] – hDDX21 + RNA<br />
 
**[[2rb4]] – hDDX25 helicase domain<BR />
**[[2rb4]] – hDDX25 helicase domain<BR />
**[[2p6n]] – hDDX41 helicase domain (mutant) <BR />
**[[2p6n]] – hDDX41 helicase domain (mutant) <BR />
 +
**[[5gvr]], [[5gvs]] – hDDX41 DEAD domain 169-399<br />
 +
**[[8dpe]] – hDDX42<br />
**[[2e29]], [[2m3d]] - hDDX50 GUCT domain - NMR<BR />
**[[2e29]], [[2m3d]] - hDDX50 GUCT domain - NMR<BR />
 +
**[[3iuy]] – hDDX53<br />
**[[1vec]] – hP54 N terminal<BR />
**[[1vec]] – hP54 N terminal<BR />
-
**[[3fho]] – Dbp5 – fission yeast<BR />
+
**[[3fho]] – fyDbp5 – fission yeast<BR />
 +
**[[8ark]] – yDbp2<br />
**[[2kbe]] – yDbp5 N terminal – NMR<BR />
**[[2kbe]] – yDbp5 N terminal – NMR<BR />
**[[2kbf]] - yDbp5 C terminal – NMR<BR />
**[[2kbf]] - yDbp5 C terminal – NMR<BR />
Line 138: Line 186:
**[[2hjv]] – BsDbpA domain 2 – ''Bacillus subtilis''<BR />
**[[2hjv]] – BsDbpA domain 2 – ''Bacillus subtilis''<BR />
**[[2g0c]] - BsDbpA RNA-binding domain<br />
**[[2g0c]] - BsDbpA RNA-binding domain<br />
-
**[[3eaq]], [[3ear]], [[3eas]] – TtHera residues 215-426 - ''Thermus thermophilus''<br />
+
**[[3eaq]], [[3ear]], [[3eas]] – TtHera residues 215-426 <br />
-
**[[3i31]] - TtHera residues 431-517<br />
+
**[[3i31]], [[4i68]], [[5mao]] - TtHera RRM residues 431-517<br />
 +
**[[4i69]] - TtHera RRM (mutant)<br />
**[[3i32]] - TtHera residues 218-517<br />
**[[3i32]] - TtHera residues 218-517<br />
**[[3nej]] - TtHera N terminal (mutant)<br />
**[[3nej]] - TtHera N terminal (mutant)<br />
 +
**[[4kbf]], [[4kbg]] - TtHera core 8-372<br />
**[[5ivl]] – GsDB CSHA - ''Geobacillus stearothermophilus''<br />
**[[5ivl]] – GsDB CSHA - ''Geobacillus stearothermophilus''<br />
**[[5b88]] - EcDbp RRM-like domain - NMR<br />
**[[5b88]] - EcDbp RRM-like domain - NMR<br />
Line 151: Line 201:
*''Dead box ATP-dependent RNA helicase complexes''
*''Dead box ATP-dependent RNA helicase complexes''
-
**[[3fmo]], [[3fhc]] – hDBP5 + Nup214<BR />
+
**[[3fmo]], [[3fhc]] – hDbp5 + Nup214<BR />
-
**[[3fht]] – hDBP5 + AMPPNP + RNA<BR />
+
**[[3fht]] – hDbp5 + AMPPNP + RNA<BR />
**[[6cz5]] - hDDX3X residues 132-607 + AMP<br />
**[[6cz5]] - hDDX3X residues 132-607 + AMP<br />
-
**[[6o5f]] - hDDX3X + RNA<br />
+
**[[6o5f]], [[7liu]] - hDDX3X + RNA<br />
 +
**[[5e7m]], [[5e7j]] – hDDX3X catalytic domain + nucleotide<br />
 +
**[[3fe2]] – hDDX5 + ADP<br />
 +
2wax, 2way, [[6f9s]] – hDDX6 C terminal + peptide
 +
**[[2pl3]] – hDDX10 DEAD domain + ADP<br />
 +
**[[6uv1]], [[6uv2]], [[6uv3]], [[6uv4]] – hDDX17 core domain + RNA<br />
 +
 
**[[6b4k]] – hDDX19B residues 54-479 + ANP<br />
**[[6b4k]] – hDDX19B residues 54-479 + ANP<br />
**[[6b4j]], [[6b4i]] – hDDX19B residues 54-479 + GLE1 + Nup42 + ANP<br />
**[[6b4j]], [[6b4i]] – hDDX19B residues 54-479 + GLE1 + Nup42 + ANP<br />
Line 160: Line 216:
**[[3g0h]] – hDDX19B residues 54-275 + ATP analog + RNA<BR />
**[[3g0h]] – hDDX19B residues 54-275 + ATP analog + RNA<BR />
**[[3ews]] - hDDX19B residues 54-275 + ADP<BR />
**[[3ews]] - hDDX19B residues 54-275 + ADP<BR />
-
**[[5e7m]], [[5e7j]] – hDDX3X catalytic domain + nucleotide<br />
+
**[[3b7g]] – hDDX20 + AMPPNP<br />
-
**[[3dkp]] – hDDX52 domain I + ADP<BR />
+
**[[6l5m]] – hDDX21 + AMP<br />
-
**[[2wax]], [[2way]] – hDDX6 C terminal + EDC3-FDF peptide<BR />
+
**[[6l5n]] – hDDX21 + RNA<br />
 +
**[[7oi6]] – hDDX28 in 39S mitoribosome – Cryo EM<br />
 +
**[[7apk]] – hDDX39B in transcription-export complex – Cryo EM<br />
 +
**[[7evn]], [[7evo]] – hDDX42 in spliceosome – Cryo EM<br />
 +
**[[8hk1]] – hDDX42 in pre-17S U2 – Cryo EM<br />
 +
**[[7q3l]] – hDDX46 in pre-17S U2 – Cryo EM<br />
 +
**[[3ber]] – hDDX47 + AMP<br />
 +
**[[6icz]] – hDDX48 in spliceosome – Cryo EM<br />
**[[2j0s]], [[2j0q]], [[2hyi]] – hDDX48 + protein mago nashi homolog + RNA-binding protein 8A + protein CASC3 + RNA<BR />
**[[2j0s]], [[2j0q]], [[2hyi]] – hDDX48 + protein mago nashi homolog + RNA-binding protein 8A + protein CASC3 + RNA<BR />
**[[2j0u]] - hDDX48 + protein CASC3<BR />
**[[2j0u]] - hDDX48 + protein CASC3<BR />
 +
**[[3dkp]] – hDDX52 domain I + ADP<br />
 +
**[[3og8]] – hDDX58 C terminal + RNA<br />
**[[2db3]] – DmVASA residues 200-623 + RNA – ''Drosophila melanogaster''<br />
**[[2db3]] – DmVASA residues 200-623 + RNA – ''Drosophila melanogaster''<br />
**[[5nt7]] – DmVASA RecA-like domain + maternal effect protein<br />
**[[5nt7]] – DmVASA RecA-like domain + maternal effect protein<br />
 +
**[[4d25]] – VASA (mutant) + RNA + AMPPNP - bee<br />
**[[3rrm]] – yDBP5 residues 91-482 (mutant) + GLE1 + NUP159 + ADP + IP6<BR />
**[[3rrm]] – yDBP5 residues 91-482 (mutant) + GLE1 + NUP159 + ADP + IP6<BR />
-
**[[3rrn]] - yDBP5 residues 91-482 (mutant) + GLE1 + IP6<BR />
+
**[[3rrn]] - yDbp5 residues 91-482 (mutant) + GLE1 + IP6<BR />
-
**[[5elx]] - yDBP5 residues 91-482 + RNA<br />
+
**[[5elx]] - yDbp5 residues 91-482 + RNA<br />
-
**[[3pew]], [[3pey]] - yDBP5 residues 91-482 (mutant) + ADP + BeF3 + RNA<BR />
+
**[[3pew]], [[3pey]] - yDbp5 residues 91-482 (mutant) + ADP + BeF3 + RNA<BR />
-
**[[3peu]], [[3pev]] - yDBP5 C-terminal (mutant) + GLE1 + IP6<BR />
+
**[[3peu]], [[3pev]] - yDbp5 C-terminal (mutant) + GLE1 + IP6<BR />
**[[3i5x]], [[3i5y]] – yMSS116 + AMPPNP + RNA<BR />
**[[3i5x]], [[3i5y]] – yMSS116 + AMPPNP + RNA<BR />
**[[3sqw]], [[3sqx]] - yMSS116 + AMPPNP + RNA<BR />
**[[3sqw]], [[3sqx]] - yMSS116 + AMPPNP + RNA<BR />
Line 177: Line 243:
**[[3i62]] - yMSS116 + ADP + AlF4 + RNA<BR />
**[[3i62]] - yMSS116 + ADP + AlF4 + RNA<BR />
**[[4tyn]] - yMSS116 + ADP + DNA<br />
**[[4tyn]] - yMSS116 + ADP + DNA<br />
 +
**[[4db2]] - yMSS116 domain 2 + RNA<br />
 +
**[[4db4]] - yMSS116 domain 2 + RNA + DNA<br />
 +
**[[8arp]] – yDbp2 + ADP<br />
**[[2xau]], [[3kx2]], [[5jpt]] – yPrp43 + nucleotide<BR />
**[[2xau]], [[3kx2]], [[5jpt]] – yPrp43 + nucleotide<BR />
**[[5i8q]] - yPrp43 + ADPNP + RNA<br />
**[[5i8q]] - yPrp43 + ADPNP + RNA<br />
Line 183: Line 252:
**[[3jrv]] – DDX3X + protein K7 – Vaccinia virus<BR />
**[[3jrv]] – DDX3X + protein K7 – Vaccinia virus<BR />
**[[3nbf]] - TtHera N terminal (mutant) + 8-oxo-ADP<br />
**[[3nbf]] - TtHera N terminal (mutant) + 8-oxo-ADP<br />
-
**[[3moj]] - BsDBPA RNA-binding domain + RNA<br />
+
**[[4i67]] - TtHera RRM + RNA<br />
 +
**[[3moj]] - BsDbpA RNA-binding domain + RNA<br />
 +
**[[7pli]], [[7pmm]], [[7pmq]] - EcDbpA + RNA<br />
**[[6aic]] – SaDB CSHA N-terminal + AMP <br />
**[[6aic]] – SaDB CSHA N-terminal + AMP <br />
 +
**[[7ase]], [[7ask]] – DDX60 in 43S preinitiation complex complex – Trypanosoma cruzi - Cryo EM<br />
* DEAH box RNA helicase
* DEAH box RNA helicase

Revision as of 08:18, 10 May 2023

3D structures of helicase

Updated on 10-May-2023

2wax, 2way, 6f9s – hDDX6 C terminal + peptide

Proteopedia Page Contributors and Editors (what is this?)

Michal Harel, Joel L. Sussman

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