1ny6

Crystal structure of sigm54 activator (AAA+ ATPase) in the active state

Method: X-RAY DIFFRACTION D_max: 165.0 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

transcriptional regulator (NtrC family)

Aquifex aeolicus

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 7 PDB declaration: heptameric（7） Consistent with protein copy count	Chain A； UniProt 122–387 Chain B； UniProt 122–387 Chain C； UniProt 122–387 Chain D； UniProt 122–387 Chain E； UniProt 122–387 Chain F； UniProt 122–387 Chain G； UniProt 122–387	Fragment：residues 122-387	ADP ADENOSINE-5'-DIPHOSPHATE × 7	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；diammonium tartrate, PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 3.10 Å R-free 0.329
2	Protein homooligomer Homooligomer Protein × 7 PDB declaration: heptameric（7） Consistent with protein copy count	Chain H； UniProt 122–387 Chain I； UniProt 122–387 Chain J； UniProt 122–387 Chain K； UniProt 122–387 Chain L； UniProt 122–387 Chain M； UniProt 122–387 Chain N； UniProt 122–387	Fragment：residues 122-387	ADP ADENOSINE-5'-DIPHOSPHATE × 7	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；diammonium tartrate, PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 3.10 Å R-free 0.329

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 1NY6	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1NY5 Crystal structure of sigm54 activator (AAA+ ATPase) in the inactive state Deposited 2003-02-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–387（387 aa） Fragment：Regulatory and Central domain Chain B 1–387（387 aa） Fragment：Regulatory and Central domain	Not recorded	MG MAGNESIUM ION × 1 PO4 PHOSPHATE ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 2 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；sodium/potasium phosphate, citric acid,imidazole,methanol,glycerol,, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.40 Å R-free 0.257
1ZY2 Crystal structure of the phosphorylated receiver domain of the transcription regulator NtrC1 from Aquifex aeolicus Deposited 2005-06-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–136（136 aa） Chain B 1–136（136 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；310 K；PEG-3350, AMMONIUM CHLORIDE, GLYCEROL, CITRIC ACID, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 310K	Resolution 3.03 Å R-free 0.283
3M0E Crystal structure of the ATP-bound state of Walker B mutant of NtrC1 ATPase domain Deposited 2010-03-02	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 7 PDB declaration: heptameric	Chain A 122–387（266 aa） Fragment：ATP-ase domain Chain B 122–387（266 aa） Fragment：ATP-ase domain Chain C 122–387（266 aa） Fragment：ATP-ase domain Chain D 122–387（266 aa） Fragment：ATP-ase domain Chain E 122–387（266 aa） Fragment：ATP-ase domain Chain F 122–387（266 aa） Fragment：ATP-ase domain Chain G 122–387（266 aa） Fragment：ATP-ase domain	Mutation：E239A Mutation：E239A Mutation：E239A Mutation：E239A Mutation：E239A Mutation：E239A Mutation：E239A	ATP ADENOSINE-5'-TRIPHOSPHATE × 7 MG MAGNESIUM ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；0.1 M SODIUM CITRATE, 0.01 M FECL3, 0-5% (V/V) JEFFAMINE M-600, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.63 Å R-free 0.241
4BT0 MuB is an AAAplus ATPase that forms helical filaments to control target selection for DNA transposition Deposited 2013-06-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 14 PDB declaration: helical	Chain A 312–384（73 aa） Fragment：AAAPLUS DOMAIN, RESIDUES 312-384 Chain B 137–309（173 aa） Fragment：AAAPLUS DOMAIN, RESIDUES 137-309	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 14	ELECTRON MICROSCOPY cryo-EM buffer 30 MM TRISHCL PH 8.0, 0.3 M KCL, 5MM MGCL2, 1MM DTT, 1 MM ATP OR ATP-GAMMA-S；pH 8；30 MM TRISHCL PH 8.0, 0.3 M KCL, 5MM MGCL2, 1MM DTT, 1 MM ATP OR ATP-GAMMA-S cryo-EM vitrification conditions Cryogen ETHANE；LIQUID ETHANE	Resolution 17.00 Å
4BT0 MuB is an AAAplus ATPase that forms helical filaments to control target selection for DNA transposition Deposited 2013-06-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 312–384（73 aa） Fragment：AAAPLUS DOMAIN, RESIDUES 312-384 Chain B 137–309（173 aa） Fragment：AAAPLUS DOMAIN, RESIDUES 137-309	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer 30 MM TRISHCL PH 8.0, 0.3 M KCL, 5MM MGCL2, 1MM DTT, 1 MM ATP OR ATP-GAMMA-S；pH 8；30 MM TRISHCL PH 8.0, 0.3 M KCL, 5MM MGCL2, 1MM DTT, 1 MM ATP OR ATP-GAMMA-S cryo-EM vitrification conditions Cryogen ETHANE；LIQUID ETHANE	Resolution 17.00 Å
4BT0 MuB is an AAAplus ATPase that forms helical filaments to control target selection for DNA transposition Deposited 2013-06-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 312–384（73 aa） Fragment：AAAPLUS DOMAIN, RESIDUES 312-384 Chain B 137–309（173 aa） Fragment：AAAPLUS DOMAIN, RESIDUES 137-309	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer 30 MM TRISHCL PH 8.0, 0.3 M KCL, 5MM MGCL2, 1MM DTT, 1 MM ATP OR ATP-GAMMA-S；pH 8；30 MM TRISHCL PH 8.0, 0.3 M KCL, 5MM MGCL2, 1MM DTT, 1 MM ATP OR ATP-GAMMA-S cryo-EM vitrification conditions Cryogen ETHANE；LIQUID ETHANE	Resolution 17.00 Å
4BT1 MuB is an AAAplus ATPase that forms helical filaments to control target selection for DNA transposition Deposited 2013-06-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 14 PDB declaration: helical	Chain A 312–384（73 aa） Fragment：AAAPLUS DOMAIN, RESIDUES 312-384 Chain B 137–309（173 aa） Fragment：AAAPLUS DOMAIN, RESIDUES 137-309	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 14	ELECTRON MICROSCOPY cryo-EM buffer 30 MM TRISHCL PH 8.0, 0.3 M KCL, 5MM MGCL2, 1MM DTT, 1 MM ATP OR ATP-GAMMA-S；pH 8；30 MM TRISHCL PH 8.0, 0.3 M KCL, 5MM MGCL2, 1MM DTT, 1 MM ATP OR ATP-GAMMA-S cryo-EM vitrification conditions Cryogen ETHANE；LIQUID ETHANE	Resolution 16.00 Å
4BT1 MuB is an AAAplus ATPase that forms helical filaments to control target selection for DNA transposition Deposited 2013-06-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 312–384（73 aa） Fragment：AAAPLUS DOMAIN, RESIDUES 312-384 Chain B 137–309（173 aa） Fragment：AAAPLUS DOMAIN, RESIDUES 137-309	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer 30 MM TRISHCL PH 8.0, 0.3 M KCL, 5MM MGCL2, 1MM DTT, 1 MM ATP OR ATP-GAMMA-S；pH 8；30 MM TRISHCL PH 8.0, 0.3 M KCL, 5MM MGCL2, 1MM DTT, 1 MM ATP OR ATP-GAMMA-S cryo-EM vitrification conditions Cryogen ETHANE；LIQUID ETHANE	Resolution 16.00 Å
4BT1 MuB is an AAAplus ATPase that forms helical filaments to control target selection for DNA transposition Deposited 2013-06-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 312–384（73 aa） Fragment：AAAPLUS DOMAIN, RESIDUES 312-384 Chain B 137–309（173 aa） Fragment：AAAPLUS DOMAIN, RESIDUES 137-309	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer 30 MM TRISHCL PH 8.0, 0.3 M KCL, 5MM MGCL2, 1MM DTT, 1 MM ATP OR ATP-GAMMA-S；pH 8；30 MM TRISHCL PH 8.0, 0.3 M KCL, 5MM MGCL2, 1MM DTT, 1 MM ATP OR ATP-GAMMA-S cryo-EM vitrification conditions Cryogen ETHANE；LIQUID ETHANE	Resolution 16.00 Å
4L4U Crystal structure of construct containing A. aeolicus NtrC1 receiver, central and DNA binding domains Deposited 2013-06-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–439（439 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å R-free 0.248
4L5E Crystal structure of A. aeolicus NtrC1 DNA binding domain Deposited 2013-06-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 393–438（46 aa） Fragment：unp residues 393-438	Not recorded	SO4 SULFATE ION × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.34 Å R-free 0.206
4LY6 Nucleotide-induced asymmetry within ATPase activator ring drives s54-RNAP interaction and ATP hydrolysis Deposited 2013-07-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 121–387（267 aa） Fragment：UNP residues 121-387 Chain B 121–387（267 aa） Fragment：UNP residues 121-387 Chain C 121–387（267 aa） Fragment：UNP residues 121-387 Chain D 121–387（267 aa） Fragment：UNP residues 121-387 Chain E 121–387（267 aa） Fragment：UNP residues 121-387 Chain F 121–387（267 aa） Fragment：UNP residues 121-387	Not recorded	08T [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium × 5 MG MAGNESIUM ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；277 K；20% ethylene glycol, pH 7.9, vapor diffusion, hanging drop, temperature 277K	Resolution 3.60 Å R-free 0.308
4LY6 Nucleotide-induced asymmetry within ATPase activator ring drives s54-RNAP interaction and ATP hydrolysis Deposited 2013-07-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain G 121–387（267 aa） Fragment：UNP residues 121-387 Chain H 121–387（267 aa） Fragment：UNP residues 121-387 Chain I 121–387（267 aa） Fragment：UNP residues 121-387 Chain J 121–387（267 aa） Fragment：UNP residues 121-387 Chain K 121–387（267 aa） Fragment：UNP residues 121-387 Chain L 121–387（267 aa） Fragment：UNP residues 121-387	Not recorded	08T [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium × 5 MG MAGNESIUM ION × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；277 K；20% ethylene glycol, pH 7.9, vapor diffusion, hanging drop, temperature 277K	Resolution 3.60 Å R-free 0.308
4LY6 Nucleotide-induced asymmetry within ATPase activator ring drives s54-RNAP interaction and ATP hydrolysis Deposited 2013-07-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain M 121–387（267 aa） Fragment：UNP residues 121-387 Chain N 121–387（267 aa） Fragment：UNP residues 121-387 Chain O 121–387（267 aa） Fragment：UNP residues 121-387 Chain P 121–387（267 aa） Fragment：UNP residues 121-387 Chain Q 121–387（267 aa） Fragment：UNP residues 121-387 Chain R 121–387（267 aa） Fragment：UNP residues 121-387	Not recorded	08T [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium × 5 MG MAGNESIUM ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；277 K；20% ethylene glycol, pH 7.9, vapor diffusion, hanging drop, temperature 277K	Resolution 3.60 Å R-free 0.308
4LY6 Nucleotide-induced asymmetry within ATPase activator ring drives s54-RNAP interaction and ATP hydrolysis Deposited 2013-07-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain S 121–387（267 aa） Fragment：UNP residues 121-387 Chain T 121–387（267 aa） Fragment：UNP residues 121-387 Chain U 121–387（267 aa） Fragment：UNP residues 121-387 Chain V 121–387（267 aa） Fragment：UNP residues 121-387 Chain W 121–387（267 aa） Fragment：UNP residues 121-387 Chain X 121–387（267 aa） Fragment：UNP residues 121-387	Not recorded	08T [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium × 5 MG MAGNESIUM ION × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；277 K；20% ethylene glycol, pH 7.9, vapor diffusion, hanging drop, temperature 277K	Resolution 3.60 Å R-free 0.308
4LZZ Nucleotide-induced asymmetry within atpase activator ring drives s54-RNAP interaction and ATP hydrolysis Deposited 2013-08-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 121–387（267 aa） Fragment：ATPase Domain (UNP residues 121-387) Chain B 121–387（267 aa） Fragment：ATPase Domain (UNP residues 121-387) Chain C 121–387（267 aa） Fragment：ATPase Domain (UNP residues 121-387) Chain D 121–387（267 aa） Fragment：ATPase Domain (UNP residues 121-387) Chain E 121–387（267 aa） Fragment：ATPase Domain (UNP residues 121-387) Chain F 121–387（267 aa） Fragment：ATPase Domain (UNP residues 121-387)	Not recorded	08T [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium × 5 MG MAGNESIUM ION × 6 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；277 K；20% ethylene glycol, crystal soaked in fresh mother liquor prior to flash cooling, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 3.21 Å R-free 0.322
4LZZ Nucleotide-induced asymmetry within atpase activator ring drives s54-RNAP interaction and ATP hydrolysis Deposited 2013-08-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain G 121–387（267 aa） Fragment：ATPase Domain (UNP residues 121-387) Chain H 121–387（267 aa） Fragment：ATPase Domain (UNP residues 121-387) Chain I 121–387（267 aa） Fragment：ATPase Domain (UNP residues 121-387) Chain J 121–387（267 aa） Fragment：ATPase Domain (UNP residues 121-387) Chain K 121–387（267 aa） Fragment：ATPase Domain (UNP residues 121-387) Chain L 121–387（267 aa） Fragment：ATPase Domain (UNP residues 121-387)	Not recorded	08T [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium × 5 MG MAGNESIUM ION × 6 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；277 K；20% ethylene glycol, crystal soaked in fresh mother liquor prior to flash cooling, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 3.21 Å R-free 0.322
4LZZ Nucleotide-induced asymmetry within atpase activator ring drives s54-RNAP interaction and ATP hydrolysis Deposited 2013-08-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain M 121–387（267 aa） Fragment：ATPase Domain (UNP residues 121-387) Chain N 121–387（267 aa） Fragment：ATPase Domain (UNP residues 121-387) Chain O 121–387（267 aa） Fragment：ATPase Domain (UNP residues 121-387) Chain P 121–387（267 aa） Fragment：ATPase Domain (UNP residues 121-387) Chain Q 121–387（267 aa） Fragment：ATPase Domain (UNP residues 121-387) Chain R 121–387（267 aa） Fragment：ATPase Domain (UNP residues 121-387)	Not recorded	08T [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium × 6 MG MAGNESIUM ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；277 K；20% ethylene glycol, crystal soaked in fresh mother liquor prior to flash cooling, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 3.21 Å R-free 0.322
4LZZ Nucleotide-induced asymmetry within atpase activator ring drives s54-RNAP interaction and ATP hydrolysis Deposited 2013-08-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain S 121–387（267 aa） Fragment：ATPase Domain (UNP residues 121-387) Chain T 121–387（267 aa） Fragment：ATPase Domain (UNP residues 121-387) Chain U 121–387（267 aa） Fragment：ATPase Domain (UNP residues 121-387) Chain V 121–387（267 aa） Fragment：ATPase Domain (UNP residues 121-387) Chain W 121–387（267 aa） Fragment：ATPase Domain (UNP residues 121-387) Chain X 121–387（267 aa） Fragment：ATPase Domain (UNP residues 121-387)	Not recorded	08T [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium × 6 MG MAGNESIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；277 K；20% ethylene glycol, crystal soaked in fresh mother liquor prior to flash cooling, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 3.21 Å R-free 0.322
9MSE de novo SigN RNA polymerase transcription initiation intermediate with pre-catalytic bEBP state (RPi1 open ring) Deposited 2025-01-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 16-meric	Chain A 121–387（267 aa） Chain B 121–387（267 aa） Chain C 121–387（267 aa） Chain D 121–387（267 aa） Chain E 121–387（267 aa） Chain F 121–387（267 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 6 MG MAGNESIUM ION × 3 POP PYROPHOSPHATE 2- × 1 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8；40 mM Tris-HCl, pH 8/RT, 200 mM KCl, 10 mM MgCl2, 1 mM DTT; fluorinated fos-choline-8 (FC8F) added to a final concentration of 1.5 mM during grid preparation cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å
9MSF de novo SigN RNA polymerase transcription initiation intermediate with post-catalytic bEBP state (RPi1 closed ring) Deposited 2025-01-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 16-meric	Chain A 121–387（267 aa） Chain B 121–387（267 aa） Chain C 121–387（267 aa） Chain D 121–387（267 aa） Chain E 121–387（267 aa） Chain F 121–387（267 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 5 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 POP PYROPHOSPHATE 2- × 1 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8；40 mM Tris-HCl, pH 8/RT, 200 mM KCl, 10 mM MgCl2, 1 mM DTT; fluorinated fos-choline-8 (FC8F) added to a final concentration of 1.5 mM during grid preparation cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.60 Å
9MSG De novo SigN RNA polymerase transcription initiation intermediate with bound SigN-RII Deposited 2025-01-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric	Chain A 121–387（267 aa） Chain B 121–387（267 aa） Chain C 121–387（267 aa） Chain D 121–387（267 aa） Chain E 121–387（267 aa） Chain F 121–387（267 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 5 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 POP PYROPHOSPHATE 2- × 1 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8；40 mM Tris-HCl, pH 8/RT, 200 mM KCl, 10 mM MgCl2, 1 mM DTT; fluorinated fos-choline-8 (FC8F) added to a final concentration of 1.5 mM during grid preparation cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å

12 other PDB entries and 22 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	O67198_AQUAE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–267； UniProt 122–387 Author chain B； PDBConstruct 1–267； UniProt 122–387 Author chain C； PDBConstruct 1–267； UniProt 122–387 Author chain D； PDBConstruct 1–267； UniProt 122–387 Author chain E； PDBConstruct 1–267； UniProt 122–387 Author chain F； PDBConstruct 1–267； UniProt 122–387 Author chain G； PDBConstruct 1–267； UniProt 122–387 Author chain H； PDBConstruct 1–267； UniProt 122–387 Author chain I； PDBConstruct 1–267； UniProt 122–387 Author chain J； PDBConstruct 1–267； UniProt 122–387 Author chain K； PDBConstruct 1–267； UniProt 122–387 Author chain L； PDBConstruct 1–267； UniProt 122–387 Author chain M； PDBConstruct 1–267； UniProt 122–387 Author chain N； PDBConstruct 1–267； UniProt 122–387

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1ny6
Deposition date deposition_date	2003-02-11
Structure title title	Crystal structure of sigm54 activator (AAA+ ATPase) in the active state
Keywords keywords	AAA+ ATPase, sigma54 activator, bacterial transcription, heptamer, TRANSCRIPTION; TRANSCRIPTION
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	51.14 Å
Radius of gyration Rg (electron density) rg_electron	50.74 Å
Forward intensity I(0) i0	2094170000.00
Molecular weight molecular_weight	397740.0 kDa
Excluded volume excluded_volume	504920 Å³
Envelope volume envelope_volume	729420 Å³
Hydration-shell volume shell_volume	117870 Å³
Envelope diameter envelope_diameter	174.8 Å
Shell Rg shell_rg	57.44 Å
Envelope Rg envelope_rg	48.35 Å
Shape Rg shape_rg	50.72 Å
Total Rg total_rg	51.06 Å
Total atoms total_atoms	28041
Residues n_residues	3456
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	165.0 Å
Rg (real space) rg_real	50.95 Å
Rg uncertainty (real space) rg_real_error	1.38 Å
I(0) (real space) i0_real	2.0940e+09
I(0) uncertainty (real space) i0_real_error	3.7810e+07
Rg (reciprocal space) rg_reciprocal	51.30 Å
I(0) (reciprocal space) i0_reciprocal	2095000000.0000
Solution quality estimate total_estimate	0.8719
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	63.9 Å
Skewness Skewness skewness	0.169
Kurtosis Kurtosis kurtosis	-0.340
Angular range angular_range	— – 0.1550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	170200000.0000
Real-space data points n_real_points	32
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.844; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.978; Smooth: 0.823

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 42 domains

SCOP 2.08 (14 domains)

Domain ID domain_id	d1ny6a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.20 — Extended AAA-ATPase domain

Domain ID domain_id	d1ny6b_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.20 — Extended AAA-ATPase domain

Domain ID domain_id	d1ny6c_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.20 — Extended AAA-ATPase domain

Domain ID domain_id	d1ny6d_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.20 — Extended AAA-ATPase domain

Domain ID domain_id	d1ny6e_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.20 — Extended AAA-ATPase domain

Domain ID domain_id	d1ny6f_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.20 — Extended AAA-ATPase domain

Domain ID domain_id	d1ny6g_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.20 — Extended AAA-ATPase domain

Domain ID domain_id	d1ny6h_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.20 — Extended AAA-ATPase domain

Domain ID domain_id	d1ny6i_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.20 — Extended AAA-ATPase domain

Domain ID domain_id	d1ny6j_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.20 — Extended AAA-ATPase domain

Domain ID domain_id	d1ny6k_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.20 — Extended AAA-ATPase domain

Domain ID domain_id	d1ny6l_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.20 — Extended AAA-ATPase domain

Domain ID domain_id	d1ny6m_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.20 — Extended AAA-ATPase domain

Domain ID domain_id	d1ny6n_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.20 — Extended AAA-ATPase domain

CATH v4.4 (28 domains)

Domain ID domain_id	1ny6A01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	1ny6A02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	60 —

Domain ID domain_id	1ny6B01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	1ny6B02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	60 —

Domain ID domain_id	1ny6C01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	1ny6C02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	60 —

Domain ID domain_id	1ny6D01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	1ny6D02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	60 —

Domain ID domain_id	1ny6E01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	1ny6E02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	60 —

Domain ID domain_id	1ny6F01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	1ny6F02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	60 —

Domain ID domain_id	1ny6G01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	1ny6G02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	60 —

Domain ID domain_id	1ny6H01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	1ny6H02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	60 —

Domain ID domain_id	1ny6I01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	1ny6I02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	60 —

Domain ID domain_id	1ny6J01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	1ny6J02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	60 —

Domain ID domain_id	1ny6K01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	1ny6K02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	60 —

Domain ID domain_id	1ny6L01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	1ny6L02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	60 —

Domain ID domain_id	1ny6M01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	1ny6M02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	60 —

Domain ID domain_id	1ny6N01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	1ny6N02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	60 —

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8. Citations (1)

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Unit-cell length a length_a	106.788 Å
Unit-cell length b length_b	108.265 Å
Unit-cell length c length_c	110.020 Å
Unit-cell angle α angle_alpha	70.25 °
Unit-cell angle β angle_beta	85.90 °
Unit-cell angle γ angle_gamma	73.27 °
Molecules per unit cell Z z_pdb	14

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.100 Å
Low-resolution limit resolution_low	19.980 Å
R factor r_factor	0.2660
R_work r_work	0.2660
R_free r_free	0.3290

Description description	transcriptional regulator (NtrC family)
Molecular weight formula_weight	30618.4 kDa
Source method src_method	man
Copy count entity_count	14

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L,M,N
Atom count atom_count	28041

Crystal structure of sigm54 activator (AAA+ ATPase) in the active state

1. Protein Identity and Related Structures Protein Identity & Related Structures

transcriptional regulator (NtrC family)

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 non-polymer

7. Fold Classification (SCOP + CATH) 42 domains

SCOP 2.08 (14 domains)

CATH v4.4 (28 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Aquifex aeolicus
NCBI Class编号 ncbi_taxonomy_id	63363
宿主生物 host_organism	Escherichia coli

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	14

fit	/app/data/saxs_computation/ny/1ny6/1ny6.fit
pddf	/app/data/pr_computation/ny/1ny6/1ny6.pr.out
profile	/app/data/saxs_computation/ny/1ny6/1ny6.dat