3j9c

CryoEM single particle reconstruction of anthrax toxin protective antigen pore at 2.9 Angstrom resolution

Method: ELECTRON MICROSCOPY D_max: 197.9 Å Quality: REASONABLE

▼

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

Protective antigen PA-63

Bacillus anthracis

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: 7-MERIC（7） Consistent with protein copy count	Chain A； UniProt 203–764	Fragment：C-terminal 63-kDa fragment (UNP residues 203-764)	CA CALCIUM ION × 14	ELECTRON MICROSCOPY cryo-EM buffer：50 mM NaOAc, pH 5.0, 0.05% Igepal CA-630；pH 5；50 mM NaOAc, pH 5.0, 0.05% Igepal CA-630 cryo-EM vitrification conditions：Cryogen ETHANE；Plunged into liguid nitrogen (FEI VITROBOT MARK IV).	Resolution 2.90 Å
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 203–764	Fragment：C-terminal 63-kDa fragment (UNP residues 203-764)	CA CALCIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer：50 mM NaOAc, pH 5.0, 0.05% Igepal CA-630；pH 5；50 mM NaOAc, pH 5.0, 0.05% Igepal CA-630 cryo-EM vitrification conditions：Cryogen ETHANE；Plunged into liguid nitrogen (FEI VITROBOT MARK IV).	Resolution 2.90 Å
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 203–764	Fragment：C-terminal 63-kDa fragment (UNP residues 203-764)	CA CALCIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer：50 mM NaOAc, pH 5.0, 0.05% Igepal CA-630；pH 5；50 mM NaOAc, pH 5.0, 0.05% Igepal CA-630 cryo-EM vitrification conditions：Cryogen ETHANE；Plunged into liguid nitrogen (FEI VITROBOT MARK IV).	Resolution 2.90 Å

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 3J9C	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1ACC ANTHRAX PROTECTIVE ANTIGEN Deposited 1997-02-05	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 30–764（735 aa）	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；277 K；PROTEIN WAS CRYSTALLIZED FROM 12-18% PEG 8K AND 50 MM CITRATE, PH 6.0 AT 4 DEGREES C. CRYSTAL FORM ""2"" (NEEDLE-LIKE CRYSTALS)., temperature 277K	Resolution 2.10 Å R-free 0.296
1T6B Crystal structure of B. anthracis Protective Antigen complexed with human Anthrax toxin receptor Deposited 2004-05-05	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain X 30–764（735 aa）	Not recorded	CA CALCIUM ION × 2 NA SODIUM ION × 2 PG4 TETRAETHYLENE GLYCOL × 1 MN MANGANESE (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9；300 K；CHES buffer, PEG400, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 300K	Resolution 2.50 Å R-free 0.266
1TZN Crystal Structure of the Anthrax Toxin Protective Antigen Heptameric Prepore bound to the VWA domain of CMG2, an anthrax toxin receptor Deposited 2004-07-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain A 203–764（562 aa） Fragment：63-kDa domain Chain B 203–764（562 aa） Fragment：63-kDa domain Chain C 203–764（562 aa） Fragment：63-kDa domain Chain D 203–764（562 aa） Fragment：63-kDa domain Chain E 203–764（562 aa） Fragment：63-kDa domain Chain F 203–764（562 aa） Fragment：63-kDa domain Chain O 203–764（562 aa） Fragment：63-kDa domain	Not recorded	CA CALCIUM ION × 14 MG MAGNESIUM ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG 8000, sodium chloride, Tris, magnesium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 4.30 Å R-free 0.330
1TZN Crystal Structure of the Anthrax Toxin Protective Antigen Heptameric Prepore bound to the VWA domain of CMG2, an anthrax toxin receptor Deposited 2004-07-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain G 203–764（562 aa） Fragment：63-kDa domain Chain H 203–764（562 aa） Fragment：63-kDa domain Chain I 203–764（562 aa） Fragment：63-kDa domain Chain J 203–764（562 aa） Fragment：63-kDa domain Chain K 203–764（562 aa） Fragment：63-kDa domain Chain L 203–764（562 aa） Fragment：63-kDa domain Chain M 203–764（562 aa） Fragment：63-kDa domain	Not recorded	CA CALCIUM ION × 14 MG MAGNESIUM ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG 8000, sodium chloride, Tris, magnesium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 4.30 Å R-free 0.330
1TZN Crystal Structure of the Anthrax Toxin Protective Antigen Heptameric Prepore bound to the VWA domain of CMG2, an anthrax toxin receptor Deposited 2004-07-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 28 PDB declaration: 28-meric	Chain A 203–764（562 aa） Fragment：63-kDa domain Chain B 203–764（562 aa） Fragment：63-kDa domain Chain C 203–764（562 aa） Fragment：63-kDa domain Chain D 203–764（562 aa） Fragment：63-kDa domain Chain E 203–764（562 aa） Fragment：63-kDa domain Chain F 203–764（562 aa） Fragment：63-kDa domain Chain G 203–764（562 aa） Fragment：63-kDa domain Chain H 203–764（562 aa） Fragment：63-kDa domain Chain I 203–764（562 aa） Fragment：63-kDa domain Chain J 203–764（562 aa） Fragment：63-kDa domain Chain K 203–764（562 aa） Fragment：63-kDa domain Chain L 203–764（562 aa） Fragment：63-kDa domain Chain M 203–764（562 aa） Fragment：63-kDa domain Chain O 203–764（562 aa） Fragment：63-kDa domain	Not recorded	CA CALCIUM ION × 28 MG MAGNESIUM ION × 14	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG 8000, sodium chloride, Tris, magnesium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 4.30 Å R-free 0.330
1TZN Crystal Structure of the Anthrax Toxin Protective Antigen Heptameric Prepore bound to the VWA domain of CMG2, an anthrax toxin receptor Deposited 2004-07-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 28 PDB declaration: 28-meric	Chain A 203–764（562 aa） Fragment：63-kDa domain Chain B 203–764（562 aa） Fragment：63-kDa domain Chain C 203–764（562 aa） Fragment：63-kDa domain Chain D 203–764（562 aa） Fragment：63-kDa domain Chain E 203–764（562 aa） Fragment：63-kDa domain Chain F 203–764（562 aa） Fragment：63-kDa domain Chain G 203–764（562 aa） Fragment：63-kDa domain Chain H 203–764（562 aa） Fragment：63-kDa domain Chain I 203–764（562 aa） Fragment：63-kDa domain Chain J 203–764（562 aa） Fragment：63-kDa domain Chain K 203–764（562 aa） Fragment：63-kDa domain Chain L 203–764（562 aa） Fragment：63-kDa domain Chain M 203–764（562 aa） Fragment：63-kDa domain Chain O 203–764（562 aa） Fragment：63-kDa domain	Not recorded	CA CALCIUM ION × 28 MG MAGNESIUM ION × 14	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG 8000, sodium chloride, Tris, magnesium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 4.30 Å R-free 0.330
1TZN Crystal Structure of the Anthrax Toxin Protective Antigen Heptameric Prepore bound to the VWA domain of CMG2, an anthrax toxin receptor Deposited 2004-07-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 28 PDB declaration: 28-meric	Chain A 203–764（562 aa） Fragment：63-kDa domain Chain B 203–764（562 aa） Fragment：63-kDa domain Chain C 203–764（562 aa） Fragment：63-kDa domain Chain D 203–764（562 aa） Fragment：63-kDa domain Chain E 203–764（562 aa） Fragment：63-kDa domain Chain F 203–764（562 aa） Fragment：63-kDa domain Chain G 203–764（562 aa） Fragment：63-kDa domain Chain H 203–764（562 aa） Fragment：63-kDa domain Chain I 203–764（562 aa） Fragment：63-kDa domain Chain J 203–764（562 aa） Fragment：63-kDa domain Chain K 203–764（562 aa） Fragment：63-kDa domain Chain L 203–764（562 aa） Fragment：63-kDa domain Chain M 203–764（562 aa） Fragment：63-kDa domain Chain O 203–764（562 aa） Fragment：63-kDa domain	Not recorded	CA CALCIUM ION × 28 MG MAGNESIUM ION × 14	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG 8000, sodium chloride, Tris, magnesium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 4.30 Å R-free 0.330
1TZO Crystal Structure of the Anthrax Toxin Protective Antigen Heptameric Prepore Deposited 2004-07-10	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 7 PDB declaration: heptameric	Chain A 203–764（562 aa） Fragment：63-kDa domain Chain B 203–764（562 aa） Fragment：63-kDa domain Chain C 203–764（562 aa） Fragment：63-kDa domain Chain D 203–764（562 aa） Fragment：63-kDa domain Chain E 203–764（562 aa） Fragment：63-kDa domain Chain F 203–764（562 aa） Fragment：63-kDa domain Chain O 203–764（562 aa） Fragment：63-kDa domain	Not recorded	CA CALCIUM ION × 14	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.25；298 K；HEPES, sodium chloride, b-octylglucoside, spermine, pH 8.25, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.60 Å R-free 0.317
1TZO Crystal Structure of the Anthrax Toxin Protective Antigen Heptameric Prepore Deposited 2004-07-10	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 7 PDB declaration: heptameric	Chain G 203–764（562 aa） Fragment：63-kDa domain Chain H 203–764（562 aa） Fragment：63-kDa domain Chain I 203–764（562 aa） Fragment：63-kDa domain Chain J 203–764（562 aa） Fragment：63-kDa domain Chain K 203–764（562 aa） Fragment：63-kDa domain Chain L 203–764（562 aa） Fragment：63-kDa domain Chain M 203–764（562 aa） Fragment：63-kDa domain	Not recorded	CA CALCIUM ION × 14	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.25；298 K；HEPES, sodium chloride, b-octylglucoside, spermine, pH 8.25, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.60 Å R-free 0.317
25PV Structure of the anthrax protective antigen in complex with a potent neutralizing antibody Deposited 2026-04-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 200–626（427 aa）	Mutation：F231S	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.03 Å
3ETB Crystal structure of the engineered neutralizing antibody M18 complexed with anthrax protective antigen domain 4 Deposited 2008-10-07	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain J 621–764（144 aa） Fragment：Domain 4 of protective antigen PA-63: UNP residues 621-764	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；10% PEG 20000, 0.05 M Tris-HCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 3.80 Å R-free 0.276
3ETB Crystal structure of the engineered neutralizing antibody M18 complexed with anthrax protective antigen domain 4 Deposited 2008-10-07	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain K 621–764（144 aa） Fragment：Domain 4 of protective antigen PA-63: UNP residues 621-764	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；10% PEG 20000, 0.05 M Tris-HCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 3.80 Å R-free 0.276
3ETB Crystal structure of the engineered neutralizing antibody M18 complexed with anthrax protective antigen domain 4 Deposited 2008-10-07	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 621–764（144 aa） Fragment：Domain 4 of protective antigen PA-63: UNP residues 621-764	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；10% PEG 20000, 0.05 M Tris-HCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 3.80 Å R-free 0.276
3ETB Crystal structure of the engineered neutralizing antibody M18 complexed with anthrax protective antigen domain 4 Deposited 2008-10-07	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain M 621–764（144 aa） Fragment：Domain 4 of protective antigen PA-63: UNP residues 621-764	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；10% PEG 20000, 0.05 M Tris-HCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 3.80 Å R-free 0.276
3INO 1.95A Resolution Structure of Protective Antigen Domain 4 Deposited 2009-08-12	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 × 2 PDB declaration: dimeric	Chain A 624–764（141 aa） Fragment：Domain 4 Chain B 624–764（141 aa） Fragment：Domain 4	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；277 K；20% PEG 8000, 100mM imidazole, 3% MPD, pH 6.5, vapor diffusion, temperature 277K	Resolution 1.95 Å R-free 0.258
3INO 1.95A Resolution Structure of Protective Antigen Domain 4 Deposited 2009-08-12	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 624–764（141 aa） Fragment：Domain 4	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；277 K；20% PEG 8000, 100mM imidazole, 3% MPD, pH 6.5, vapor diffusion, temperature 277K	Resolution 1.95 Å R-free 0.258
3INO 1.95A Resolution Structure of Protective Antigen Domain 4 Deposited 2009-08-12	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 624–764（141 aa） Fragment：Domain 4	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；277 K；20% PEG 8000, 100mM imidazole, 3% MPD, pH 6.5, vapor diffusion, temperature 277K	Resolution 1.95 Å R-free 0.258
3KWV Structural basis for the unfolding of anthrax lethal factor by protective antigen oligomers Deposited 2009-12-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 197–764（568 aa） Fragment：UNP residues 197-764 Chain B 197–764（568 aa） Fragment：UNP residues 197-764	Mutation：V303P, H304G Mutation：V303P, H304G	CA CALCIUM ION × 16	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；291 K；16% PEG 3000, 0.1M cacodylic acid, 0.2M magnesium chloride, 10 mM Tris-Cl, 75 mM sodium chloride, 10 mM adenosine-5'-triphosphate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.10 Å R-free 0.281
3KWV Structural basis for the unfolding of anthrax lethal factor by protective antigen oligomers Deposited 2009-12-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain D 197–764（568 aa） Fragment：UNP residues 197-764 Chain E 197–764（568 aa） Fragment：UNP residues 197-764	Mutation：V303P, H304G Mutation：V303P, H304G	CA CALCIUM ION × 16	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；291 K；16% PEG 3000, 0.1M cacodylic acid, 0.2M magnesium chloride, 10 mM Tris-Cl, 75 mM sodium chloride, 10 mM adenosine-5'-triphosphate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.10 Å R-free 0.281
3MHZ 1.7A structure of 2-fluorohistidine labeled Protective Antigen Deposited 2010-04-09	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 30–764（735 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 2 PG4 TETRAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.2；293 K；30% PEG 400, 0.1M Tris, pH 8.2, vapor diffusion, temperature 293K	Resolution 1.70 Å R-free 0.222
3Q8A Crystal structure of WT Protective Antigen (pH 5.5) Deposited 2011-01-06	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 30–764（735 aa）	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.5；293 K；25 %(w/v) PEG 1500, 100 mM SPG Buffer, pH 5.5, vapor diffusion, temperature 293K	Resolution 3.13 Å R-free 0.279
3Q8B Crystal structure of WT Protective Antigen (pH 9.0) Deposited 2011-01-06	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 30–764（735 aa）	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 9；293 K；25 %(w/v) PEG 1500, 100 mM MMT Buffer, pH 9.0, vapor diffusion, temperature 293K	Resolution 2.00 Å R-free 0.258
3Q8C Crystal structure of Protective Antigen W346F (pH 5.5) Deposited 2011-01-06	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 30–764（735 aa）	Mutation：W346F	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.5；293 K；25%(w/v) PEG 1500, 100mM SPG Buffer, pH 5.5, vapor diffusion, temperature 293K	Resolution 2.85 Å R-free 0.271
3Q8E Crystal structure of Protective Antigen W346F (pH 8.5) Deposited 2011-01-06	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 30–764（735 aa）	Mutation：W346F	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；293 K；25%(w/v) PEG 1500, 100mM SPG Buffer, pH 8.5, vapor diffusion, temperature 293K	Resolution 2.10 Å R-free 0.248
3Q8F Crystal structure of 2-Fluorohistine labeled Protective Antigen (pH 5.8) Deposited 2011-01-06	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 30–764（735 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 2 PG4 TETRAETHYLENE GLYCOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；293 K；30% PEG 400, 100mM MES, pH 7.0, vapor diffusion, temperature 293K	Resolution 2.10 Å R-free 0.267
3TEZ Crystal Structure of Anthrax Protective Antigen Mutant S337C N664C and dithiolacetone modified to 1.8-A resolution Deposited 2011-08-15	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 30–764（735 aa）	Mutation：S337C,N664C	CA CALCIUM ION × 2 MXE 2-METHOXYETHANOL × 2 ACN ACETONE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；292 K；20% PEG-ME 2000, 0.1M Tris-Cl, 0.2M Trimethylamine-N-oxide, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 1.83 Å R-free 0.226
4EE2 Crystal Structure of Anthrax Protective Antigen K446M Mutant to 1.91-A Resolution Deposited 2012-03-28	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 30–764（735 aa） Fragment：Protective antigen	Mutation：K446M	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；292 K；0.1M tris, 20% peg2k-MME, 0.2M TMAO, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 1.91 Å R-free 0.265
4H2A Crystal structure of wild type protective antigen to 1.62 A (pH 7.5) Deposited 2012-09-12	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 30–764（735 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 4 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；280 K；protein crystallised from 0.1 M HEPES pH 7.5, 10 % PEG 8000, 8 % ethylene glycol by sitting drop vapour diffusion at temperature 280 K., VAPOR DIFFUSION, SITTING DROP	Resolution 1.62 Å R-free 0.219
4NAM 1.7A structure of 5-Fluoro Tryptophan Labeled Protective Antigen (W206Y) Deposited 2013-10-22	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 30–764（735 aa）	Mutation：W206Y Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；293 K；35% (v/v) Pentaerythritol propoxylate (5/4 PO/OH), 0.05 M HEPES, 0.2 M Potassium chloride, pH 7.5, vapor diffusion, temperature 293K	Resolution 1.70 Å R-free 0.208
5FR3 X-ray crystal structure of aggregation-resistant protective antigen of Bacillus anthracis (mutant S559L T576E) Deposited 2015-12-15	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 43–764（722 aa）	Mutation：YES	CA CALCIUM ION × 2 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions 20 MM MGCL2, 100 MM HEPES PH 7.5, 22% POLY(ACRYLIC ACID SODIUM SALT) 5100	Resolution 1.94 Å R-free 0.227
6PSN Anthrax toxin protective antigen channels bound to lethal factor Deposited 2019-07-12	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 197–764（568 aa） Chain B 197–764（568 aa） Chain C 197–764（568 aa） Chain D 197–764（568 aa） Chain E 197–764（568 aa） Chain F 197–764（568 aa） Chain G 197–764（568 aa）	Not recorded	CA CALCIUM ION × 14	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.60 Å
6UJI Low resolution crystal structure (5.5 A) of the anthrax toxin protective antigen heptamer prepore D425A mutant Deposited 2019-10-03	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 7 PDB declaration: heptameric	Chain A 197–764（568 aa） Chain B 197–764（568 aa） Chain C 197–764（568 aa） Chain D 197–764（568 aa） Chain E 197–764（568 aa） Chain F 197–764（568 aa） Chain G 197–764（568 aa）	Mutation：D425A Mutation：D425A Mutation：D425A Mutation：D425A Mutation：D425A Mutation：D425A Mutation：D425A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；10% (v/v) ethanol, 0.1 M Tris	Resolution 5.50 Å R-free 0.278
6UJI Low resolution crystal structure (5.5 A) of the anthrax toxin protective antigen heptamer prepore D425A mutant Deposited 2019-10-03	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 7 PDB declaration: heptameric	Chain H 197–764（568 aa） Chain I 197–764（568 aa） Chain J 197–764（568 aa） Chain K 197–764（568 aa） Chain L 197–764（568 aa） Chain M 197–764（568 aa） Chain N 197–764（568 aa）	Mutation：D425A Mutation：D425A Mutation：D425A Mutation：D425A Mutation：D425A Mutation：D425A Mutation：D425A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；10% (v/v) ethanol, 0.1 M Tris	Resolution 5.50 Å R-free 0.278
6UZB Anthrax toxin protective antigen channels bound to edema factor Deposited 2019-11-14	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 30–764（735 aa） Chain B 30–764（735 aa） Chain C 30–764（735 aa） Chain D 30–764（735 aa） Chain E 30–764（735 aa） Chain F 30–764（735 aa） Chain G 30–764（735 aa）	Not recorded	CA CALCIUM ION × 14	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
6UZD Anthrax toxin protective antigen channels bound to edema factor Deposited 2019-11-14	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain A 30–764（735 aa） Chain B 30–764（735 aa） Chain C 30–764（735 aa） Chain D 30–764（735 aa） Chain E 30–764（735 aa） Chain F 30–764（735 aa） Chain G 30–764（735 aa）	Not recorded	CA CALCIUM ION × 14	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
6UZE Anthrax toxin protective antigen channels bound to edema factor Deposited 2019-11-15	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain A 30–764（735 aa） Chain B 30–764（735 aa） Chain C 30–764（735 aa） Chain D 30–764（735 aa） Chain E 30–764（735 aa） Chain F 30–764（735 aa） Chain G 30–764（735 aa）	Not recorded	CA CALCIUM ION × 14	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
6VRA Anthrax octamer prechannel bound to full-length edema factor Deposited 2020-02-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 33–764（732 aa） Chain B 33–764（732 aa） Chain C 33–764（732 aa） Chain D 33–764（732 aa） Chain E 33–764（732 aa） Chain F 33–764（732 aa） Chain G 33–764（732 aa） Chain H 33–764（732 aa）	Mutation：K245G, R252N Mutation：D512K Mutation：K245G, R252N Mutation：D512K Mutation：K245G, R252N Mutation：D512K Mutation：K245G, R252N Mutation：D512K	CA CALCIUM ION × 16	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
6WJJ Anthrax octamer prechannel bound to full-length lethal factor Deposited 2020-04-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 33–764（732 aa） Chain B 33–764（732 aa） Chain C 33–764（732 aa） Chain D 33–764（732 aa） Chain E 33–764（732 aa） Chain F 33–764（732 aa） Chain G 33–764（732 aa） Chain H 33–764（732 aa）	Not recorded	CA CALCIUM ION × 16 SO4 SULFATE ION × 4 ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
7KXR Protective antigen pore translocating lethal factor N-terminal domain Deposited 2020-12-04	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 203–764（562 aa） Fragment：UNP Residues 203-764 Chain B 203–764（562 aa） Fragment：UNP Residues 203-764 Chain C 203–764（562 aa） Fragment：UNP Residues 203-764 Chain D 203–764（562 aa） Fragment：UNP Residues 203-764 Chain E 203–764（562 aa） Fragment：UNP Residues 203-764 Chain F 203–764（562 aa） Fragment：UNP Residues 203-764 Chain G 203–764（562 aa） Fragment：UNP Residues 203-764	Not recorded	CA CALCIUM ION × 14	ELECTRON MICROSCOPY cryo-EM buffer pH 5.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
7O85 Anthrax toxin prepore in complex with the neutralizing Fab cAb29 Deposited 2021-04-14	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 21 PDB declaration: 21-meric	Chain A 203–643（441 aa） Chain D 203–643（441 aa） Chain G 203–643（441 aa） Chain J 203–643（441 aa） Chain M 203–643（441 aa） Chain P 203–643（441 aa） Chain S 203–643（441 aa）	Not recorded	CA CALCIUM ION × 14	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å

28 other PDB entries and 40 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PAG_BACAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–562； UniProt 203–764

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

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	3j9c
Deposition date deposition_date	2014-12-25
Structure title title	CryoEM single particle reconstruction of anthrax toxin protective antigen pore at 2.9 Angstrom resolution
Keywords keywords	bacterial toxin, anthrax toxin, protective antigen, protein translocation channel, TOXIN, TRANSPORT PROTEIN; TOXIN, TRANSPORT PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

▼

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

Radius of gyration Rg (Guinier) rg_guinier	43.15 Å
Radius of gyration Rg (electron density) rg_electron	45.52 Å
Forward intensity I(0) i0	37812500.00
Molecular weight molecular_weight	47249.0 kDa
Excluded volume excluded_volume	58686 Å³
Envelope volume envelope_volume	105890 Å³
Hydration-shell volume shell_volume	24210 Å³
Envelope diameter envelope_diameter	190.1 Å
Shell Rg shell_rg	36.39 Å
Envelope Rg envelope_rg	57.72 Å
Shape Rg shape_rg	45.63 Å
Total Rg total_rg	44.46 Å
Total atoms total_atoms	3328
Residues n_residues	423
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

▼

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

Maximum dimension Dmax dmax	197.9 Å
Rg (real space) rg_real	45.88 Å
Rg uncertainty (real space) rg_real_error	4.64 Å
I(0) (real space) i0_real	3.7810e+07
I(0) uncertainty (real space) i0_real_error	8.9740e+05
Rg (reciprocal space) rg_reciprocal	43.16 Å
I(0) (reciprocal space) i0_reciprocal	37690000.0000
Solution quality estimate total_estimate	0.6104
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.7 Å
Skewness Skewness skewness	1.206
Kurtosis Kurtosis kurtosis	0.525
Angular range angular_range	— – 0.1850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2983000.0000
Real-space data points n_real_points	38
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.000; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.000; Smooth: 0.929

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Protective antigen PA-63
Molecular weight formula_weight	63019.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3328

TVPDRDNDGIPDSLEVEGYTVDVKNKRTFLSPWISNIHEKKGLTKYKSSPEKWSTASDPYSDFEKVTGRIDKNVSPEARHPLVAAYPIVHVDMENIILSKNEDQSTQNTDSQTRTISKNTSTSRTHTSEVHGNAEVHASFFDIGGSVSAGFSNSNSSTVAIDHSLSLAGERTWAETMGLNTADTARLNANIRYVNTGTAPIYNVLPTTSLVLGKNQTLATIKAKENQLSQILAPNNYYPSKNLAPIALNAQDDFSSTPITMNYNQFLELEKTKQLRLDTDQVYGNIATYNFENGRVRVDTGSNWSEVLPQIQETTARIIFNGKDLNLVERRIAAVNPSDPLETTKPDMTLKEALKIAFGFNEPNGNLQYQGKDITEFDFNFDQQTSQNIKNQLAELNATNIYTVLDKIKLNAKMNILIRDKRFHYDRNNIAVGADESVVKEAHREVINSSTEGLLLNIDKDIRKILSGYIVEIEDTEGLKEVINDRYDMLNISSLRQDGKTFIDFKKYNDKLPLYISNPNYKVNVYAVTKENTIINPSENGDTSTNGIKKILIFSKKGYEIG

来源 Source

来源生物 organism	Bacillus anthracis
通用名 common_name	anthrax
NCBI Class编号 ncbi_taxonomy_id	1392
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	2

▼

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3j9ca1
Class class	b — All beta proteins
Fold Fold fold	b.179 — Anthrax protective antigen N-terminal-like
Superfamily Superfamily superfamily	b.179.1 — PA14-like
Family Family family	b.179.1.1 — PA14

CATH v4.4 (1 domains)

Domain ID domain_id	3j9cA03
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	110 —

▶

8. Citations (1)

▶

Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	1

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

Resolution resolution	2.90 Å
Resolution测定方法 resolution_method	Maximum a posteriori optimization
颗粒数 num_particles	60455

fit	/app/data/saxs_computation/j9/3j9c/3j9c.fit
pddf	/app/data/pr_computation/j9/3j9c/3j9c.pr.out
profile	/app/data/saxs_computation/j9/3j9c/3j9c.dat