SAXSdb — 3er9

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

;Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase ;

vaccinia virus WR

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–RNA Heteromer Protein × 2 RNA 1 PDB declaration: trimeric（3） Consistent with all polymer counts	Chain A； UniProt 1–297	Mutation：R140A,K142A,R143A	Poly(A) polymerase catalytic subunit × 1 （P23371） 5'-R(UPU)-3' × 1 GOL* GLYCEROL × 3 3AT 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.7；295 K；proteins(4-5mg.ml) in 10mM tris-HCl, pH 8.7, 75 mM NaCl, 0.5 mM DTT, mixed with equal volume buffer which composed of 10mM Tris-HCl, pH 8.7, 15-20% PEG 4000, 5% glycerol, 0.5 mM DTT. Room temperature for several days., VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.06 Å R-free 0.250

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 3ER9	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AV6 VACCINIA METHYLTRANSFERASE VP39 COMPLEXED WITH M7G CAPPED RNA HEXAMER AND S-ADENOSYLHOMOCYSTEINE Deposited 1997-09-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 3–297（295 aa）	Mutation：C-TERMINAL DELETION OF 26 RESIDUES	MGT 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；pH 8.50	Resolution 2.80 Å R-free 0.285
1B42 VACCINIA METHYLTRANSFERASE VP39 COMPLEXED WITH M1ADE AND S-ADENOSYLHOMOCYSTEINE Deposited 1999-01-05	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 1–297（297 aa）	Mutation：C-TERMINAL DELETION OF 26 RESIDUES	SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 M1A 6-AMINO-1-METHYLPURINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 2.20 Å R-free 0.256
1BKY VACCINIA METHYLTRANSFERASE VP39 COMPLEXED WITH M1CYT AND S-ADENOSYLHOMOCYSTEINE Deposited 1998-07-13	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 1–307（307 aa）	Mutation：C-TERMINAL DELETION OF 26 RESIDUES	SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 1MC 1-METHYLCYTOSINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 2.00 Å R-free 0.261
1EAM VACCINIA METHYLTRANSFERASE VP39 MUTANT (EC: 2.7.7.19) Deposited 1999-01-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–307（307 aa）	Mutation：C-TERMINAL DELETION OF 26 RESIDUES & E233A	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 2.00 Å R-free 0.268
1EQA VACCINIA METHYLTRANSFERASE VP39 MUTANT E233Q COMPLEXED WITH M7G AND S-ADENOSYLHOMOCYSTEINE Deposited 1999-01-05	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 1–297（297 aa）	Mutation：C-TERMINAL DELETION OF 26 RESIDUES	SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 MG7 7-METHYLGUANOSINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 2.20 Å R-free 0.255
1JSZ Crystal Structure Analysis of N7,9-dimethylguanine-VP39 complex Deposited 2001-08-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–307（307 aa） Fragment：residues 1-307	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 NDM 7,9-DIMETHYLGUANINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；298 K；PEG 8000, sodium citrate, ammonium sulphate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.93 Å R-free 0.252
1JTE Crystal Structure Analysis of VP39 F180W mutant Deposited 2001-08-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–307（307 aa） Fragment：residues 1-307	Mutation：F180W	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；298 K；PEG 8000, sodium citrate, ammonium sulphate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.00 Å R-free 0.285
1JTF Crystal Structure Analysis of VP39-F180W mutant and m7GpppG complex Deposited 2001-08-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–307（307 aa） Fragment：residues 1-307	Mutation：F180W	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 M7G 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；298 K；PEG 8000, sodium citrate, ammonium sulphate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.60 Å R-free 0.279
1P39 DC26 MUTANT OF VACCINIA VIRUS PROTEIN VP39 IN COMPLEX WITH S-ADENOSYLHOMOCYSTEINE AND M7G(5')PPPG Deposited 1996-12-16	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 1–307（307 aa）	Mutation：26 C-TERMINAL RESIDUES DELETED	SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 MGT 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.5；DC26 CRYSTALLIZED IN 2MM ADOHCY AND 2MM M7GPPPG., pH 4.5	Resolution 2.00 Å
1V39 DC26 MUTANT OF VACCINIA VIRUS PROTEIN VP39 IN COMPLEX WITH S-ADENOSYLHOMOCYSTEINE AND M7G(5')PPPG Deposited 1996-12-16	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 1–307（307 aa）	Mutation：26 C-TERMINAL RESIDUES DELETED	SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 M7G 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；DC26/ADOHCY CRYSTAL SOAKED IN 10MM M7GPPPG., pH 6.5	Resolution 1.80 Å
1VP3 VACCINIA VIRUS PROTEIN VP39 IN COMPLEX WITH S-ADENOSYLHOMOCYSTEINE Deposited 1996-11-21	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 1–333（333 aa）	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.5；pH 4.5	Resolution 1.90 Å
1VP9 DC26 MUTANT OF VACCINIA VIRUS PROTEIN VP39 IN COMPLEX WITH S-ADENOSYLHOMOCYSTEINE Deposited 1996-11-23	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 1–307（307 aa）	Mutation：26 C-TERMINAL RESIDUES DELETED	SAH S-ADENOSYL-L-HOMOCYSTEINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 1.95 Å
1VPT AS11 VARIANT OF VACCINIA VIRUS PROTEIN VP39 IN COMPLEX WITH S-ADENOSYL-L-METHIONINE Deposited 1996-03-20	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 1–333（333 aa）	Mutation：AS11 VARIANT (R140A, K142A, R143A)	SAM S-ADENOSYLMETHIONINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.5；pH 4.5	Resolution 1.80 Å R-free 0.250
2GA9 Crystal Structure of the Heterodimeric Vaccinia Virus Polyadenylate Polymerase with Bound ATP-gamma-S Deposited 2006-03-08	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–297（297 aa）	Mutation：R140A K142A R143A	CA CALCIUM ION × 2 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.7；293 K；20% PEG 4000, 0.240 M CaCl2, 5% glycerol, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.30 Å R-free 0.260
2GAF Crystal Structure of the Vaccinia Polyadenylate Polymerase Heterodimer (apo form) Deposited 2006-03-08	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–297（297 aa）	Mutation：R140A, K142A, R143A Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.7；293 K；20% PEG 4000, 0.24 M CaCl2, 5% glycerol, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.40 Å R-free 0.288
2VP3 DC26 MUTANT OF VACCINIA VIRUS PROTEIN VP39 IN COMPLEX WITH S-ADENOSYLHOMOCYSTEINE AND M7G(5')PPPG Deposited 1996-12-16	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 1–307（307 aa）	Mutation：26 C-TERMINAL RESIDUES DELETED	SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 M7G 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；DC26/ADOHCY CRYSTAL SOAKED IN 10MM M7GDP., pH 6.5	Resolution 1.95 Å
3ER8 Crystal structure of the heterodimeric vaccinia virus mRNA polyadenylate polymerase complex with two fragments of RNA Deposited 2008-10-01	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain A 1–297（297 aa）	Mutation：R140A,K142A,R143A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.7；295 K；proteins(4-5mg.ml) in 10mM Tris-HCl, pH8.7, 75 mM NaCl, 0.5 mM DTT, mixed with equal volume buffer which composed of 10mM Tris-HCl, pH 8.7, 15-20% PEG 4000, 5% glycerol, 0.5 mM DTT. room temperature for several days., VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 3.18 Å R-free 0.285
3ER8 Crystal structure of the heterodimeric vaccinia virus mRNA polyadenylate polymerase complex with two fragments of RNA Deposited 2008-10-01	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain B 1–297（297 aa）	Mutation：R140A,K142A,R143A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.7；295 K；proteins(4-5mg.ml) in 10mM Tris-HCl, pH8.7, 75 mM NaCl, 0.5 mM DTT, mixed with equal volume buffer which composed of 10mM Tris-HCl, pH 8.7, 15-20% PEG 4000, 5% glycerol, 0.5 mM DTT. room temperature for several days., VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 3.18 Å R-free 0.285
3ERC Crystal structure of the heterodimeric vaccinia virus mRNA polyadenylate polymerase with three fragments of RNA and 3'-deoxy ATP Deposited 2008-10-01	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain A 1–297（297 aa）	Mutation：R140A,K142A,R143A	U5P URIDINE-5'-MONOPHOSPHATE × 1 3AT 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.7；295 K；Proteins(4-5mg.ml) in 10mM Tris-HCl, pH8.7, 75 mM NaCl, 0.5 mM DTT, mixed with equal volume buffer which composed of 10mM Tris-HCl, pH 8.7, 15-20% PEG 4000, 5% glycerol, 0.5 mM DTT. Room temperature for several days., VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 3.21 Å R-free 0.309
3ERC Crystal structure of the heterodimeric vaccinia virus mRNA polyadenylate polymerase with three fragments of RNA and 3'-deoxy ATP Deposited 2008-10-01	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–RNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain B 1–297（297 aa）	Mutation：R140A,K142A,R143A	U5P URIDINE-5'-MONOPHOSPHATE × 1 3AT 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.7；295 K；Proteins(4-5mg.ml) in 10mM Tris-HCl, pH8.7, 75 mM NaCl, 0.5 mM DTT, mixed with equal volume buffer which composed of 10mM Tris-HCl, pH 8.7, 15-20% PEG 4000, 5% glycerol, 0.5 mM DTT. Room temperature for several days., VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 3.21 Å R-free 0.309
3MAG VACCINIA METHYLTRANSFERASE VP39 COMPLEXED WITH M3ADE AND S-ADENOSYLHOMOCYSTEINE Deposited 1998-07-12	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 1–307（307 aa）	Mutation：C-TERMINAL DELETION OF 26 RESIDUES	SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 3MA 6-AMINO-3-METHYLPURINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 1.80 Å R-free 0.251
3MCT VACCINIA METHYLTRANSFERASE VP39 COMPLEXED WITH M3CYT AND S-ADENOSYLHOMOCYSTEINE Deposited 1999-01-05	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 1–297（297 aa）	Mutation：C-TERMINAL DELETION OF 26 RESIDUES	SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 3MC 3-METHYLCYTOSINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 2.00 Å R-free 0.285
4DCG VACCINIA METHYLTRANSFERASE VP39 MUTANT D182A COMPLEXED WITH M7G AND S-ADENOSYLHOMOCYSTEINE Deposited 1998-07-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–307（307 aa）	Mutation：D182A, C-TERMINAL DELETION OF 26 RESIDUES	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 MG7 7-METHYLGUANOSINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 1.80 Å R-free 0.258

21 other PDB entries and 23 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PAP2_VACCV
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–297； UniProt 1–297

Poly(A) polymerase catalytic subunit

vaccinia virus WR

UniProt P23371

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–RNA Heteromer Protein × 2 RNA 1 PDB declaration: trimeric（3） Consistent with all polymer counts	Chain B； UniProt 1–479	Mutation：L36S	;Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase ; × 1 （P07617） 5'-R(UPU)-3' × 1 GOL* GLYCEROL × 3 3AT 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.7；295 K；proteins(4-5mg.ml) in 10mM tris-HCl, pH 8.7, 75 mM NaCl, 0.5 mM DTT, mixed with equal volume buffer which composed of 10mM Tris-HCl, pH 8.7, 15-20% PEG 4000, 5% glycerol, 0.5 mM DTT. Room temperature for several days., VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.06 Å R-free 0.250

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 3ER9	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2GA9 Crystal Structure of the Heterodimeric Vaccinia Virus Polyadenylate Polymerase with Bound ATP-gamma-S Deposited 2006-03-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 11–479（469 aa）	Mutation：L36S	CA CALCIUM ION × 2 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.7；293 K；20% PEG 4000, 0.240 M CaCl2, 5% glycerol, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.30 Å R-free 0.260
2GAF Crystal Structure of the Vaccinia Polyadenylate Polymerase Heterodimer (apo form) Deposited 2006-03-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 11–479（469 aa）	Mutation：L36S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.7；293 K；20% PEG 4000, 0.24 M CaCl2, 5% glycerol, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.40 Å R-free 0.288
3ER8 Crystal structure of the heterodimeric vaccinia virus mRNA polyadenylate polymerase complex with two fragments of RNA Deposited 2008-10-01	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain D 1–479（479 aa）	Mutation：L36S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.7；295 K；proteins(4-5mg.ml) in 10mM Tris-HCl, pH8.7, 75 mM NaCl, 0.5 mM DTT, mixed with equal volume buffer which composed of 10mM Tris-HCl, pH 8.7, 15-20% PEG 4000, 5% glycerol, 0.5 mM DTT. room temperature for several days., VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 3.18 Å R-free 0.285
3ER8 Crystal structure of the heterodimeric vaccinia virus mRNA polyadenylate polymerase complex with two fragments of RNA Deposited 2008-10-01	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain C 1–479（479 aa）	Mutation：L36S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.7；295 K；proteins(4-5mg.ml) in 10mM Tris-HCl, pH8.7, 75 mM NaCl, 0.5 mM DTT, mixed with equal volume buffer which composed of 10mM Tris-HCl, pH 8.7, 15-20% PEG 4000, 5% glycerol, 0.5 mM DTT. room temperature for several days., VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 3.18 Å R-free 0.285
3ERC Crystal structure of the heterodimeric vaccinia virus mRNA polyadenylate polymerase with three fragments of RNA and 3'-deoxy ATP Deposited 2008-10-01	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain D 1–479（479 aa）	Mutation：L36S	U5P URIDINE-5'-MONOPHOSPHATE × 1 3AT 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.7；295 K；Proteins(4-5mg.ml) in 10mM Tris-HCl, pH8.7, 75 mM NaCl, 0.5 mM DTT, mixed with equal volume buffer which composed of 10mM Tris-HCl, pH 8.7, 15-20% PEG 4000, 5% glycerol, 0.5 mM DTT. Room temperature for several days., VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 3.21 Å R-free 0.309
3ERC Crystal structure of the heterodimeric vaccinia virus mRNA polyadenylate polymerase with three fragments of RNA and 3'-deoxy ATP Deposited 2008-10-01	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–RNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain C 1–479（479 aa）	Mutation：L36S	U5P URIDINE-5'-MONOPHOSPHATE × 1 3AT 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.7；295 K；Proteins(4-5mg.ml) in 10mM Tris-HCl, pH8.7, 75 mM NaCl, 0.5 mM DTT, mixed with equal volume buffer which composed of 10mM Tris-HCl, pH 8.7, 15-20% PEG 4000, 5% glycerol, 0.5 mM DTT. Room temperature for several days., VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 3.21 Å R-free 0.309
3OWG Crystal structure of vaccinia virus Polyadenylate polymerase(vp55) Deposited 2010-09-17	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–479（479 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；12-16%PEG 3350,200mM Na-citate, 5% glycero, 1mM DTT, pH ~9, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.86 Å R-free 0.316
3OWG Crystal structure of vaccinia virus Polyadenylate polymerase(vp55) Deposited 2010-09-17	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–479（479 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；12-16%PEG 3350,200mM Na-citate, 5% glycero, 1mM DTT, pH ~9, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.86 Å R-free 0.316

5 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PAP1_VACCV
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–479； UniProt 1–479

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3er9
Deposition date deposition_date	2008-10-01
Structure title title	Crystal structure of the heterodimeric vaccinia virus mRNA polyadenylate polymerase complex with UU and 3'-deoxy ATP
Keywords keywords	;Polyadenylate polymerase, translocation, single tranded RNA poly(A) polymerase, RNA protein complex, processivity, heterodimer, nucleotidyltransferase, poxvirus; Methyltransferase, mRNA capping, mRNA processing, S-adenosyl-L-methionine, Transcription, Transferase, Transferase-RNA COMPLEX ;; Transcription, Transferase/RNA
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	29.07 Å
Radius of gyration Rg (electron density) rg_electron	28.02 Å
Forward intensity I(0) i0	114911000.00
Molecular weight molecular_weight	86888.0 kDa
Excluded volume excluded_volume	109760 Å³
Envelope volume envelope_volume	131280 Å³
Hydration-shell volume shell_volume	38236 Å³
Envelope diameter envelope_diameter	90.9 Å
Shell Rg shell_rg	36.14 Å
Envelope Rg envelope_rg	28.09 Å
Shape Rg shape_rg	28.02 Å
Total Rg total_rg	28.83 Å
Total atoms total_atoms	6099
Residues n_residues	735
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	89.3 Å
Rg (real space) rg_real	28.96 Å
Rg uncertainty (real space) rg_real_error	0.59 Å
I(0) (real space) i0_real	1.1490e+08
I(0) uncertainty (real space) i0_real_error	1.4240e+06
Rg (reciprocal space) rg_reciprocal	29.01 Å
I(0) (reciprocal space) i0_reciprocal	114900000.0000
Solution quality estimate total_estimate	0.9098
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	34.1 Å
Skewness Skewness skewness	0.181
Kurtosis Kurtosis kurtosis	-0.598
Angular range angular_range	— – 0.2750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	39890000.0000
Real-space data points n_real_points	56
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.957; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.952

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	;Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase ;
Molecular weight formula_weight	34589.0 kDa
EC 编号 ec_number	2.1.1.57
Mutation mutation	R140A,K142A,R143A
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	6416

MDVVSLDKPFMYFEEIDNELDYEPESANEVAKKLPYQGQLKLLLGELFFLSKLQRHGILDGATVVYIGSAPGTHIRYLRDHFYNLGVIIKWMLIDGRHHDPILNGLRDVTLVTRFVDEEYLRSIKKQLHPSKIILISDVASAAGGNEPSTADLLSNYALQNVMISILNPVASSLKWRCPFPDQWIKDFYIPHGNKMLQPFAPSYSAEMRLLSIYTGENMRLTRVTKSDAVNYEKKMYYLNKIVRNKVVVNFDYPNQEYDYFHMYFMLRTVYCNKTFPTTKAKVLFLQQSIFRFLNIP

来源 Source

来源生物 organism	vaccinia virus WR
NCBI Class编号 ncbi_taxonomy_id	10254
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Poly(A) polymerase catalytic subunit
Molecular weight formula_weight	55574.1 kDa
EC 编号 ec_number	2.7.7.19
Mutation mutation	L36S
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MNRNPDQNTLPNITLKIIETYLGRVPSVNEYHMLKSQARNIQKITVFNKDIFVSLVKKNKKRFFSDVNTSASEIKDRILSYFSKQTQTYNIGKLFTIIELQSVLVTTYTDILGVLTIKAPNVISSKISYNVTSMEELARDMLNSMNVAVIDKAKVMGRHNVSSLVKNVNKLMEEYLRRHNKSCICYGSYSLYLINPNIRYGDIDILQTNSRTFLIDLAFLIKFITGNNIILSKIPYLRNYMVIKDENDNHIIDSFNIRQDTMNVVPKIFIDNIYIVDPTFQLLNMIKMFSQIDRLEDLSKDPEKFNARMATMLEYVRYTHGIVFDGKRNNMPMKCIIDENNRIVTVTTKDYFSFKKCLVYLDENVLSSDILDLNADTSCDFESVTNSVYLIHDNIMYTYFSNTILLSDKGKVHEISARGLCAHILLYQMLTSGEYKQCLSDLLNSMMNRDKIPIYSHTERDKKPGRHGFINIEKDIIVF

来源 Source

来源生物 organism	vaccinia virus WR
NCBI Class编号 ncbi_taxonomy_id	10254
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	5'-R(UP*U)-3'
Molecular weight formula_weight	567.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	D

UU

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 non-polymer

Description description	3'-DEOXYADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	491.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

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

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	317

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7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3er9a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
Superfamily Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
Family Family family	c.66.1.25 — mRNA cap methylase

Domain ID domain_id	d3er9b_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.69 — Poly(A) polymerase catalytic subunit-like
Superfamily Superfamily superfamily	e.69.1 — Poly(A) polymerase catalytic subunit-like
Family Family family	e.69.1.1 — Poxvirus poly(A) polymerase catalytic subunit-like

CATH v4.4 (3 domains)

Domain ID domain_id	3er9A00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

Domain ID domain_id	3er9B01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
Homologous superfamily homologous superfamily	320 — Poxvirus poly(A) polymerase, N domain

Domain ID domain_id	3er9B03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	460 — Beta Polymerase; domain 2
Homologous superfamily homologous superfamily	60 — Poxvirus poly(A) polymerase, nucleotidyltransferase domain

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8. Citations (2)

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Unit-cell length a length_a	69.531 Å
Unit-cell length b length_b	91.977 Å
Unit-cell length c length_c	133.734 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.060 Å
Low-resolution limit resolution_low	42.690 Å
R factor r_factor	0.2080
R_work r_work	0.2080
R_free r_free	0.2500

fit	/app/data/saxs_computation/er/3er9/3er9.fit
pddf	/app/data/pr_computation/er/3er9/3er9.pr.out
profile	/app/data/saxs_computation/er/3er9/3er9.dat

Crystal structure of the heterodimeric vaccinia virus mRNA polyadenylate polymerase complex with UU and 3'-deoxy ATP

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

;Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase ;

State in the Current Structure

Other States of the Same Protein in the Database

Poly(A) polymerase catalytic subunit

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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)