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1ne6

Crystal structure of Sp-cAMP binding R1a subunit of cAMP-dependent protein kinase

Method: X-RAY DIFFRACTION Dmax: 71.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

cAMP-dependent protein kinase type I-alpha regulatory chain

Bos taurus

UniProt P00514

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 94–376 Fragment：1-91 deletion mutant SP1 6-(6-AMINO-PURIN-9-YL)-2-THIOXO-TETRAHYDRO-2-FURO[3,2-D][1,3,2]DIOXAPHOSPHININE-2,7-DIOL × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.5；295.5 K；amino sulfate, glycerol, DTT, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295.5K Resolution 2.30 Å R-free 0.241

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 1NE6 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1NE4 Crystal Structure of Rp-cAMP Binding R1a Subunit of cAMP-dependent Protein Kinase Deposited 2002-12-10 Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 94–376（283 aa） Fragment：1-91 deletion mutant
Not recorded RP1 6-(6-AMINO-PURIN-9-YL)-2-THIOXO-TETRAHYDRO-2-FURO[3,2-D][1,3,2]DIOXAPHOSPHININE-2,7-DIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；295.5 K；amino sulfate, glycerol, DTT, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295.5K
Resolution 2.40 Å R-free 0.253
1RGS REGULATORY SUBUNIT OF CAMP DEPENDENT PROTEIN KINASE Deposited 1995-06-21 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 92–379（288 aa） Fragment：REGULATORY SUBUNIT
Mutation：DEL(1-91) CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.80 Å
1RL3 Crystal structure of cAMP-free R1a subunit of PKA Deposited 2003-11-24 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 92–379（288 aa）
Not recorded PCG CYCLIC GUANOSINE MONOPHOSPHATE × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295.5 K；NH4SO4, glycerol, DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295.5K
Resolution 2.70 Å R-free 0.285
1RL3 Crystal structure of cAMP-free R1a subunit of PKA Deposited 2003-11-24 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 92–379（288 aa）
Not recorded PCG CYCLIC GUANOSINE MONOPHOSPHATE × 1 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295.5 K；NH4SO4, glycerol, DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295.5K
Resolution 2.70 Å R-free 0.285
2EZW Solution structure of the docking and dimerization domain of the type I alpha regulatory subunit of protein kinase A (RIalpha D/D) Deposited 2005-11-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 12–61（50 aa） Fragment：dimerization-anchoring domain (residues 12-61)
Chain B 12–61（50 aa） Fragment：dimerization-anchoring domain (residues 12-61)
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 4；310 K；Ionic strength (raw mmCIF value) 50mM sodium acetate, 150mM sodium chloride；Pressure 1
NMR sample composition R1a(12-61) at 1.2-1.6 mM dimer, 50mM sodium acetate, 150mM sodium chloride, pH 4.0, 90% H2O, 10% D2O | 90% H2O/10% D2O
NMR sample composition 15N-enriched R1a(12-61), 5% H2O, 95% D2O | 5% H2O, 95% D2O
NMR sample composition 15N-enriched R1a(12-61), 90% H2O, 10% D2O | 90% H2O/10% D2O
NMR sample composition 13C/15N-enriched R1a(12-61), 5% H2O, 95% D2O | 5% H2O, 95% D2O
NMR sample composition asymmetrically enriched 13C/15N-12C/14N R1a(12-61), 5% H2O,95% D2O | 5% H2O,95% D2O
Resolution not provided
2QCS A complex structure between the Catalytic and Regulatory subunit of Protein Kinase A that represents the inhibited state Deposited 2007-06-19 Different construct 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 B 91–380（290 aa） Fragment：REGULATORY SUBUNIT
Mutation：R333K MN MANGANESE (II) ION × 2 SO4 SULFATE ION × 6 ACT ACETATE ION × 1 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 TAM TRIS(HYDROXYETHYL)AMINOMETHANE × 1 GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；298 K；2.0M(NH4)2SO4, 0.1M Citrate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.20 Å R-free 0.225
3FHI Crystal structure of a complex between the catalytic and regulatory (RI{alpha}) subunits of PKA Deposited 2008-12-09 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 B 92–245（154 aa） Fragment：UNP residues 92-245
Not recorded ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 MN MANGANESE (II) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；20 % PEG 2000, 0.1 M Tris-HCl, 4 % 1,3-Propanediol, 2.0 mM Cyclohexyl-pentyl-D-maltoside, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.00 Å R-free 0.226
3IIA Crystal structure of apo (91-244) RIa subunit of cAMP-dependent protein kinase Deposited 2009-07-31 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 92–245（154 aa） Fragment：The RIa subunit: UNP residues 92-245
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.1 M Sodium cacodylate trihydrate pH 6.5, 30% w/v PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 2.70 Å R-free 0.285
3IM3 Crystal structure of PKA RI alpha dimerization/docking domain Deposited 2009-08-09 Different construct 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 13–62（50 aa） Fragment：Dimerization and docking domain: UNP residues 13-62
Not recorded FMT FORMIC ACID × 4 X-RAY DIFFRACTION
X-ray crystallization conditions MICROBATCH；pH 9；298 K；30% PEG 3350, 0.2 mM Sodium formate, 0.1 M Bis-Tris propane pH 9.0, MICROBATCH, temperature 298K
Resolution 2.00 Å R-free 0.249
3IM4 Crystal structure of cAMP-dependent Protein Kinase A Regulatory Subunit I alpha in complex with dual-specific A-Kinase Anchoring Protein 2 Deposited 2009-08-09 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 13–62（50 aa） Fragment：Dimerization and docking domain: UNP residues 13-62
Chain B 13–62（50 aa） Fragment：Dimerization and docking domain: UNP residues 13-62
Not recorded ZN ZINC ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions MICROBATCH；pH 5.5；298 K；10% PEG 6000, 0.01 M ZnCl2, 0.1 M MES, pH 5.5, MICROBATCH, temperature 298K
Resolution 2.29 Å R-free 0.254
3PLQ Crystal structure of PKA type I regulatory subunit bound with Rp-8-Br-cAMPS Deposited 2010-11-15 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 92–245（154 aa） Fragment：residues 91-244
Not recorded RP2 (2R,4aR,6R,7R,7aS)-6-(6-amino-8-bromo-9H-purin-9-yl)tetrahydro-4H-furo[3,2-d][1,3,2]dioxaphosphinine-2,7-diol 2-sulfide × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions hanging drop；pH 6.5；298 K；pH 6.5, hanging drop, temperature 298K
Resolution 2.30 Å R-free 0.328
3PNA Crystal Structure of cAMP bound (91-244)RIa Subunit of cAMP-dependent Protein Kinase Deposited 2010-11-18 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 92–245（154 aa） Fragment：N-terminal cAMP binding domain (UNP residues 92-245)
Not recorded CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；0.1 M sodium acetate trihydrate, 2.0 M ammonium sulfate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.50 Å R-free 0.182
3PNA Crystal Structure of cAMP bound (91-244)RIa Subunit of cAMP-dependent Protein Kinase Deposited 2010-11-18 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 92–245（154 aa） Fragment：N-terminal cAMP binding domain (UNP residues 92-245)
Not recorded CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；0.1 M sodium acetate trihydrate, 2.0 M ammonium sulfate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.50 Å R-free 0.182
3PNA Crystal Structure of cAMP bound (91-244)RIa Subunit of cAMP-dependent Protein Kinase Deposited 2010-11-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 92–245（154 aa） Fragment：N-terminal cAMP binding domain (UNP residues 92-245)
Chain B 92–245（154 aa） Fragment：N-terminal cAMP binding domain (UNP residues 92-245)
Not recorded CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 4 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；0.1 M sodium acetate trihydrate, 2.0 M ammonium sulfate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.50 Å R-free 0.182
3PVB Crystal structure of (73-244)RIa:C holoenzyme of cAMP-dependent Protein kinase Deposited 2010-12-06 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 B 85–244（160 aa） Fragment：unp residues 85-244
Not recorded ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 MN MANGANESE (II) ION × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；The RIa(73-244):C complex was crystallized in 0.1M MES pH 6.0 and 12% PEG 20,000 by using a Douglas Instruments Oryx8 crystallography robot as 1:1 protein solution:crystallizing solution, VAPOR DIFFUSION, SITTING DROP, temperature 298.0 K
Resolution 3.30 Å R-free 0.290
4JV4 Crystal Structure of RIalpha(91-379) bound to HE33, a N6 di-propyl substituted cAMP analog Deposited 2013-03-25 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 92–379（288 aa） Fragment：RIalpha (93-380)
Mutation：deletion mutant 1OR (2R,4aR,6R,7R,7aS)-6-[6-(dipropylamino)-9H-purin-9-yl]tetrahydro-4H-furo[3,2-d][1,3,2]dioxaphosphinine-2,7-diol 2-oxide × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；6.3% PEG 3350, 0.074 M sodium malonate (pH 7.0) after 3 weeks of growth, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 2.95 Å R-free 0.286
4MX3 Crystal Structure of PKA RIalpha Homodimer Deposited 2013-09-25 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 2–380（379 aa）
Chain B 2–380（379 aa）
Not recorded CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；298 K；0.125 M sodium acetate (pH 5), 2M sodium formate with the protein at a final concentration of 4 mg/ml grown in a 2 ul drop, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 3.88 Å R-free 0.287
4MX3 Crystal Structure of PKA RIalpha Homodimer Deposited 2013-09-25 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–380（379 aa）
Not recorded CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；298 K；0.125 M sodium acetate (pH 5), 2M sodium formate with the protein at a final concentration of 4 mg/ml grown in a 2 ul drop, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 3.88 Å R-free 0.287
4MX3 Crystal Structure of PKA RIalpha Homodimer Deposited 2013-09-25 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 2–380（379 aa）
Not recorded CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；298 K；0.125 M sodium acetate (pH 5), 2M sodium formate with the protein at a final concentration of 4 mg/ml grown in a 2 ul drop, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 3.88 Å R-free 0.287
4X6R An Isoform-specific Myristylation Switch Targets RIIb PKA Holoenzymes to Membranes Deposited 2014-12-09 Different construct 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 B 91–380（290 aa）
Mutation：R333K SO4 SULFATE ION × 6 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 TAM TRIS(HYDROXYETHYL)AMINOMETHANE × 1 GOL GLYCEROL × 2 MYR MYRISTIC ACID × 1 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions BATCH MODE；298 K；Crystallization of RIb(91-379,R333K): myrC(K7C) heterodimer :RC heterodimer that was concentrated to 14 mg/mL and screened against different ammonium sulfate concentrations ranging from 0.8-2.5 M in 0.1 M sodium citrate buffer and also varying the pH from 5.0-6.0 using the hanging drop vapor diffusion method. The crystal used for structure determination was obtained from a 4 uL drop containing 1:1 protein to well solution with the well solution containing 1.6 M ammonium sulfate and 0.1 M sodium citrate at pH 5.5
Resolution 2.40 Å R-free 0.234
5HVZ Crystal structure of smAKAP AKB domain bound RIa dimerization/docking (D/D) complex at 2.0 A resolution Deposited 2016-01-28 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 13–62（50 aa）
Chain B 13–62（50 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions MICROBATCH；pH 3.5；297 K；a 2:3 ratio of protein solution:crystallizing (crystallizing solution: 0.1 M Citric acid pH 3.5, 28% w/v Polyethylene glycol 8,000)
Resolution 2.00 Å R-free 0.241
5JR7 Crystal structure of an ACRDYS heterodimer [RIa(92-365):C] of PKA Deposited 2016-05-05 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 B 92–366（275 aa） Fragment：UNP residues 92-366
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；0.2 M Sodium thiocyanate and 20% PEG 3350 with the protein at a final concentration of 5 mg/ml in a 1.6 ul drop
Resolution 3.56 Å R-free 0.322
5JR7 Crystal structure of an ACRDYS heterodimer [RIa(92-365):C] of PKA Deposited 2016-05-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 92–366（275 aa） Fragment：UNP residues 92-366
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；0.2 M Sodium thiocyanate and 20% PEG 3350 with the protein at a final concentration of 5 mg/ml in a 1.6 ul drop
Resolution 3.56 Å R-free 0.322
6BYR Structures of the PKA RI alpha holoenzyme with the FLHCC driver J-PKAc alpha or native PKAc alpha Deposited 2017-12-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 2–380（379 aa）
Chain D 2–380（379 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；100 mM NaCl, 16-18% pentaerythritol propoxylate and 10% dimethyl sulfoxide
Resolution 3.66 Å R-free 0.249
6BYR Structures of the PKA RI alpha holoenzyme with the FLHCC driver J-PKAc alpha or native PKAc alpha Deposited 2017-12-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 2–380（379 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；100 mM NaCl, 16-18% pentaerythritol propoxylate and 10% dimethyl sulfoxide
Resolution 3.66 Å R-free 0.249
6BYR Structures of the PKA RI alpha holoenzyme with the FLHCC driver J-PKAc alpha or native PKAc alpha Deposited 2017-12-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 2–380（379 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；100 mM NaCl, 16-18% pentaerythritol propoxylate and 10% dimethyl sulfoxide
Resolution 3.66 Å R-free 0.249
6BYS Structures of the PKA RI alpha holoenzyme with the FLHCC driver J-PKAc alpha or native PRKAc alpha Deposited 2017-12-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 2–380（379 aa）
Chain H 2–380（379 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；100 mM HEPES sodium-MOPS (acid) pH 7.5, 90 mM NPS (30 mM sodium nitrate, 30 mM sodium phosphate dibasic, 30 mM ammonium sulfate), 40-42% Precipitant Mix 2 (40% ethylene glycol; 20% PEG 8000), 3% D-(+)-Glucose monohydrate
Resolution 4.75 Å R-free 0.255
6BYS Structures of the PKA RI alpha holoenzyme with the FLHCC driver J-PKAc alpha or native PRKAc alpha Deposited 2017-12-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 2–380（379 aa）
Chain F 2–380（379 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；100 mM HEPES sodium-MOPS (acid) pH 7.5, 90 mM NPS (30 mM sodium nitrate, 30 mM sodium phosphate dibasic, 30 mM ammonium sulfate), 40-42% Precipitant Mix 2 (40% ethylene glycol; 20% PEG 8000), 3% D-(+)-Glucose monohydrate
Resolution 4.75 Å R-free 0.255
6BYS Structures of the PKA RI alpha holoenzyme with the FLHCC driver J-PKAc alpha or native PRKAc alpha Deposited 2017-12-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 2–380（379 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；100 mM HEPES sodium-MOPS (acid) pH 7.5, 90 mM NPS (30 mM sodium nitrate, 30 mM sodium phosphate dibasic, 30 mM ammonium sulfate), 40-42% Precipitant Mix 2 (40% ethylene glycol; 20% PEG 8000), 3% D-(+)-Glucose monohydrate
Resolution 4.75 Å R-free 0.255
6BYS Structures of the PKA RI alpha holoenzyme with the FLHCC driver J-PKAc alpha or native PRKAc alpha Deposited 2017-12-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 2–380（379 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；100 mM HEPES sodium-MOPS (acid) pH 7.5, 90 mM NPS (30 mM sodium nitrate, 30 mM sodium phosphate dibasic, 30 mM ammonium sulfate), 40-42% Precipitant Mix 2 (40% ethylene glycol; 20% PEG 8000), 3% D-(+)-Glucose monohydrate
Resolution 4.75 Å R-free 0.255
6BYS Structures of the PKA RI alpha holoenzyme with the FLHCC driver J-PKAc alpha or native PRKAc alpha Deposited 2017-12-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 2–380（379 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；100 mM HEPES sodium-MOPS (acid) pH 7.5, 90 mM NPS (30 mM sodium nitrate, 30 mM sodium phosphate dibasic, 30 mM ammonium sulfate), 40-42% Precipitant Mix 2 (40% ethylene glycol; 20% PEG 8000), 3% D-(+)-Glucose monohydrate
Resolution 4.75 Å R-free 0.255
6BYS Structures of the PKA RI alpha holoenzyme with the FLHCC driver J-PKAc alpha or native PRKAc alpha Deposited 2017-12-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 2–380（379 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；100 mM HEPES sodium-MOPS (acid) pH 7.5, 90 mM NPS (30 mM sodium nitrate, 30 mM sodium phosphate dibasic, 30 mM ammonium sulfate), 40-42% Precipitant Mix 2 (40% ethylene glycol; 20% PEG 8000), 3% D-(+)-Glucose monohydrate
Resolution 4.75 Å R-free 0.255
6NO7 Crystal Structure of the full-length wild-type PKA RIa Holoenzyme Deposited 2019-01-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–380（380 aa）
Chain D 1–380（380 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；296 K；mixing 1 ul of the protein solution (7.5 mg/ml) and 1 ul of the reservoir solution (100 mM imidazole/MES pH=7.0, 100 mM NPS, 16.8% v/v Ethylene glycol, 8.4 % w/v PEG 8000).
Resolution 3.55 Å R-free 0.269
6NO7 Crystal Structure of the full-length wild-type PKA RIa Holoenzyme Deposited 2019-01-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain F 1–380（380 aa）
Chain H 1–380（380 aa）
Not recorded MG MAGNESIUM ION × 4 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；296 K；mixing 1 ul of the protein solution (7.5 mg/ml) and 1 ul of the reservoir solution (100 mM imidazole/MES pH=7.0, 100 mM NPS, 16.8% v/v Ethylene glycol, 8.4 % w/v PEG 8000).
Resolution 3.55 Å R-free 0.269
7LZ4 Crystal structure of A211D mutant of Protein Kinase A RIa subunit, a Carney Complex mutation Deposited 2021-03-08 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 109–377（269 aa）
Mutation：A211D CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；295.5 K；The protein was concentrated to 8 mg/mL, and crystallized in 2 uL hanging drops using the vapor diffusion method with 75 mM Sodium Acetate (pH 5.0), 2.0 M sodium formate, and four-fold molar excess cAMP at room temperature
Resolution 4.16 Å R-free 0.270
7LZ4 Crystal structure of A211D mutant of Protein Kinase A RIa subunit, a Carney Complex mutation Deposited 2021-03-08 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 109–377（269 aa）
Mutation：A211D CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；295.5 K；The protein was concentrated to 8 mg/mL, and crystallized in 2 uL hanging drops using the vapor diffusion method with 75 mM Sodium Acetate (pH 5.0), 2.0 M sodium formate, and four-fold molar excess cAMP at room temperature
Resolution 4.16 Å R-free 0.270
7LZ4 Crystal structure of A211D mutant of Protein Kinase A RIa subunit, a Carney Complex mutation Deposited 2021-03-08 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 109–377（269 aa）
Mutation：A211D CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；295.5 K；The protein was concentrated to 8 mg/mL, and crystallized in 2 uL hanging drops using the vapor diffusion method with 75 mM Sodium Acetate (pH 5.0), 2.0 M sodium formate, and four-fold molar excess cAMP at room temperature
Resolution 4.16 Å R-free 0.270
7LZ4 Crystal structure of A211D mutant of Protein Kinase A RIa subunit, a Carney Complex mutation Deposited 2021-03-08 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 109–377（269 aa）
Mutation：A211D CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；295.5 K；The protein was concentrated to 8 mg/mL, and crystallized in 2 uL hanging drops using the vapor diffusion method with 75 mM Sodium Acetate (pH 5.0), 2.0 M sodium formate, and four-fold molar excess cAMP at room temperature
Resolution 4.16 Å R-free 0.270
7LZ4 Crystal structure of A211D mutant of Protein Kinase A RIa subunit, a Carney Complex mutation Deposited 2021-03-08 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain E 109–377（269 aa）
Mutation：A211D CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；295.5 K；The protein was concentrated to 8 mg/mL, and crystallized in 2 uL hanging drops using the vapor diffusion method with 75 mM Sodium Acetate (pH 5.0), 2.0 M sodium formate, and four-fold molar excess cAMP at room temperature
Resolution 4.16 Å R-free 0.270
7LZ4 Crystal structure of A211D mutant of Protein Kinase A RIa subunit, a Carney Complex mutation Deposited 2021-03-08 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain F 109–377（269 aa）
Mutation：A211D CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；295.5 K；The protein was concentrated to 8 mg/mL, and crystallized in 2 uL hanging drops using the vapor diffusion method with 75 mM Sodium Acetate (pH 5.0), 2.0 M sodium formate, and four-fold molar excess cAMP at room temperature
Resolution 4.16 Å R-free 0.270
7LZ4 Crystal structure of A211D mutant of Protein Kinase A RIa subunit, a Carney Complex mutation Deposited 2021-03-08 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 7 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain G 109–377（269 aa）
Mutation：A211D CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；295.5 K；The protein was concentrated to 8 mg/mL, and crystallized in 2 uL hanging drops using the vapor diffusion method with 75 mM Sodium Acetate (pH 5.0), 2.0 M sodium formate, and four-fold molar excess cAMP at room temperature
Resolution 4.16 Å R-free 0.270
7LZ4 Crystal structure of A211D mutant of Protein Kinase A RIa subunit, a Carney Complex mutation Deposited 2021-03-08 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 8 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain H 109–377（269 aa）
Mutation：A211D CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；295.5 K；The protein was concentrated to 8 mg/mL, and crystallized in 2 uL hanging drops using the vapor diffusion method with 75 mM Sodium Acetate (pH 5.0), 2.0 M sodium formate, and four-fold molar excess cAMP at room temperature
Resolution 4.16 Å R-free 0.270
9EDC Reset Type-I Protein Kinase A Holoenzyme Deposited 2024-11-16 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 B 1–380（380 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.18 Å
9EDD Reset Type-I Protein Kinase A Holoenzyme Deposited 2024-11-16 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 B 1–380（380 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.30 Å
9EDE Reset Type-I Protein Kinase A Holoenzyme Deposited 2024-11-16 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 B 1–380（380 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.90 Å
9FQR 96-nm repeat of axonemal doublet microtubules from bovine sperm Deposited 2024-06-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 1574 PDB declaration: 1574-meric
Chain Xk 1–380（380 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 342 MG MAGNESIUM ION × 345 GDP GUANOSINE-5'-DIPHOSPHATE × 345 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 5.00 Å

25 other PDB entries and 46 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name KAP0_BOVIN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–283； UniProt 94–376

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

SAXS profile for 1ne6

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1ne6
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1ne6
Deposition date deposition_date2002-12-10
Structure title titleCrystal structure of Sp-cAMP binding R1a subunit of cAMP-dependent protein kinase
Keywords keywordscAMP-dependent protein kinase, R1a subunit, cAMP analog, Sp-cAMP, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier21.34 Å
Radius of gyration Rg (electron density) rg_electron20.36 Å
Forward intensity I(0) i016540300.00
Molecular weight molecular_weight30449.0 kDa
Excluded volume excluded_volume37998 ų
Envelope volume envelope_volume44828 ų
Hydration-shell volume shell_volume19033 ų
Envelope diameter envelope_diameter75.9 Å
Shell Rg shell_rg26.22 Å
Envelope Rg envelope_rg20.64 Å
Shape Rg shape_rg20.37 Å
Total Rg total_rg21.14 Å
Total atoms total_atoms2141
Residues n_residues268
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax71.8 Å
Rg (real space) rg_real21.36 Å
Rg uncertainty (real space) rg_real_error0.65 Å
I(0) (real space) i0_real1.6540e+07
I(0) uncertainty (real space) i0_real_error2.4310e+05
Rg (reciprocal space) rg_reciprocal21.36 Å
I(0) (reciprocal space) i0_reciprocal16540000.0000
Solution quality estimate total_estimate0.7993
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary24.3 Å
Skewness Skewness skewness0.373
Kurtosis Kurtosis kurtosis-0.348
Angular range angular_range— – 0.3700 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3054000.0000
Real-space data points n_real_points69
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.811; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.954; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1ne6a1
Class classb — All beta proteins
Fold Fold foldb.82 — Double-stranded beta-helix
Superfamily Superfamily superfamilyb.82.3 — cAMP-binding domain-like
Family Family familyb.82.3.2 — cAMP-binding domain
Domain ID domain_idd1ne6a2
Class classb — All beta proteins
Fold Fold foldb.82 — Double-stranded beta-helix
Superfamily Superfamily superfamilyb.82.3 — cAMP-binding domain-like
Family Family familyb.82.3.2 — cAMP-binding domain

CATH v4.4 (2 domains)

Domain ID domain_id1ne6A01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily10 — Jelly Rolls
Domain ID domain_id1ne6A02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily10 — Jelly Rolls
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8. Citations (1)

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9. Files and Curves (10)