3im3

Crystal structure of PKA RI alpha dimerization/docking domain

Method: X-RAY DIFFRACTION D_max: 52.0 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 subunit

Bos taurus

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 13–62	Fragment：Dimerization and docking domain: UNP residues 13-62	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

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 3IM3	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 construct 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 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
1NE6 Crystal structure of Sp-cAMP binding R1a subunit of cAMP-dependent protein kinase Deposited 2002-12-10	Different construct 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 94–376（283 aa） Fragment：1-91 deletion mutant	Not recorded	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
1RGS REGULATORY SUBUNIT OF CAMP DEPENDENT PROTEIN KINASE Deposited 1995-06-21	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 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 oligomeric state 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 oligomeric state 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 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 oligomeric state 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
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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 1–50； UniProt 13–62

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

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

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

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3im3
Deposition date deposition_date	2009-08-09
Structure title title	Crystal structure of PKA RI alpha dimerization/docking domain
Keywords keywords	;helix-turn-helix, Acetylation, cAMP, cAMP-binding, Disulfide bond, Nucleotide-binding, Phosphoprotein, STRUCTURAL PROTEIN, SIGNALING PROTEIN ;; STRUCTURAL PROTEIN, SIGNALING PROTEIN
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	14.93 Å
Radius of gyration Rg (electron density) rg_electron	13.62 Å
Forward intensity I(0) i0	881323.00
Molecular weight molecular_weight	6071.0 kDa
Excluded volume excluded_volume	7623 Å³
Envelope volume envelope_volume	9961 Å³
Hydration-shell volume shell_volume	6988 Å³
Envelope diameter envelope_diameter	50.3 Å
Shell Rg shell_rg	17.71 Å
Envelope Rg envelope_rg	14.07 Å
Shape Rg shape_rg	13.55 Å
Total Rg total_rg	14.94 Å
Total atoms total_atoms	425
Residues n_residues	50
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	52.0 Å
Rg (real space) rg_real	14.99 Å
Rg uncertainty (real space) rg_real_error	0.42 Å
I(0) (real space) i0_real	8.8130e+05
I(0) uncertainty (real space) i0_real_error	9.9060e+03
Rg (reciprocal space) rg_reciprocal	14.98 Å
I(0) (reciprocal space) i0_reciprocal	881300.0000
Solution quality estimate total_estimate	0.8724
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	15.8 Å
Skewness Skewness skewness	0.283
Kurtosis Kurtosis kurtosis	-0.457
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	67610.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.880; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.789; Smooth: 0.907

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	cAMP-dependent protein kinase type I-alpha regulatory subunit
Molecular weight formula_weight	6006.0 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	463

SLRECELYVQKHNIQALLKDSIVQLCTARPERPMAFLREYFEKLEKEEAK

来源 Source

来源生物 organism	Bos taurus
通用名 common_name	bovine
NCBI Class编号 ncbi_taxonomy_id	9913
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	FORMIC ACID
Molecular weight formula_weight	46.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	29

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3im3a_
Class class	a — All alpha proteins
Fold Fold fold	a.31 — Dimerization-anchoring domain of cAMP-dependent PK regulatory subunit
Superfamily Superfamily superfamily	a.31.1 — Dimerization-anchoring domain of cAMP-dependent PK regulatory subunit
Family Family family	a.31.1.1 — Dimerization-anchoring domain of cAMP-dependent PK regulatory subunit

CATH v4.4 (1 domains)

Domain ID domain_id	3im3A00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	890 — cAMP-dependent Protein Kinase, Chain A
Homologous superfamily homologous superfamily	10 — cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain

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8. Citations (1)

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Unit-cell length a length_a	44.122 Å
Unit-cell length b length_b	44.122 Å
Unit-cell length c length_c	93.036 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 62 2 2
Space-group number int_tables_number	180
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	24.081 Å
R factor r_factor	0.1930
R_work r_work	0.1871
R_free r_free	0.2488

fit	/app/data/saxs_computation/im/3im3/3im3.fit
pddf	/app/data/pr_computation/im/3im3/3im3.pr.out
profile	/app/data/saxs_computation/im/3im3/3im3.dat