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4jva

Crystal Structure of RIIbeta(108-402) bound to HE33, a N6 di-propyl substituted cAMP analog

Method: X-RAY DIFFRACTION Dmax: 62.6 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

cAMP-dependent protein kinase type II-beta regulatory subunit

Rattus norvegicus

UniProt P12369

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 112–416 Fragment：RIIbeta(108-402) of cAMP-dependent Protein Kinase 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 under oil (VDUO)；pH 6；298 K；20% PEG 4000, 80 mM Bis-Tris 6.0, and 50 mM MgCl2 using the Oryx crystallization robot (Douglas Instruments) in modified microbatch mode, vapor diffusion under oil (VDUO) , temperature 298.0K Resolution 2.50 Å R-free 0.278

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 4JVA Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1CX4 CRYSTAL STRUCTURE OF A DELETION MUTANT OF THE TYPE II BETA REGULATORY SUBUNIT OF CAMP-DEPENDENT PROTEIN KINASE Deposited 1999-08-28 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 112–416（305 aa） Fragment：CAMP BINDING DOMAINS
Not recorded CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.75；pH 7.75
Resolution 2.45 Å R-free 0.198
3IDB Crystal structure of (108-268)RIIb:C holoenzyme of cAMP-dependent protein kinase Deposited 2009-07-20 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 108–268（161 aa） Fragment：UNP residues 108-268
Not recorded MN MANGANESE (II) ION × 2 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION UNDER OIL (VDUO)；pH 7.5；298 K；8% PEG 3350, 40 mM Bis-Tris pH 7.5, 0.05 mM Na Acetate, VAPOR DIFFUSION UNDER OIL (VDUO), temperature 298.0K
Resolution 1.62 Å R-free 0.230
3IDC Crystal structure of (102-265)RIIb:C holoenzyme of cAMP-dependent protein kinase Deposited 2009-07-20 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 102–265（164 aa） Fragment：UNP residues 102-265
Not recorded MN MANGANESE (II) ION × 2 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION UNDER OIL (VDUO)；pH 7.5；298 K；8% PEG 3350, 40 mM Bis-Tris pH 7.5, 0.05 mM Na Acetate, VAPOR DIFFUSION UNDER OIL (VDUO), temperature 298K
Resolution 2.70 Å R-free 0.319
6WJF PKA RIIbeta holoenzyme with DnaJB1-PKAc fusion in fibrolamellar hepatoceullar carcinoma Deposited 2020-04-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–416（416 aa）
Chain D 1–416（416 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 5.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.50 Å
6WJG PKA RIIbeta holoenzyme with DnaJB1-PKAc fusion in fibrolamellar hepatoceullar carcinoma Deposited 2020-04-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–416（416 aa）
Chain D 1–416（416 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 5.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.20 Å

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

View Construct and Data Evidence
UniProt name KAP3_RAT
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–305； UniProt 112–416

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 4jva

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4jva
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4jva
Deposition date deposition_date2013-03-25
Structure title titleCrystal Structure of RIIbeta(108-402) bound to HE33, a N6 di-propyl substituted cAMP analog
Keywords keywords;cAMP-dependent protein kinase, cyclic nucleotide analogs, isoform selectivity, fluorescence anisotropy, TRANSFERASE-TRANSFERASE INHIBITOR complex ;; TRANSFERASE/TRANSFERASE INHIBITOR
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_guinier19.88 Å
Radius of gyration Rg (electron density) rg_electron18.70 Å
Forward intensity I(0) i016077600.00
Molecular weight molecular_weight29506.0 kDa
Excluded volume excluded_volume36650 ų
Envelope volume envelope_volume42948 ų
Hydration-shell volume shell_volume19213 ų
Envelope diameter envelope_diameter64.2 Å
Shell Rg shell_rg25.06 Å
Envelope Rg envelope_rg18.91 Å
Shape Rg shape_rg18.70 Å
Total Rg total_rg19.60 Å
Total atoms total_atoms2072
Residues n_residues264
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 dmax62.6 Å
Rg (real space) rg_real19.74 Å
Rg uncertainty (real space) rg_real_error0.28 Å
I(0) (real space) i0_real1.6080e+07
I(0) uncertainty (real space) i0_real_error1.7460e+05
Rg (reciprocal space) rg_reciprocal19.76 Å
I(0) (reciprocal space) i0_reciprocal16080000.0000
Solution quality estimate total_estimate0.8998
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary25.6 Å
Skewness Skewness skewness0.121
Kurtosis Kurtosis kurtosis-0.494
Angular range angular_range— – 0.4000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2438000.0000
Real-space data points n_real_points72
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.910; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.965
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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_idd4jvaa1
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_idd4jvaa2
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_id4jvaA01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily10 — Jelly Rolls
Domain ID domain_id4jvaA02
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)