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1cx4

CRYSTAL STRUCTURE OF A DELETION MUTANT OF THE TYPE II BETA REGULATORY SUBUNIT OF CAMP-DEPENDENT PROTEIN KINASE

Method: X-RAY DIFFRACTION Dmax: 64.2 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

CAMP-DEPENDENT PROTEIN KINASE REGULATORY SUBUNIT TYPE II BETA

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：CAMP BINDING DOMAINS 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

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 1CX4 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3IDB Crystal structure of (108-268)RIIb:C holoenzyme of cAMP-dependent protein kinase Deposited 2009-07-20 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 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 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
4JVA Crystal Structure of RIIbeta(108-402) 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 112–416（305 aa） 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
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 1cx4

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1cx4
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1cx4
Deposition date deposition_date1999-08-28
Structure title titleCRYSTAL STRUCTURE OF A DELETION MUTANT OF THE TYPE II BETA REGULATORY SUBUNIT OF CAMP-DEPENDENT PROTEIN KINASE
Keywords keywordsBETA BARREL, CAMP-DEPENDENT PROTEIN KINASE, CAMP-BINDING, REGULATORY SUBUNIT, SIGNALING PROTEIN; SIGNALING PROTEIN
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_guinier20.55 Å
Radius of gyration Rg (electron density) rg_electron19.50 Å
Forward intensity I(0) i018097900.00
Molecular weight molecular_weight31515.0 kDa
Excluded volume excluded_volume39170 ų
Envelope volume envelope_volume45838 ų
Hydration-shell volume shell_volume19871 ų
Envelope diameter envelope_diameter65.1 Å
Shell Rg shell_rg25.70 Å
Envelope Rg envelope_rg19.57 Å
Shape Rg shape_rg19.50 Å
Total Rg total_rg20.34 Å
Total atoms total_atoms2207
Residues n_residues275
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 dmax64.2 Å
Rg (real space) rg_real20.46 Å
Rg uncertainty (real space) rg_real_error0.33 Å
I(0) (real space) i0_real1.8100e+07
I(0) uncertainty (real space) i0_real_error2.2000e+05
Rg (reciprocal space) rg_reciprocal20.48 Å
I(0) (reciprocal space) i0_reciprocal18100000.0000
Solution quality estimate total_estimate0.9067
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary25.1 Å
Skewness Skewness skewness0.192
Kurtosis Kurtosis kurtosis-0.451
Angular range angular_range— – 0.3850 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3171000.0000
Real-space data points n_real_points70
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.931; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.993
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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_idd1cx4a1
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_idd1cx4a2
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_id1cx4A01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily10 — Jelly Rolls
Domain ID domain_id1cx4A02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily10 — Jelly Rolls
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8. Citations (2)

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9. Files and Curves (10)