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3tnq

Structure and Allostery of the PKA RIIb Tetrameric Holoenzyme

Method: X-RAY DIFFRACTION Dmax: 90.0 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Protein kinase, cAMP-dependent, catalytic, alpha

Rattus norvegicus

UniProt A1L1M0

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 2–351 Non-standard monomer：Yes (specific site not provided by mmCIF) cAMP-dependent protein kinase type II-beta regulatory subunit × 1 （P31324） MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；The RII (R230K)2:C2 holoenzyme complex was crystallized at room temperature in 10% PEG8000, 8% ethylene glycol, pH7.5 HEPES buffer by using vapor diffusion at a 1:1 ratio of protein to crystallization solution. VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 3.10 Å R-free 0.275

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name A1L1M0_RAT
Isoform —
PDB entities 1
Chains and sequence ranges Author chain B； PDBConstruct 1–350； UniProt 2–351

cAMP-dependent protein kinase type II-beta regulatory subunit

Mus musculus

UniProt P31324

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1–416 Mutation：R230K Non-standard monomer：Yes (specific site not provided by mmCIF) Protein kinase, cAMP-dependent, catalytic, alpha × 1 （A1L1M0） MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；The RII (R230K)2:C2 holoenzyme complex was crystallized at room temperature in 10% PEG8000, 8% ethylene glycol, pH7.5 HEPES buffer by using vapor diffusion at a 1:1 ratio of protein to crystallization solution. VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 3.10 Å R-free 0.275

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 3TNQ Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3TNP Structure and Allostery of the PKA RIIb Tetrameric Holoenzyme Deposited 2011-09-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–416（416 aa）
Chain E 1–416（416 aa）
Mutation：R230K Mutation：R230K No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；The RII (R230K)2:C2 holoenzyme complex was crystallized at room temperature in 10% PEG8000, 8% ethylene glycol, pH7.5 HEPES buffer by using vapor diffusion at a 1:1 ratio of protein to crystallization solution. VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.30 Å R-free 0.235
3TNP Structure and Allostery of the PKA RIIb Tetrameric Holoenzyme Deposited 2011-09-01 Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–416（416 aa）
Mutation：R230K No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；The RII (R230K)2:C2 holoenzyme complex was crystallized at room temperature in 10% PEG8000, 8% ethylene glycol, pH7.5 HEPES buffer by using vapor diffusion at a 1:1 ratio of protein to crystallization solution. VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.30 Å R-free 0.235
3TNP Structure and Allostery of the PKA RIIb Tetrameric Holoenzyme Deposited 2011-09-01 Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 1–416（416 aa）
Mutation：R230K No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；The RII (R230K)2:C2 holoenzyme complex was crystallized at room temperature in 10% PEG8000, 8% ethylene glycol, pH7.5 HEPES buffer by using vapor diffusion at a 1:1 ratio of protein to crystallization solution. VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.30 Å R-free 0.235
4WBB Single Turnover Autophosphorylation Cycle of the PKA RIIb Holoenzyme Deposited 2014-09-02 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–416（416 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) CA CALCIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions BATCH MODE；298 K；The RIIb (R230K):C apo complex was crystallized in 20%PEG8000, 8% Ethylene Glycol, 20mM MESpH7.5 HEPES . To make CaATP binding holoenzyme crystals, the apo holoenzyme crystals were soaked with 20%PEG8000, 8% Ethylene Glycol, 20mM MESpH7.5 HEPES, 5mM CaCl2 and 1mM ATP at pH5.8 solution overnight
Resolution 2.80 Å R-free 0.279
4X6Q An Isoform-specific Myristylation Switch Targets RIIb PKA Holoenzymes to Membranes Deposited 2014-12-08 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–416（416 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions BATCH MODE；298 K；The RIIb(R230K)2: myrC(K7C)2 holoenzyme was concentrated to 12 mg/mL. The crystal used for structure determination was obtained from a 3 uL drop containing 1:1 protein to well solution with the well solution containing 10% PEG8000, 8% ethylene glycol, 20mM MES, at pH5.8.
Resolution 2.52 Å R-free 0.261

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

View Construct and Data Evidence
UniProt name KAP3_MOUSE
Isoform —
PDB entities 2
Chains and sequence ranges Author chain A； PDBConstruct 1–416； UniProt 1–416

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 3tnq

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3tnq
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3tnq
Deposition date deposition_date2011-09-01
Structure title titleStructure and Allostery of the PKA RIIb Tetrameric Holoenzyme
Keywords keywordsPKA RIIb tetrameric holoenzyme, TRANSFERASE; TRANSFERASE
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_guinier28.01 Å
Radius of gyration Rg (electron density) rg_electron26.93 Å
Forward intensity I(0) i079096100.00
Molecular weight molecular_weight70193.0 kDa
Excluded volume excluded_volume88144 ų
Envelope volume envelope_volume109390 ų
Hydration-shell volume shell_volume33792 ų
Envelope diameter envelope_diameter95.6 Å
Shell Rg shell_rg34.33 Å
Envelope Rg envelope_rg27.12 Å
Shape Rg shape_rg26.91 Å
Total Rg total_rg27.77 Å
Total atoms total_atoms4929
Residues n_residues599
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 dmax90.0 Å
Rg (real space) rg_real27.91 Å
Rg uncertainty (real space) rg_real_error0.50 Å
I(0) (real space) i0_real7.9100e+07
I(0) uncertainty (real space) i0_real_error1.0400e+06
Rg (reciprocal space) rg_reciprocal27.94 Å
I(0) (reciprocal space) i0_reciprocal79100000.0000
Solution quality estimate total_estimate0.9009
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary33.2 Å
Skewness Skewness skewness0.234
Kurtosis Kurtosis kurtosis-0.444
Angular range angular_range— – 0.2850 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha15110000.0000
Real-space data points n_real_points58
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.915; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.962
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd3tnqb_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamilyd.144.1 — Protein kinase-like (PK-like)
Family Family familyd.144.1.7 — Protein kinases, catalytic subunit

CATH v4.4 (4 domains)

Domain ID domain_id3tnqA01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily10 — Jelly Rolls
Domain ID domain_id3tnqA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily10 — Jelly Rolls
Domain ID domain_id3tnqB01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
Domain ID domain_id3tnqB02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
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8. Citations (1)

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9. Files and Curves (10)