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2lg1

Solution structure of the human AKAP13 PH domain and stabilizing DH helix

Method: SOLUTION NMR Dmax: 52.9 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

A-kinase anchor protein 13

Homo sapiens

UniProt Q12802

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 2164–2346 Fragment：PH domain residues 2164-2346 No other associated polymer SOLUTION NMR NMR measurement conditions：pH 7；293 K；Ionic strength (raw mmCIF value) 150.00；Pressure 1.00 NMR sample composition：0.5 mM [U-100% 13C; U-100% 15N] AKAP13a_A10, 50.0 mM sodium phosphate, 150.0 mM sodium chloride, 0.1 mM Sodium azide, 90% H2O/10% D2O | 90% H2O/10% D2O Resolution not provided

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 2LG1 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4D0N AKAP13 (AKAP-Lbc) RhoGEF domain in complex with RhoA Deposited 2014-04-29 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 1968–2338（371 aa） Fragment：RHOGEF DOMAIN, RESIDUES 1968-2338
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 SO4 SULFATE ION × 5 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.5；0.2 M AMMONIUM SULPHATE, 0.1 M BIS-TRIS PH 5.5, 25% (W/V) PEG 3350
Resolution 2.10 Å R-free 0.239
4D0O AKAP13 (AKAP-Lbc) DH domain Deposited 2014-04-29 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1972–2207（236 aa） Fragment：RHOGEF DOMAIN, RESIDUES 1972-2207
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.5；0.2 M AMMONIUM SULPHATE, 0.1 M BIS-TRIS PH 5.5, 25% (W/V) PEG 3350
Resolution 2.75 Å R-free 0.308
4D0O AKAP13 (AKAP-Lbc) DH domain Deposited 2014-04-29 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1972–2207（236 aa） Fragment：RHOGEF DOMAIN, RESIDUES 1972-2207
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.5；0.2 M AMMONIUM SULPHATE, 0.1 M BIS-TRIS PH 5.5, 25% (W/V) PEG 3350
Resolution 2.75 Å R-free 0.308
6BCA A Complex between PH Domain of LbcRhoGEF (AKAP-Lbc) and Activated RhoA Bound to a GTP Analog Deposited 2017-10-20 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 2173–2313（141 aa）
Not recorded MG MAGNESIUM ION × 1 GSP 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；24-26% PEG 3350, 100mM Bis-Tris, 200mM ammonium sulfate
Resolution 2.00 Å R-free 0.234
6BCA A Complex between PH Domain of LbcRhoGEF (AKAP-Lbc) and Activated RhoA Bound to a GTP Analog Deposited 2017-10-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 2173–2313（141 aa）
Not recorded MG MAGNESIUM ION × 1 GSP 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；24-26% PEG 3350, 100mM Bis-Tris, 200mM ammonium sulfate
Resolution 2.00 Å R-free 0.234

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

View Construct and Data Evidence
UniProt name AKP13_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–185； UniProt 2164–2346

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 2lg1

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2lg1
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2lg1
Deposition date deposition_date2011-07-19
Structure title titleSolution structure of the human AKAP13 PH domain and stabilizing DH helix
Keywords keywordsMETAL BINDING PROTEIN; METAL BINDING PROTEIN
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier16.55 Å
Radius of gyration Rg (electron density) rg_electron16.08 Å
Forward intensity I(0) i02397730000.00
Molecular weight molecular_weight420420.0 kDa
Excluded volume excluded_volume528770 ų
Envelope volume envelope_volume37188 ų
Hydration-shell volume shell_volume17803 ų
Envelope diameter envelope_diameter61.8 Å
Shell Rg shell_rg23.81 Å
Envelope Rg envelope_rg17.82 Å
Shape Rg shape_rg16.06 Å
Total Rg total_rg16.25 Å
Total atoms total_atoms59900
Residues n_residues3700
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 dmax52.9 Å
Rg (real space) rg_real16.46 Å
Rg uncertainty (real space) rg_real_error0.27 Å
I(0) (real space) i0_real2.3980e+09
I(0) uncertainty (real space) i0_real_error2.5010e+07
Rg (reciprocal space) rg_reciprocal16.47 Å
I(0) (reciprocal space) i0_reciprocal2398000000.0000
Solution quality estimate total_estimate0.8945
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary22.0 Å
Skewness Skewness skewness0.162
Kurtosis Kurtosis kurtosis-0.372
Angular range angular_range— – 0.4800 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha893500.0000
Real-space data points n_real_points78
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.881; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.986
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id2lg1A01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily2510 —
Domain ID domain_id2lg1A02
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology29 — PH-domain like
Homologous superfamily homologous superfamily30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)
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8. Citations (2)

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9. Files and Curves (10)