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3mne

Crystal structure of the agonist form of mouse glucocorticoid receptor stabilized by F608S mutation at 1.96A

Method: X-RAY DIFFRACTION Dmax: 64.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Glucocorticoid receptor

Mus musculus

UniProt P06537

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 527–783 Fragment：UNP residues 527-783 Mutation：F608S Nuclear receptor coactivator 2 peptide × 1 （Q61026） GOL GLYCEROL × 2 DEX DEXAMETHASONE × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；0.5 M ammonium sulfate, 0.9 M sodium tartrate, 0.1 M PIPES pH 7.0, VAPOR DIFFUSION, SITTING DROP Resolution 1.96 Å R-free 0.185

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 3MNE Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3MNO Crystal structure of the agonist form of mouse glucocorticoid receptor stabilized by (A611V, F608S) mutations at 1.55A Deposited 2010-04-22 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 527–783（257 aa） Fragment：UNP residues 527-783
Mutation：A611V, F608S GOL GLYCEROL × 2 DEX DEXAMETHASONE × 1 SCN THIOCYANATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；0.2 M sodium thiocyanate, 0.1 M Bis-Tris pH 6.5, 0.7 M lithium sulfate, 10 % Glycerol, VAPOR DIFFUSION, HANGING DROP
Resolution 1.55 Å R-free 0.187
3MNP Crystal structure of the agonist form of mouse glucocorticoid receptor stabilized by (A611V, V708A, E711G) mutations at 1.50A Deposited 2010-04-22 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 527–783（257 aa） Fragment：UNP residues 527-783
Mutation：A611V, V708A, E711G GOL GLYCEROL × 2 DEX DEXAMETHASONE × 1 SCN THIOCYANATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；0.1 M Tris pH 8.5, 0.1 M sodium thiocyanate, 9 % PEG 10000, VAPOR DIFFUSION, SITTING DROP
Resolution 1.50 Å R-free 0.201

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GCR_MOUSE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 5–261； UniProt 527–783

Nuclear receptor coactivator 2 peptide

OrganismNot specified

UniProt Q61026

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 740–752 Fragment：TIF2 coactivator motif, residues 740-752 Glucocorticoid receptor × 1 （P06537） GOL GLYCEROL × 2 DEX DEXAMETHASONE × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；0.5 M ammonium sulfate, 0.9 M sodium tartrate, 0.1 M PIPES pH 7.0, VAPOR DIFFUSION, SITTING DROP Resolution 1.96 Å R-free 0.185

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 3MNE Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1L2I Human Estrogen Receptor alpha Ligand-binding Domain in Complex with (R,R)-5,11-cis-diethyl-5,6,11,12-tetrahydrochrysene-2,8-diol and a Glucocorticoid Receptor Interacting Protein 1 NR box II Peptide Deposited 2002-02-21 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 C 686–698（13 aa） Fragment：NR box II (residues 686-698)
Chain D 686–698（13 aa） Fragment：NR box II (residues 686-698)
Not recorded CL CHLORIDE ION × 1 ETC (R,R)-5,11-CIS-DIETHYL-5,6,11,12-TETRAHYDROCHRYSENE-2,8-DIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.8；293 K；16% (w/v) PEG 4000, 50 mM Magnesium chloride, 53 mM Tris pH 8.8 292-294 K, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.95 Å R-free 0.243
1L2I Human Estrogen Receptor alpha Ligand-binding Domain in Complex with (R,R)-5,11-cis-diethyl-5,6,11,12-tetrahydrochrysene-2,8-diol and a Glucocorticoid Receptor Interacting Protein 1 NR box II Peptide Deposited 2002-02-21 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 C 686–698（13 aa） Fragment：NR box II (residues 686-698)
Chain D 686–698（13 aa） Fragment：NR box II (residues 686-698)
Not recorded CL CHLORIDE ION × 1 ETC (R,R)-5,11-CIS-DIETHYL-5,6,11,12-TETRAHYDROCHRYSENE-2,8-DIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.8；293 K；16% (w/v) PEG 4000, 50 mM Magnesium chloride, 53 mM Tris pH 8.8 292-294 K, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.95 Å R-free 0.243
1OSV STRUCTURAL BASIS FOR BILE ACID BINDING AND ACTIVATION OF THE NUCLEAR RECEPTOR FXR Deposited 2003-03-20 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 741–752（12 aa） Fragment：Residues (741-752)
Not recorded CHC 6-ETHYL-CHENODEOXYCHOLIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；283 K；PEG 8000,Ethylene Glycol, PIPES , pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Resolution 2.50 Å R-free 0.276
1OSV STRUCTURAL BASIS FOR BILE ACID BINDING AND ACTIVATION OF THE NUCLEAR RECEPTOR FXR Deposited 2003-03-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 741–752（12 aa） Fragment：Residues (741-752)
Chain E 741–752（12 aa） Fragment：Residues (741-752)
Not recorded CHC 6-ETHYL-CHENODEOXYCHOLIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；283 K；PEG 8000,Ethylene Glycol, PIPES , pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Resolution 2.50 Å R-free 0.276
1WM0 PPARgamma in complex with a 2-BABA compound Deposited 2004-07-01 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain Y 684–697（14 aa）
Not recorded PLB 2-[(2,4-DICHLOROBENZOYL)AMINO]-5-(PYRIMIDIN-2-YLOXY)BENZOIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；PEG3000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.90 Å R-free 0.295
3MNO Crystal structure of the agonist form of mouse glucocorticoid receptor stabilized by (A611V, F608S) mutations at 1.55A Deposited 2010-04-22 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 740–752（13 aa） Fragment：TIF2 coactivator motif, residues 740-752
Not recorded GOL GLYCEROL × 2 DEX DEXAMETHASONE × 1 SCN THIOCYANATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；0.2 M sodium thiocyanate, 0.1 M Bis-Tris pH 6.5, 0.7 M lithium sulfate, 10 % Glycerol, VAPOR DIFFUSION, HANGING DROP
Resolution 1.55 Å R-free 0.187
3MNP Crystal structure of the agonist form of mouse glucocorticoid receptor stabilized by (A611V, V708A, E711G) mutations at 1.50A Deposited 2010-04-22 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 740–752（13 aa） Fragment：TIF2 coactivator motif, residues 740-752
Not recorded GOL GLYCEROL × 2 DEX DEXAMETHASONE × 1 SCN THIOCYANATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；0.1 M Tris pH 8.5, 0.1 M sodium thiocyanate, 9 % PEG 10000, VAPOR DIFFUSION, SITTING DROP
Resolution 1.50 Å R-free 0.201

5 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NCOA2_MOUSE
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–13； UniProt 740–752

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 3mne

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id3mne
Deposition date deposition_date2010-04-21
Structure title titleCrystal structure of the agonist form of mouse glucocorticoid receptor stabilized by F608S mutation at 1.96A
Keywords keywordsprotein-ligand complex, steroid nuclear receptor, mouse, agonist, co-activator, HORMONE RECEPTOR; HORMONE RECEPTOR
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_guinier19.95 Å
Radius of gyration Rg (electron density) rg_electron18.51 Å
Forward intensity I(0) i015246400.00
Molecular weight molecular_weight30747.0 kDa
Excluded volume excluded_volume39127 ų
Envelope volume envelope_volume45927 ų
Hydration-shell volume shell_volume20318 ų
Envelope diameter envelope_diameter66.8 Å
Shell Rg shell_rg25.40 Å
Envelope Rg envelope_rg19.18 Å
Shape Rg shape_rg18.49 Å
Total Rg total_rg19.63 Å
Total atoms total_atoms2155
Residues n_residues263
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 dmax64.4 Å
Rg (real space) rg_real19.83 Å
Rg uncertainty (real space) rg_real_error0.30 Å
I(0) (real space) i0_real1.5250e+07
I(0) uncertainty (real space) i0_real_error1.7050e+05
Rg (reciprocal space) rg_reciprocal19.85 Å
I(0) (reciprocal space) i0_reciprocal15250000.0000
Solution quality estimate total_estimate0.8918
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary25.4 Å
Skewness Skewness skewness0.196
Kurtosis Kurtosis kurtosis-0.369
Angular range angular_range— – 0.4000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3853000.0000
Real-space data points n_real_points72
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.864; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.998
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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) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd3mnea1
Class classa — All alpha proteins
Fold Fold folda.123 — Nuclear receptor ligand-binding domain
Superfamily Superfamily superfamilya.123.1 — Nuclear receptor ligand-binding domain
Family Family familya.123.1.1 — Nuclear receptor ligand-binding domain
Domain ID domain_idd3mnea2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id3mneA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology565 — Retinoid X Receptor
Homologous superfamily homologous superfamily10 — Retinoid X Receptor
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8. Citations (1)

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9. Files and Curves (10)