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1nty

Crystal structure of the first DH/PH domain of Trio to 1.7 A

Method: X-RAY DIFFRACTION Dmax: 77.2 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Triple functional domain protein

Homo sapiens

UniProt O75962

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 1225–1535 Fragment：N-terminal DH/PH domains, residues 1225-1535 No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：Batch Method.；pH 7.5；277 K；DTT, pH 7.5, Batch Method., temperature 277K Resolution 1.70 Å R-free 0.214

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 1NTY Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2NZ8 N-terminal DHPH cassette of Trio in complex with nucleotide-free Rac1 Deposited 2006-11-22 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1226–1535（310 aa） Fragment：N-terminal DH/PH cassette (residues 1226-1535)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；291 K；100 mM sodium cacodylate pH 5.5 to 6.5, 14 to 18% (w/v) PEG 8000, and 300-500 mM calcium acetate, pH 6.0, VAPOR DIFFUSION, temperature 291K
Resolution 2.00 Å R-free 0.249
6D8Z Crystal Structure of the C-terminal Guanine Nucleotide Exchange Factor Module of Human Trio Deposited 2018-04-27 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1960–2275（316 aa） Fragment：UNP RESIDUES 1960-2275
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；14% PEG 3350, 100MM HEPES PH 7.5, HANGING DROP, 293K, VAPOR DIFFUSION, HANGING DROP
Resolution 2.65 Å R-free 0.266
6D8Z Crystal Structure of the C-terminal Guanine Nucleotide Exchange Factor Module of Human Trio Deposited 2018-04-27 Different construct Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1960–2275（316 aa） Fragment：UNP RESIDUES 1960-2275
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；14% PEG 3350, 100MM HEPES PH 7.5, HANGING DROP, 293K, VAPOR DIFFUSION, HANGING DROP
Resolution 2.65 Å R-free 0.266
6D8Z Crystal Structure of the C-terminal Guanine Nucleotide Exchange Factor Module of Human Trio Deposited 2018-04-27 Different construct Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1960–2275（316 aa） Fragment：UNP RESIDUES 1960-2275
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；14% PEG 3350, 100MM HEPES PH 7.5, HANGING DROP, 293K, VAPOR DIFFUSION, HANGING DROP
Resolution 2.65 Å R-free 0.266
7SJ4 Human Trio residues 1284-1959 in complex with Rac1 Deposited 2021-10-15 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1284–1959（676 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；Blot force 10
Resolution 2.86 Å

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

View Construct and Data Evidence
UniProt name TRIO_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–311； UniProt 1225–1535

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 1nty

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1nty
Deposition date deposition_date2003-01-30
Structure title titleCrystal structure of the first DH/PH domain of Trio to 1.7 A
Keywords keywordsDbl, Pleckstrin, GEF, Rho, GTPase, Guanine-nucleotide releasing factor, Phosphorylation, 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_guinier24.51 Å
Radius of gyration Rg (electron density) rg_electron23.56 Å
Forward intensity I(0) i021367300.00
Molecular weight molecular_weight35614.0 kDa
Excluded volume excluded_volume44811 ų
Envelope volume envelope_volume55416 ų
Hydration-shell volume shell_volume20239 ų
Envelope diameter envelope_diameter78.4 Å
Shell Rg shell_rg29.61 Å
Envelope Rg envelope_rg23.66 Å
Shape Rg shape_rg23.56 Å
Total Rg total_rg24.37 Å
Total atoms total_atoms2504
Residues n_residues305
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 dmax77.2 Å
Rg (real space) rg_real24.51 Å
Rg uncertainty (real space) rg_real_error0.54 Å
I(0) (real space) i0_real2.1370e+07
I(0) uncertainty (real space) i0_real_error2.8070e+05
Rg (reciprocal space) rg_reciprocal24.51 Å
I(0) (reciprocal space) i0_reciprocal21370000.0000
Solution quality estimate total_estimate0.9047
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary23.3 Å
Skewness Skewness skewness0.260
Kurtosis Kurtosis kurtosis-0.588
Angular range angular_range— – 0.3250 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4559000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.945; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.951; Smooth: 0.971
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1ntya1
Class classa — All alpha proteins
Fold Fold folda.87 — DBL homology domain (DH-domain)
Superfamily Superfamily superfamilya.87.1 — DBL homology domain (DH-domain)
Family Family familya.87.1.1 — DBL homology domain (DH-domain)
Domain ID domain_idd1ntya2
Class classb — All beta proteins
Fold Fold foldb.55 — PH domain-like barrel
Superfamily Superfamily superfamilyb.55.1 — PH domain-like
Family Family familyb.55.1.1 — Pleckstrin-homology domain (PH domain)

CATH v4.4 (2 domains)

Domain ID domain_id1ntyA01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology900 — Dbl Homology Domain; Chain A
Homologous superfamily homologous superfamily10 — Dbl homology (DH) domain
Domain ID domain_id1ntyA02
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 (1)

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9. Files and Curves (10)