SAXSdb — 6d8z

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Triple functional domain protein

Homo sapiens

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 1960–2275	Fragment：UNP RESIDUES 1960-2275	No other associated polymer	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
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1960–2275	Fragment：UNP RESIDUES 1960-2275	No other associated polymer	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
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 1960–2275	Fragment：UNP RESIDUES 1960-2275	No other associated polymer	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

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 6D8Z	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1NTY Crystal structure of the first DH/PH domain of Trio to 1.7 A Deposited 2003-01-30	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1225–1535（311 aa） Fragment：N-terminal DH/PH domains, residues 1225-1535	Not recorded	No recorded non-water small molecule	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
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
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 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TRIO_HUMAN
Isoform	O75962-2
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–319； UniProt 1960–2275 Author chain B； PDBConstruct 4–319； UniProt 1960–2275 Author chain C； PDBConstruct 4–319； UniProt 1960–2275

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6d8z
Deposition date deposition_date	2018-04-27
Structure title title	Crystal Structure of the C-terminal Guanine Nucleotide Exchange Factor Module of Human Trio
Keywords keywords	RhoGEF, Dbl Family member, Dbl Homology, Pleckstrin Homology, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	36.27 Å
Radius of gyration Rg (electron density) rg_electron	35.74 Å
Forward intensity I(0) i0	171024000.00
Molecular weight molecular_weight	106750.0 kDa
Excluded volume excluded_volume	134470 Å³
Envelope volume envelope_volume	183250 Å³
Hydration-shell volume shell_volume	43855 Å³
Envelope diameter envelope_diameter	131.7 Å
Shell Rg shell_rg	40.79 Å
Envelope Rg envelope_rg	35.71 Å
Shape Rg shape_rg	35.74 Å
Total Rg total_rg	36.12 Å
Total atoms total_atoms	7499
Residues n_residues	907
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	126.1 Å
Rg (real space) rg_real	36.37 Å
Rg uncertainty (real space) rg_real_error	1.20 Å
I(0) (real space) i0_real	1.7100e+08
I(0) uncertainty (real space) i0_real_error	2.8940e+06
Rg (reciprocal space) rg_reciprocal	36.31 Å
I(0) (reciprocal space) i0_reciprocal	171000000.0000
Solution quality estimate total_estimate	0.8671
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	43.0 Å
Skewness Skewness skewness	0.412
Kurtosis Kurtosis kurtosis	-0.218
Angular range angular_range	— – 0.2200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	25990000.0000
Real-space data points n_real_points	45
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.823; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.936; Smooth: 0.862

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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) 13 domains

SCOP 2.08 (7 domains)

Domain ID domain_id	d6d8za1
Class class	a — All alpha proteins
Fold Fold fold	a.87 — DBL homology domain (DH-domain)
Superfamily Superfamily superfamily	a.87.1 — DBL homology domain (DH-domain)
Family Family family	a.87.1.1 — DBL homology domain (DH-domain)

Domain ID domain_id	d6d8za2
Class class	b — All beta proteins
Fold Fold fold	b.55 — PH domain-like barrel
Superfamily Superfamily superfamily	b.55.1 — PH domain-like
Family Family family	b.55.1.1 — Pleckstrin-homology domain (PH domain)

Domain ID domain_id	d6d8zb1
Class class	a — All alpha proteins
Fold Fold fold	a.87 — DBL homology domain (DH-domain)
Superfamily Superfamily superfamily	a.87.1 — DBL homology domain (DH-domain)
Family Family family	a.87.1.1 — DBL homology domain (DH-domain)

Domain ID domain_id	d6d8zb2
Class class	b — All beta proteins
Fold Fold fold	b.55 — PH domain-like barrel
Superfamily Superfamily superfamily	b.55.1 — PH domain-like
Family Family family	b.55.1.1 — Pleckstrin-homology domain (PH domain)

Domain ID domain_id	d6d8zb3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d6d8zc1
Class class	a — All alpha proteins
Fold Fold fold	a.87 — DBL homology domain (DH-domain)
Superfamily Superfamily superfamily	a.87.1 — DBL homology domain (DH-domain)
Family Family family	a.87.1.1 — DBL homology domain (DH-domain)

Domain ID domain_id	d6d8zc2
Class class	b — All beta proteins
Fold Fold fold	b.55 — PH domain-like barrel
Superfamily Superfamily superfamily	b.55.1 — PH domain-like
Family Family family	b.55.1.1 — Pleckstrin-homology domain (PH domain)

CATH v4.4 (6 domains)

Domain ID domain_id	6d8zA01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	900 — Dbl Homology Domain; Chain A
Homologous superfamily homologous superfamily	10 — Dbl homology (DH) domain

Domain ID domain_id	6d8zA02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	29 — PH-domain like
Homologous superfamily homologous superfamily	30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)

Domain ID domain_id	6d8zB01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	900 — Dbl Homology Domain; Chain A
Homologous superfamily homologous superfamily	10 — Dbl homology (DH) domain

Domain ID domain_id	6d8zB02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	29 — PH-domain like
Homologous superfamily homologous superfamily	30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)

Domain ID domain_id	6d8zC01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	900 — Dbl Homology Domain; Chain A
Homologous superfamily homologous superfamily	10 — Dbl homology (DH) domain

Domain ID domain_id	6d8zC02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	29 — PH-domain like
Homologous superfamily homologous superfamily	30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)

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8. Citations (1)

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Unit-cell length a length_a	59.181 Å
Unit-cell length b length_b	95.787 Å
Unit-cell length c length_c	182.431 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.650 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	0.2270
R_work r_work	0.2250
R_free r_free	0.2660

Description description	Triple functional domain protein
Molecular weight formula_weight	37482.3 kDa
EC 编号 ec_number	2.7.11.1
Source method src_method	man
Copy count entity_count	3

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	7525

Crystal Structure of the C-terminal Guanine Nucleotide Exchange Factor Module of Human Trio

1. Protein Identity and Related Structures Protein Identity & Related Structures

Triple functional domain protein

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 13 domains

SCOP 2.08 (7 domains)

CATH v4.4 (6 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli BL21(DE3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	26

fit	/app/data/saxs_computation/d8/6d8z/6d8z.fit
pddf	/app/data/pr_computation/d8/6d8z/6d8z.pr.out
profile	/app/data/saxs_computation/d8/6d8z/6d8z.dat