SAXSdb — 6zsh

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

EH domain-binding protein 1

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1060–1162 Chain B； UniProt 440–550	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M di-Ammonium hydrogen citrate 20% (w/v) PEG 3350	Resolution 2.20 Å R-free 0.230
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 1060–1162 Chain D； UniProt 440–550	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M di-Ammonium hydrogen citrate 20% (w/v) PEG 3350	Resolution 2.20 Å R-free 0.230

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 6ZSH	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6ZSI The mechanism of activation of the actin binding protein EHBP1 by Rab8 family members. Deposited 2020-07-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1060–1212（153 aa）	Mutation：M1116A	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 PEG DI(HYDROXYETHYL)ETHER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1 M Mes pH 6.0 5% w/v PEG 3000 30% v/v PEG 200	Resolution 1.91 Å R-free 0.267
6ZSI The mechanism of activation of the actin binding protein EHBP1 by Rab8 family members. Deposited 2020-07-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1060–1212（153 aa）	Mutation：M1116A	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 PEG DI(HYDROXYETHYL)ETHER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1 M Mes pH 6.0 5% w/v PEG 3000 30% v/v PEG 200	Resolution 1.91 Å R-free 0.267
6ZSJ The mechanism of activation of the actin binding protein EHBP1 by Rab8 family members. Deposited 2020-07-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1060–1212（153 aa）	Mutation：F1120A	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1M Mes pH 6.5 10 % (w/v) Peg-MME5000 12% (v/v) 1-propanol	Resolution 2.00 Å R-free 0.291
6ZSJ The mechanism of activation of the actin binding protein EHBP1 by Rab8 family members. Deposited 2020-07-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1060–1212（153 aa）	Mutation：F1120A	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1M Mes pH 6.5 10 % (w/v) Peg-MME5000 12% (v/v) 1-propanol	Resolution 2.00 Å R-free 0.291

2 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	EHBP1_HUMAN
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 4–106； UniProt 1060–1162 Author chain C； PDBConstruct 4–106； UniProt 1060–1162 Author chain B； PDBConstruct 4–114； UniProt 440–550 Author chain D； PDBConstruct 4–114； UniProt 440–550

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	6zsh
Deposition date deposition_date	2020-07-15
Structure title title	The mechanism of activation of the actin binding protein EHBP1 by Rab8 family members
Keywords keywords	Rab GTPase, EHBP1, bMERB domain, CH domain, ENDOCYTOSIS; ENDOCYTOSIS
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	33.72 Å
Radius of gyration Rg (electron density) rg_electron	33.96 Å
Forward intensity I(0) i0	33373700.00
Molecular weight molecular_weight	45417.0 kDa
Excluded volume excluded_volume	57006 Å³
Envelope volume envelope_volume	79789 Å³
Hydration-shell volume shell_volume	21911 Å³
Envelope diameter envelope_diameter	134.5 Å
Shell Rg shell_rg	35.83 Å
Envelope Rg envelope_rg	34.43 Å
Shape Rg shape_rg	33.99 Å
Total Rg total_rg	34.05 Å
Total atoms total_atoms	3190
Residues n_residues	388
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	125.7 Å
Rg (real space) rg_real	34.06 Å
Rg uncertainty (real space) rg_real_error	1.58 Å
I(0) (real space) i0_real	3.3370e+07
I(0) uncertainty (real space) i0_real_error	6.0260e+05
Rg (reciprocal space) rg_reciprocal	33.85 Å
I(0) (reciprocal space) i0_reciprocal	33370000.0000
Solution quality estimate total_estimate	0.7610
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.1 Å
Skewness Skewness skewness	0.492
Kurtosis Kurtosis kurtosis	-0.313
Angular range angular_range	— – 0.2350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2561000.0000
Real-space data points n_real_points	48
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.576; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.260; Smooth: 0.899

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	EH domain-binding protein 1
Molecular weight formula_weight	12631.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	3320

GHMDEVLNKGFKDTSQYVVGELAALENEQKQIDTRAALVEKRLRYLMDTGRNTEEEEAMMQEWFMLVNKKNALIRRMNQLSLLEKEHDLERRYELLNRELRAMLAI

来源 Source

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

Entity 2 Entity 2 polymer

Description description	EH domain-binding protein 1
Molecular weight formula_weight	13050.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

GHMGRKPNASQSLLVWCKEVTKNYRGVKITNFTTSWRNGLSFCAILHHFRPDLIDYKSLNPQDIKENNKKAYDGFASIGISRLLEPSDMVLLAIPDKLTVMTYLYQIRAHFSGQ

来源 Source

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

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	130

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d6zshb_
Class class	a — All alpha proteins
Fold Fold fold	a.40 — CH domain-like
Superfamily Superfamily superfamily	a.40.1 — Calponin-homology domain, CH-domain
Family Family family	a.40.1.0 — automated matches

Domain ID domain_id	d6zshd_
Class class	a — All alpha proteins
Fold Fold fold	a.40 — CH domain-like
Superfamily Superfamily superfamily	a.40.1 — Calponin-homology domain, CH-domain
Family Family family	a.40.1.0 — automated matches

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8. Citations (1)

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Unit-cell length a length_a	54.060 Å
Unit-cell length b length_b	48.190 Å
Unit-cell length c length_c	100.300 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	97.48 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	44.820 Å
R factor r_factor	0.1796
R_work r_work	0.1770
R_free r_free	0.2298

fit	/app/data/saxs_computation/zs/6zsh/6zsh.fit
pddf	/app/data/pr_computation/zs/6zsh/6zsh.pr.out
profile	/app/data/saxs_computation/zs/6zsh/6zsh.dat

The mechanism of activation of the actin binding protein EHBP1 by Rab8 family members

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

EH domain-binding protein 1

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)