3ehz

X-ray structure of the pentameric ligand gated ion channel of Gloebacter violaceus (GLIC) in a presumptive open conformation

Method: X-RAY DIFFRACTION Dmax: 123.7 Å Quality: GOOD

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

Glr4197 protein

Gloeobacter violaceus

UniProt Q7NDN8

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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain A; UniProt 50–359 Chain B; UniProt 50–359 Chain C; UniProt 50–359 Chain D; UniProt 50–359 Chain E; UniProt 50–359 Fragment:UNP residues 50-359 No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 4;277.15 K;9% PEG4000, 50mM CH3COONa, 200mM (NH4)2SO4, pH4.0, vapor diffusion, hanging drop, temperature 277.15K, VAPOR DIFFUSION, HANGING DROP Resolution 3.10 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.

129 other PDB entries and 135 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q7NDN8_GLOVI
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 8–317; UniProt 50–359 Author chain B; PDBConstruct 8–317; UniProt 50–359 Author chain C; PDBConstruct 8–317; UniProt 50–359 Author chain D; PDBConstruct 8–317; UniProt 50–359 Author chain E; PDBConstruct 8–317; UniProt 50–359

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 3ehz

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id3ehz
Deposition date deposition_date2008-09-15
Structure title titleX-ray structure of the pentameric ligand gated ion channel of Gloebacter violaceus (GLIC) in a presumptive open conformation
Keywords keywordspentameric ligand gated ion channel, membrane protein, prokaryotic cys-loop receptor, cation selective channel; MEMBRANE PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier37.79
Radius of gyration Rg (electron density) rg_electron37.00
Forward intensity I(0) i0398075000.00
Molecular weight molecular_weight177630.0 kDa
Excluded volume excluded_volume228330 ų
Envelope volume envelope_volume290910 ų
Hydration-shell volume shell_volume64007 ų
Envelope diameter envelope_diameter128.5
Shell Rg shell_rg44.68
Envelope Rg envelope_rg36.71
Shape Rg shape_rg36.98
Total Rg total_rg37.59
Total atoms total_atoms12605
Residues n_residues1550
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

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

Maximum dimension Dmax dmax123.7
Rg (real space) rg_real37.69
Rg uncertainty (real space) rg_real_error1.02
I(0) (real space) i0_real3.9810e+08
I(0) uncertainty (real space) i0_real_error6.5010e+06
Rg (reciprocal space) rg_reciprocal37.75
I(0) (reciprocal space) i0_reciprocal398100000.0000
Solution quality estimate total_estimate0.8771
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary47.1
Skewness Skewness skewness0.319
Kurtosis Kurtosis kurtosis-0.268
Angular range angular_range— – 0.2100 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha70700000.0000
Real-space data points n_real_points43
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.829; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.922

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

7. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

Domain ID domain_id3ehzA01
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain
Domain ID domain_id3ehzA02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily390 — Neurotransmitter-gated ion-channel transmembrane domain
Domain ID domain_id3ehzB01
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain
Domain ID domain_id3ehzB02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily390 — Neurotransmitter-gated ion-channel transmembrane domain
Domain ID domain_id3ehzC01
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain
Domain ID domain_id3ehzC02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily390 — Neurotransmitter-gated ion-channel transmembrane domain
Domain ID domain_id3ehzD01
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain
Domain ID domain_id3ehzD02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily390 — Neurotransmitter-gated ion-channel transmembrane domain
Domain ID domain_id3ehzE01
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology170 — Acetylcholine Binding Protein; Chain: A,
Homologous superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain
Domain ID domain_id3ehzE02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily390 — Neurotransmitter-gated ion-channel transmembrane domain

8. Citations (1)

9. Files and Curves (10)