3uub

The GLIC pentameric Ligand-Gated Ion Channel Loop2-21' mutant reduced in solution

Method: X-RAY DIFFRACTION Dmax: 219.9 Å Quality: REASONABLE

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 44–359 Chain B; UniProt 44–359 Chain C; UniProt 44–359 Chain D; UniProt 44–359 Chain E; UniProt 44–359 Fragment:UNP residues 44-359 Mutation:C27S,K33C,N245C PLC DIUNDECYL PHOSPHATIDYL CHOLINE × 15 LMT DODECYL-BETA-D-MALTOSIDE × 6 NA SODIUM ION × 1 CL CHLORIDE ION × 5 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 4;293 K;15% PEG4000, 0.4 M sodium thiocyanate, 0.1 M sodium acetate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.90 Å R-free 0.221
2 Protein homooligomer Homooligomer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain F; UniProt 44–359 Chain G; UniProt 44–359 Chain H; UniProt 44–359 Chain I; UniProt 44–359 Chain J; UniProt 44–359 Fragment:UNP residues 44-359 Mutation:C27S,K33C,N245C PLC DIUNDECYL PHOSPHATIDYL CHOLINE × 15 LMT DODECYL-BETA-D-MALTOSIDE × 6 NA SODIUM ION × 1 CL CHLORIDE ION × 5 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 4;293 K;15% PEG4000, 0.4 M sodium thiocyanate, 0.1 M sodium acetate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.90 Å R-free 0.221

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 134 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 6–321; UniProt 44–359 Author chain B; PDBConstruct 6–321; UniProt 44–359 Author chain C; PDBConstruct 6–321; UniProt 44–359 Author chain D; PDBConstruct 6–321; UniProt 44–359 Author chain E; PDBConstruct 6–321; UniProt 44–359 Author chain F; PDBConstruct 6–321; UniProt 44–359 Author chain G; PDBConstruct 6–321; UniProt 44–359 Author chain H; PDBConstruct 6–321; UniProt 44–359 Author chain I; PDBConstruct 6–321; UniProt 44–359 Author chain J; PDBConstruct 6–321; UniProt 44–359

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 3uub

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3uub
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id3uub
Deposition date deposition_date2011-11-28
Structure title titleThe GLIC pentameric Ligand-Gated Ion Channel Loop2-21' mutant reduced in solution
Keywords keywordsCys-loop receptor family, MEMBRANE PROTEIN, TRANSPORT PROTEIN; MEMBRANE PROTEIN, TRANSPORT PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier87.12
Radius of gyration Rg (electron density) rg_electron88.11
Forward intensity I(0) i01451760000.00
Molecular weight molecular_weight366290.0 kDa
Excluded volume excluded_volume474250 ų
Envelope volume envelope_volume767110 ų
Hydration-shell volume shell_volume70968 ų
Envelope diameter envelope_diameter279.2
Shell Rg shell_rg93.56
Envelope Rg envelope_rg83.37
Shape Rg shape_rg88.11
Total Rg total_rg88.17
Total atoms total_atoms25942
Residues n_residues3110
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 dmax219.9
Rg (real space) rg_real83.12
Rg uncertainty (real space) rg_real_error1.08
I(0) (real space) i0_real1.4000e+09
I(0) uncertainty (real space) i0_real_error2.9470e+07
Rg (reciprocal space) rg_reciprocal81.43
I(0) (reciprocal space) i0_reciprocal1427000000.0000
Solution quality estimate total_estimate0.6377
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary48.9
Skewness Skewness skewness0.222
Kurtosis Kurtosis kurtosis-1.397
Angular range angular_range— – 0.0900 −1
Current regularization parameter α current_alpha0.2049
Highest regularization parameter α highest_alpha47140000.0000
Real-space data points n_real_points19
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.110; Stabil: 0.928; Sysdev: 1.000; Positv: 1.000; Valcen: 0.179; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 20 domains

CATH v4.4 (20 domains)

Domain ID domain_id3uubA01
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_id3uubA02
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_id3uubB01
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_id3uubB02
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_id3uubC01
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_id3uubC02
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_id3uubD01
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_id3uubD02
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_id3uubE01
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_id3uubE02
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_id3uubF01
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_id3uubF02
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_id3uubG01
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_id3uubG02
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_id3uubH01
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_id3uubH02
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_id3uubI01
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_id3uubI02
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_id3uubJ01
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_id3uubJ02
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)