6hjz

Xray structure of GLIC in complex with succinate

Method: X-RAY DIFFRACTION Dmax: 209.6 Å Quality: REASONABLE

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

Proton-gated ion channel

Gloeobacter violaceus (strain PCC 7421)

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 43–359 Chain B; UniProt 43–359 Chain C; UniProt 43–359 Chain D; UniProt 43–359 Chain E; UniProt 43–359 Not recorded PLC DIUNDECYL PHOSPHATIDYL CHOLINE × 15 CL CHLORIDE ION × 7 NA SODIUM ION × 6 LMT DODECYL-BETA-D-MALTOSIDE × 6 SIN SUCCINIC ACID × 10 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;293 K;100 mM NaSuccinate pH4 400 mM NaIsothiocynate 12-15% PEG4000 2% DMSO 15% glycerol Resolution 2.50 Å R-free 0.227
2 Protein homooligomer Homooligomer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain F; UniProt 43–359 Chain G; UniProt 43–359 Chain H; UniProt 43–359 Chain I; UniProt 43–359 Chain J; UniProt 43–359 Not recorded PLC DIUNDECYL PHOSPHATIDYL CHOLINE × 15 CL CHLORIDE ION × 7 NA SODIUM ION × 6 LMT DODECYL-BETA-D-MALTOSIDE × 6 SIN SUCCINIC ACID × 10 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;293 K;100 mM NaSuccinate pH4 400 mM NaIsothiocynate 12-15% PEG4000 2% DMSO 15% glycerol Resolution 2.50 Å R-free 0.227

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 GLIC_GLOVI
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–317; UniProt 43–359 Author chain B; PDBConstruct 1–317; UniProt 43–359 Author chain C; PDBConstruct 1–317; UniProt 43–359 Author chain D; PDBConstruct 1–317; UniProt 43–359 Author chain E; PDBConstruct 1–317; UniProt 43–359 Author chain F; PDBConstruct 1–317; UniProt 43–359 Author chain G; PDBConstruct 1–317; UniProt 43–359 Author chain H; PDBConstruct 1–317; UniProt 43–359 Author chain I; PDBConstruct 1–317; UniProt 43–359 Author chain J; PDBConstruct 1–317; UniProt 43–359

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 6hjz

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6hjz
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6hjz
Deposition date deposition_date2018-09-04
Structure title titleXray structure of GLIC in complex with succinate
Keywords keywordsPentameric Ligand-Gated Ion channel, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier69.87
Radius of gyration Rg (electron density) rg_electron68.74
Forward intensity I(0) i01521400000.00
Molecular weight molecular_weight371150.0 kDa
Excluded volume excluded_volume481520 ų
Envelope volume envelope_volume639770 ų
Hydration-shell volume shell_volume85694 ų
Envelope diameter envelope_diameter237.1
Shell Rg shell_rg55.67
Envelope Rg envelope_rg68.86
Shape Rg shape_rg68.71
Total Rg total_rg68.54
Total atoms total_atoms26280
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 dmax209.6
Rg (real space) rg_real70.37
Rg uncertainty (real space) rg_real_error1.61
I(0) (real space) i0_real1.5200e+09
I(0) uncertainty (real space) i0_real_error3.1340e+07
Rg (reciprocal space) rg_reciprocal67.29
I(0) (reciprocal space) i0_reciprocal1512000000.0000
Solution quality estimate total_estimate0.6979
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary47.6
Skewness Skewness skewness0.513
Kurtosis Kurtosis kurtosis-0.829
Angular range angular_range— – 0.1100 −1
Current regularization parameter α current_alpha0.0032
Highest regularization parameter α highest_alpha380000000.0000
Real-space data points n_real_points23
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.434; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.766; Smooth: 0.004

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 20 domains

CATH v4.4 (20 domains)

Domain ID domain_id6hjzA01
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_id6hjzA02
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_id6hjzB01
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_id6hjzB02
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_id6hjzC01
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_id6hjzC02
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_id6hjzD01
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_id6hjzD02
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_id6hjzE01
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_id6hjzE02
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_id6hjzF01
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_id6hjzF02
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_id6hjzG01
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_id6hjzG02
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_id6hjzH01
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_id6hjzH02
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_id6hjzI01
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_id6hjzI02
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_id6hjzJ01
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_id6hjzJ02
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)