10ex

SK5A-Matured apo state in complex with GluN1-GluN2B, full refinement

Method: ELECTRON MICROSCOPY Dmax: 214.4 Å Quality: GOOD

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

Isoform 4 of Glutamate receptor ionotropic, NMDA 1

Homo sapiens

UniProt Q5R1P0

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 heterocomplex Heteromer Protein × 8 PDB declaration: octameric(8) Consistent with protein copy count Chain A; UniProt 25–838 Chain C; UniProt 25–838 Not recorded Glutamate receptor ionotropic, NMDA 2B × 2 (Q13224) Light chain × 2 Heavy chain × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 4.08 Å

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.

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

View Construct and Data Evidence
UniProt name NMDZ1_CANLF
Isoform Q5R1P0-4
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–814; UniProt 25–838 Author chain C; PDBConstruct 1–814; UniProt 25–838

Glutamate receptor ionotropic, NMDA 2B

Homo sapiens

UniProt Q13224

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 heterocomplex Heteromer Protein × 8 PDB declaration: octameric(8) Consistent with protein copy count Chain B; UniProt 59–845 Chain D; UniProt 59–845 Not recorded Isoform 4 of Glutamate receptor ionotropic, NMDA 1 × 2 (Q5R1P0) Light chain × 2 Heavy chain × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 4.08 Å

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.

35 other PDB entries and 42 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NMDE2_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–787; UniProt 59–845 Author chain D; PDBConstruct 1–787; UniProt 59–845

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 10ex

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 10ex
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2. Structure Basics 2. Structure Basics

Entry ID entry_id10ex
Deposition date deposition_date2026-01-15
Structure title titleSK5A-Matured apo state in complex with GluN1-GluN2B, full refinement
Keywords keywordsNMDAR, antibody, SIGNALING PROTEIN, SIGNALING PROTEIN-Immune System complex; SIGNALING PROTEIN/Immune System
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier61.01
Radius of gyration Rg (electron density) rg_electron61.26
Forward intensity I(0) i01912570000.00
Molecular weight molecular_weight368790.0 kDa
Excluded volume excluded_volume461950 ų
Envelope volume envelope_volume713140 ų
Hydration-shell volume shell_volume103860 ų
Envelope diameter envelope_diameter216.5
Shell Rg shell_rg57.34
Envelope Rg envelope_rg59.36
Shape Rg shape_rg61.26
Total Rg total_rg61.15
Total atoms total_atoms26017
Residues n_residues3535
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 dmax214.4
Rg (real space) rg_real61.10
Rg uncertainty (real space) rg_real_error2.41
I(0) (real space) i0_real1.9130e+09
I(0) uncertainty (real space) i0_real_error4.4080e+07
Rg (reciprocal space) rg_reciprocal60.90
I(0) (reciprocal space) i0_reciprocal1912000000.0000
Solution quality estimate total_estimate0.8112
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary66.0
Skewness Skewness skewness0.326
Kurtosis Kurtosis kurtosis-0.387
Angular range angular_range— – 0.1300 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha125100000.0000
Real-space data points n_real_points27
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.848; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

8. Citations (1)

9. Files and Curves (10)