7qhh

Desensitized state of GluA1/2 AMPA receptor in complex with TARP-gamma 8 (TMD-LBD)

Method: ELECTRON MICROSCOPY Dmax: 133.6 Å Quality: GOOD

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

Isoform Flip of Glutamate receptor 1

Rattus norvegicus

UniProt P19490

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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain A; UniProt 1–907 Chain C; UniProt 1–907 Not recorded Isoform Flip of Glutamate receptor 2 × 2 (P19491) Voltage-dependent calcium channel gamma-8 subunit × 2 (Q8VHW5) GLU GLUTAMIC ACID × 4 PAM PALMITOLEIC ACID × 10 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 2 79N (2S)-2,3-dihydroxypropyl (7Z)-hexadec-7-enoate × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 8;25 mM TRIS 150 mM NaCl 0.02 % GDN 87 uM CTZ 100 mM L-Glu cryo-EM vitrification conditions:Cryogen ETHANE;3-4 second blots Resolution 3.60 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.

32 other PDB entries and 34 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GRIA1_RAT
Isoform P19490-2
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–915; UniProt 1–907 Author chain C; PDBConstruct 1–915; UniProt 1–907

Isoform Flip of Glutamate receptor 2

Rattus norvegicus

UniProt P19491

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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain B; UniProt 1–860 Chain D; UniProt 1–860 Not recorded Isoform Flip of Glutamate receptor 1 × 2 (P19490) Voltage-dependent calcium channel gamma-8 subunit × 2 (Q8VHW5) GLU GLUTAMIC ACID × 4 PAM PALMITOLEIC ACID × 10 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 2 79N (2S)-2,3-dihydroxypropyl (7Z)-hexadec-7-enoate × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 8;25 mM TRIS 150 mM NaCl 0.02 % GDN 87 uM CTZ 100 mM L-Glu cryo-EM vitrification conditions:Cryogen ETHANE;3-4 second blots Resolution 3.60 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.

333 other PDB entries and 482 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GRIA2_RAT
Isoform P19491-2
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–860; UniProt 1–860 Author chain D; PDBConstruct 1–860; UniProt 1–860

Voltage-dependent calcium channel gamma-8 subunit

Rattus norvegicus

UniProt Q8VHW5

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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain I; UniProt 2–417 Chain J; UniProt 2–417 Not recorded Isoform Flip of Glutamate receptor 1 × 2 (P19490) Isoform Flip of Glutamate receptor 2 × 2 (P19491) GLU GLUTAMIC ACID × 4 PAM PALMITOLEIC ACID × 10 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 2 79N (2S)-2,3-dihydroxypropyl (7Z)-hexadec-7-enoate × 2 ELECTRON MICROSCOPY cryo-EM buffer:pH 8;25 mM TRIS 150 mM NaCl 0.02 % GDN 87 uM CTZ 100 mM L-Glu cryo-EM vitrification conditions:Cryogen ETHANE;3-4 second blots Resolution 3.60 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.

11 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CCG8_RAT
Isoform
PDB entities 3
Chains and sequence ranges Author chain I; PDBConstruct 2–417; UniProt 2–417 Author chain J; PDBConstruct 2–417; UniProt 2–417

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 7qhh

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7qhh
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7qhh
Deposition date deposition_date2021-12-12
Structure title titleDesensitized state of GluA1/2 AMPA receptor in complex with TARP-gamma 8 (TMD-LBD)
Keywords keywordsglutamate, AMPA receptor, TARPs, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier42.74
Radius of gyration Rg (electron density) rg_electron41.96
Forward intensity I(0) i0511919000.00
Molecular weight molecular_weight192290.0 kDa
Excluded volume excluded_volume242650 ų
Envelope volume envelope_volume350560 ų
Hydration-shell volume shell_volume69040 ų
Envelope diameter envelope_diameter136.0
Shell Rg shell_rg47.86
Envelope Rg envelope_rg41.03
Shape Rg shape_rg41.99
Total Rg total_rg42.18
Total atoms total_atoms13626
Residues n_residues1978
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 dmax133.6
Rg (real space) rg_real42.55
Rg uncertainty (real space) rg_real_error0.71
I(0) (real space) i0_real5.1190e+08
I(0) uncertainty (real space) i0_real_error8.1910e+06
Rg (reciprocal space) rg_reciprocal42.74
I(0) (reciprocal space) i0_reciprocal512000000.0000
Solution quality estimate total_estimate0.8965
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary54.1
Skewness Skewness skewness0.114
Kurtosis Kurtosis kurtosis-0.580
Angular range angular_range— – 0.1850 −1
Current regularization parameter α current_alpha0.0006
Highest regularization parameter α highest_alpha60770000.0000
Real-space data points n_real_points38
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.948; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.820

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id7qhhI01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
Homologous superfamily homologous superfamily150
Domain ID domain_id7qhhJ01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
Homologous superfamily homologous superfamily150

8. Citations (1)

9. Files and Curves (10)