7y96

Crystal structure of the carboxy-terminal domain of a coronavirus M protein fused with a split GFP

Method: X-RAY DIFFRACTION Dmax: 136.3 Å Quality: GOOD

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

Green fluorescent protein,Membrane protein

Aequorea victoria

UniProt A3EXD6

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Homooligomer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 116–203 Chain B; UniProt 116–203 Fragment:carboxy-terminal domain Mutation:R30S,Y39N,M153T,V163A,I171A,A206V Non-standard monomer:Yes (specific site not provided by mmCIF) No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5.3;293 K;0.4 M ammonium sulfate, 0.1 M Bis-Tris pH 5.3, PEG 3350 27%, 0.5% ethyl acetate Resolution 3.42 Å R-free 0.265

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 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name VME1_BCHK5
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 148–235; UniProt 116–203 Author chain B; PDBConstruct 148–235; UniProt 116–203

Green fluorescent protein,Membrane protein

Aequorea victoria

UniProt P42212

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Homooligomer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 1–144 Chain A; UniProt 146–230 Chain B; UniProt 1–144 Chain B; UniProt 146–230 Fragment:carboxy-terminal domain Mutation:R30S,Y39N,M153T,V163A,I171A,A206V Non-standard monomer:Yes (specific site not provided by mmCIF) No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5.3;293 K;0.4 M ammonium sulfate, 0.1 M Bis-Tris pH 5.3, PEG 3350 27%, 0.5% ethyl acetate Resolution 3.42 Å R-free 0.265

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.

568 other PDB entries and 744 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GFP_AEQVI
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–142; UniProt 1–144 Author chain A; PDBConstruct 239–323; UniProt 146–230 Author chain B; PDBConstruct 1–142; UniProt 1–144 Author chain B; PDBConstruct 239–323; UniProt 146–230

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 7y96

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7y96
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7y96
Deposition date deposition_date2022-06-24
Structure title titleCrystal structure of the carboxy-terminal domain of a coronavirus M protein fused with a split GFP
Keywords keywordsM protein, Cytosolic domain, SARS-COV-2 related, 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_guinier35.67
Radius of gyration Rg (electron density) rg_electron35.83
Forward intensity I(0) i077310100.00
Molecular weight molecular_weight69472.0 kDa
Excluded volume excluded_volume86952 ų
Envelope volume envelope_volume130190 ų
Hydration-shell volume shell_volume32714 ų
Envelope diameter envelope_diameter141.9
Shell Rg shell_rg37.84
Envelope Rg envelope_rg37.32
Shape Rg shape_rg35.79
Total Rg total_rg36.15
Total atoms total_atoms4890
Residues n_residues621
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 dmax136.3
Rg (real space) rg_real36.22
Rg uncertainty (real space) rg_real_error1.78
I(0) (real space) i0_real7.7310e+07
I(0) uncertainty (real space) i0_real_error1.4680e+06
Rg (reciprocal space) rg_reciprocal35.87
I(0) (reciprocal space) i0_reciprocal77290000.0000
Solution quality estimate total_estimate0.7503
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary31.0
Skewness Skewness skewness0.710
Kurtosis Kurtosis kurtosis0.143
Angular range angular_range— – 0.2200 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha13030000.0000
Real-space data points n_real_points45
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.518; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.384; Smooth: 0.810

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (1)

8. Citations (1)

9. Files and Curves (10)