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2k84

Solution Structure of the equine infectious anemia virus p9 GAG protein

Method: SOLUTION NMR Dmax: 33.5 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

P9

OrganismNot specified

UniProt P69732

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 457–486 Fragment：UNP residues 457-486 No other associated polymer SOLUTION NMR NMR measurement conditions：pH 3；300 K；Pressure ambient NMR sample composition：2-3 mM p9 (22-51), 50% H2O/50% CF3CD2OH | 50% H2O/50% CF3CD2OH Resolution not provided

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.

Other PDB Difference from Current Entry 2K84 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1EIA X-RAY CRYSTAL STRUCTURE OF EQUINE INFECTIOUS ANEMIA VIRUS (EIAV) CAPSID PROTEIN P26 Deposited 1998-07-15 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 140–346（207 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；pH 6.5
Resolution 2.70 Å R-free 0.275
2BL6 Solution structure of the Zn complex of EIAV NCp11(22-58) peptide, including two CCHC Zn-binding motifs. Deposited 2005-03-02 Different construct Different ligand/ion Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 381–417（37 aa） Fragment：RESIDUES 381-417
Not recorded ZN ZINC ION × 2 SOLUTION NMR
NMR measurement conditions pH 5.8；293 K；Ionic strength (raw mmCIF value) 210；Pressure 1.0
NMR sample composition 10% WATER/90% D2O
Resolution not provided
2EIA X-RAY CRYSTAL STRUCTURE OF EQUINE INFECTIOUS ANEMIA VIRUS (EIAV) CAPSID PROTEIN P26 Deposited 1998-07-15 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 141–346（206 aa）
Chain B 141–346（206 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；0.1M SODIUM CITRATE, 10% PEG 3350, 15% ISOPROPANOL, PH 6.5
Resolution 2.70 Å R-free 0.294
2R03 Crystal Structure of ALIX/AIP1 in complex with the YPDL Late Domain Deposited 2007-08-17 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 456–463（8 aa） Fragment：UNP residues 456-463
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.9；286 K；0.20-0.25 M MgCl2, 7-10% PEG 4000, 0.1 M NaMES, pH 5.9, VAPOR DIFFUSION, SITTING DROP, temperature 286K
Resolution 2.59 Å R-free 0.286

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GAG_EIAVY
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–30； UniProt 457–486

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 2k84

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2k84
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2k84
Deposition date deposition_date2008-09-02
Structure title titleSolution Structure of the equine infectious anemia virus p9 GAG protein
Keywords keywords;polypeptide, Capsid protein, Core protein, Host-virus interaction, Metal-binding, Viral matrix protein, Viral nucleoprotein, Virion, Zinc, Zinc-finger, VIRAL PROTEIN ;; VIRAL PROTEIN
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier12.20 Å
Radius of gyration Rg (electron density) rg_electron13.65 Å
Forward intensity I(0) i072446500.00
Molecular weight molecular_weight72980.0 kDa
Excluded volume excluded_volume91731 ų
Envelope volume envelope_volume10676 ų
Hydration-shell volume shell_volume7195 ų
Envelope diameter envelope_diameter53.3 Å
Shell Rg shell_rg18.45 Å
Envelope Rg envelope_rg16.02 Å
Shape Rg shape_rg13.66 Å
Total Rg total_rg13.75 Å
Total atoms total_atoms10140
Residues n_residues600
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax33.5 Å
Rg (real space) rg_real11.33 Å
Rg uncertainty (real space) rg_real_error0.07 Å
I(0) (real space) i0_real6.9280e+07
I(0) uncertainty (real space) i0_real_error5.3560e+05
Rg (reciprocal space) rg_reciprocal12.61 Å
I(0) (reciprocal space) i0_reciprocal72450000.0000
Solution quality estimate total_estimate0.5776
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary7.6 Å
Skewness Skewness skewness0.410
Kurtosis Kurtosis kurtosis-0.819
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha4.2820
Highest regularization parameter α highest_alpha4012.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.001; Oscil: 0.825; Stabil: 0.954; Sysdev: 0.000; Positv: 1.000; Valcen: 0.204; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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8. Citations (1)

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9. Files and Curves (10)