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5nhq

Nuclear Magnetic Resonance Structure of the Human Polyoma JC Virus Agnoprotein

Method: SOLUTION NMR Dmax: 102.7 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Agnoprotein

OrganismNot specified

UniProt P03086

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 1–71 Not recorded No other associated polymer SOLUTION NMR NMR measurement conditions：pH 3；313 K；Ionic strength (raw mmCIF value) 200 mM NaCl；Pressure pa NMR sample composition：0.2 mM no labelling agnoprotein, trifluoroethanol/water | trifluoroethanol/water 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 5NHQ Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2MJ2 Structure of the dimerization domain of the human polyoma, JC virus agnoprotein is an amphipathic alpha-helix. Deposited 2013-12-23 Different construct Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 17–52（36 aa） Fragment：UNP residues 17-52
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 3；293 K；Ionic strength (raw mmCIF value) no salts；Pressure ambient
NMR measurement conditions pH 3；303 K；Ionic strength (raw mmCIF value) no salts；Pressure ambient
NMR measurement conditions pH 3；313 K；Ionic strength (raw mmCIF value) no salts；Pressure ambient
NMR sample composition 0.5 mM AGNO, 70 v/v H2O, 30 v/v [U-100% 2H] TFE, water with 30% (v/v) TFE (Trifluoroethanol, CF3CH2OH) | water with 30% (v/v) TFE (Trifluoroethanol, CF3CH2OH)
Resolution not provided
9CMT The crystal structure of HP1alpha CSD-Agno complex Deposited 2024-07-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 4–19（16 aa）
Chain F 4–19（16 aa）
Not recorded F6Z 3',6'-DIHYDROXY-3-OXO-3H-SPIRO[2-BENZOFURAN-1,9'-XANTHENE]-5-CARBOXYLIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；1 uL protein solution (about 10 mg/ml) and 1 uL reservoir solution containing 0.01 M NiCl2, 0.1 M Tris-HCl, pH 8.5, and 20% PEG2000MME (v/v)
Resolution 3.17 Å R-free 0.286

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

View Construct and Data Evidence
UniProt name AGNO_POVJC
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–71； UniProt 1–71

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 5nhq

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5nhq
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5nhq
Deposition date deposition_date2017-03-22
Structure title titleNuclear Magnetic Resonance Structure of the Human Polyoma JC Virus Agnoprotein
Keywords keywords;Agnoprotein, dimer, oligomer, polyomavirus, JCV, SV40, BKV, Merkel cell, DNA replication, progressive multifocal leukoencephalopathy, alpha-helix, intrinsically unstructured, 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_guinier24.33 Å
Radius of gyration Rg (electron density) rg_electron23.56 Å
Forward intensity I(0) i0141967000.00
Molecular weight molecular_weight97062.0 kDa
Excluded volume excluded_volume122640 ų
Envelope volume envelope_volume116000 ų
Hydration-shell volume shell_volume34808 ų
Envelope diameter envelope_diameter108.8 Å
Shell Rg shell_rg34.57 Å
Envelope Rg envelope_rg29.13 Å
Shape Rg shape_rg23.52 Å
Total Rg total_rg24.61 Å
Total atoms total_atoms14016
Residues n_residues852
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 dmax102.7 Å
Rg (real space) rg_real24.53 Å
Rg uncertainty (real space) rg_real_error1.43 Å
I(0) (real space) i0_real1.4200e+08
I(0) uncertainty (real space) i0_real_error2.2820e+06
Rg (reciprocal space) rg_reciprocal24.48 Å
I(0) (reciprocal space) i0_reciprocal142000000.0000
Solution quality estimate total_estimate0.7024
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary24.5 Å
Skewness Skewness skewness0.562
Kurtosis Kurtosis kurtosis0.273
Angular range angular_range— – 0.3250 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha719400.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.266; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.330; Smooth: 0.999
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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 (2)

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9. Files and Curves (10)