3c6d

The pseudo-atomic structure of dengue immature virus

Method: ELECTRON MICROSCOPY Dmax: 179.9 Å Quality: GOOD

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

Polyprotein

OrganismNot specified

UniProt O11875

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 × 360 PDB declaration: 360-meric(360) Consistent with protein copy count Chain A; UniProt 281–675 Chain B; UniProt 281–675 Chain C; UniProt 281–675 Not recorded prM × 180 (P14337) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.6;12 mM Tris-HCl, 120 mM NaCl, 1 mM EDTA cryo-EM vitrification conditions:Cryogen ETHANE Resolution 12.50 Å
2 Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain A; UniProt 281–675 Chain B; UniProt 281–675 Chain C; UniProt 281–675 Not recorded prM × 3 (P14337) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.6;12 mM Tris-HCl, 120 mM NaCl, 1 mM EDTA cryo-EM vitrification conditions:Cryogen ETHANE Resolution 12.50 Å
3 Protein heterocomplex Heteromer Protein × 30 PDB declaration: 30-meric(30) Consistent with protein copy count Chain A; UniProt 281–675 Chain B; UniProt 281–675 Chain C; UniProt 281–675 Not recorded prM × 15 (P14337) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.6;12 mM Tris-HCl, 120 mM NaCl, 1 mM EDTA cryo-EM vitrification conditions:Cryogen ETHANE Resolution 12.50 Å
4 Protein heterocomplex Heteromer Protein × 36 PDB declaration: 36-meric(36) Consistent with protein copy count Chain A; UniProt 281–675 Chain B; UniProt 281–675 Chain C; UniProt 281–675 Not recorded prM × 18 (P14337) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.6;12 mM Tris-HCl, 120 mM NaCl, 1 mM EDTA cryo-EM vitrification conditions:Cryogen ETHANE Resolution 12.50 Å
5 Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain A; UniProt 281–675 Chain B; UniProt 281–675 Chain C; UniProt 281–675 Not recorded prM × 3 (P14337) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.6;12 mM Tris-HCl, 120 mM NaCl, 1 mM EDTA cryo-EM vitrification conditions:Cryogen ETHANE Resolution 12.50 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.

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

View Construct and Data Evidence
UniProt name O11875_9FLAV
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–395; UniProt 281–675 Author chain B; PDBConstruct 1–395; UniProt 281–675 Author chain C; PDBConstruct 1–395; UniProt 281–675

prM

OrganismNot specified

UniProt P14337

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 × 360 PDB declaration: 360-meric(360) Consistent with protein copy count Chain D; UniProt 115–195 Chain E; UniProt 115–195 Chain F; UniProt 115–195 Not recorded Polyprotein × 180 (O11875) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.6;12 mM Tris-HCl, 120 mM NaCl, 1 mM EDTA cryo-EM vitrification conditions:Cryogen ETHANE Resolution 12.50 Å
2 Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain D; UniProt 115–195 Chain E; UniProt 115–195 Chain F; UniProt 115–195 Not recorded Polyprotein × 3 (O11875) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.6;12 mM Tris-HCl, 120 mM NaCl, 1 mM EDTA cryo-EM vitrification conditions:Cryogen ETHANE Resolution 12.50 Å
3 Protein heterocomplex Heteromer Protein × 30 PDB declaration: 30-meric(30) Consistent with protein copy count Chain D; UniProt 115–195 Chain E; UniProt 115–195 Chain F; UniProt 115–195 Not recorded Polyprotein × 15 (O11875) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.6;12 mM Tris-HCl, 120 mM NaCl, 1 mM EDTA cryo-EM vitrification conditions:Cryogen ETHANE Resolution 12.50 Å
4 Protein heterocomplex Heteromer Protein × 36 PDB declaration: 36-meric(36) Consistent with protein copy count Chain D; UniProt 115–195 Chain E; UniProt 115–195 Chain F; UniProt 115–195 Not recorded Polyprotein × 18 (O11875) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.6;12 mM Tris-HCl, 120 mM NaCl, 1 mM EDTA cryo-EM vitrification conditions:Cryogen ETHANE Resolution 12.50 Å
5 Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain D; UniProt 115–195 Chain E; UniProt 115–195 Chain F; UniProt 115–195 Not recorded Polyprotein × 3 (O11875) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.6;12 mM Tris-HCl, 120 mM NaCl, 1 mM EDTA cryo-EM vitrification conditions:Cryogen ETHANE Resolution 12.50 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.

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name POLG_DEN28
Isoform
PDB entities 2
Chains and sequence ranges Author chain D; PDBConstruct 1–81; UniProt 115–195 Author chain E; PDBConstruct 1–81; UniProt 115–195 Author chain F; PDBConstruct 1–81; UniProt 115–195

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 3c6d

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3c6d
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3c6d
Deposition date deposition_date2008-02-04
Structure title titleThe pseudo-atomic structure of dengue immature virus
Keywords keywords;icosahedral virion, Helicase, Hydrolase, Nucleotide-binding, RNA replication, Transmembrane, ATP-binding, Capsid protein, Cleavage on pair of basic residues, Endoplasmic reticulum, Envelope protein, Glycoprotein, Metal-binding, Multifunctional enzyme, Nucleotidyltransferase, Nucleus, Phosphoprotein, Protease, Ribonucleoprotein, RNA-binding, RNA-directed RNA polymerase, Secreted, Serine protease, Transcription, Transcription regulation, Transferase, Viral nucleoprotein, icosahedral virus, VIRUS ;; VIRUS
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier55.35
Radius of gyration Rg (electron density) rg_electron55.68
Forward intensity I(0) i0369306000.00
Molecular weight molecular_weight157790.0 kDa
Excluded volume excluded_volume192350 ų
Envelope volume envelope_volume219360 ų
Hydration-shell volume shell_volume37274 ų
Envelope diameter envelope_diameter176.0
Shell Rg shell_rg51.37
Envelope Rg envelope_rg50.84
Shape Rg shape_rg55.78
Total Rg total_rg55.56
Total atoms total_atoms
Residues n_residues
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 dmax179.9
Rg (real space) rg_real55.28
Rg uncertainty (real space) rg_real_error1.59
I(0) (real space) i0_real3.6930e+08
I(0) uncertainty (real space) i0_real_error7.6690e+06
Rg (reciprocal space) rg_reciprocal55.37
I(0) (reciprocal space) i0_reciprocal369300000.0000
Solution quality estimate total_estimate0.8616
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary83.5
Skewness Skewness skewness-0.002
Kurtosis Kurtosis kurtosis-0.803
Angular range angular_range— – 0.1400 −1
Current regularization parameter α current_alpha0.0002
Highest regularization parameter α highest_alpha9039000.0000
Real-space data points n_real_points29
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.817; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.962; Smooth: 0.783

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

8. Citations (1)

9. Files and Curves (10)