← Back to search
3j35

Cryo-EM reconstruction of Dengue virus at 37 C

Method: ELECTRON MICROSCOPY Dmax: 212.3 Å Quality: REASONABLE
▼

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

envelope protein

OrganismNot specified

UniProt D0EPS0

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 homooligomer Homooligomer Protein × 180 PDB declaration: 180-meric（180） Consistent with protein copy count Chain A； UniProt 281–675 Chain B； UniProt 281–675 Chain C； UniProt 281–675 Fragment：UNP residues 281-675 No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer：NTE；pH 7.3；NTE cryo-EM vitrification conditions：100 K；Cryogen ETHANE；Plunged into liquid ethane using a homemade plunger. Resolution 35.00 Å
2 Protein homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain A； UniProt 281–675 Chain B； UniProt 281–675 Chain C； UniProt 281–675 Fragment：UNP residues 281-675 No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer：NTE；pH 7.3；NTE cryo-EM vitrification conditions：100 K；Cryogen ETHANE；Plunged into liquid ethane using a homemade plunger. Resolution 35.00 Å
3 Protein homooligomer Homooligomer Protein × 15 PDB declaration: pentadecameric（15） Consistent with protein copy count Chain A； UniProt 281–675 Chain B； UniProt 281–675 Chain C； UniProt 281–675 Fragment：UNP residues 281-675 No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer：NTE；pH 7.3；NTE cryo-EM vitrification conditions：100 K；Cryogen ETHANE；Plunged into liquid ethane using a homemade plunger. Resolution 35.00 Å
4 Protein homooligomer Homooligomer Protein × 18 PDB declaration: octadecameric（18） Consistent with protein copy count Chain A； UniProt 281–675 Chain B； UniProt 281–675 Chain C； UniProt 281–675 Fragment：UNP residues 281-675 No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer：NTE；pH 7.3；NTE cryo-EM vitrification conditions：100 K；Cryogen ETHANE；Plunged into liquid ethane using a homemade plunger. Resolution 35.00 Å
5 Protein homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain A； UniProt 281–675 Chain B； UniProt 281–675 Chain C； UniProt 281–675 Fragment：UNP residues 281-675 No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer：NTE；pH 7.3；NTE cryo-EM vitrification conditions：100 K；Cryogen ETHANE；Plunged into liquid ethane using a homemade plunger. Resolution 35.00 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.

Other PDB Difference from Current Entry 3J35 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6WER DENV2 NS1 in complex with neutralizing 2B7 Fab fragment Deposited 2020-04-02 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 A 775–1127（353 aa）
Chain B 775–1127（353 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.2；293 K；23% PEG 3350, 0.25 M MgCl2, 0.1 M sodium acetate pH 5.2
Resolution 3.96 Å R-free 0.311
6WY1 Crystal structure of an engineered thermostable dengue virus 2 envelope protein dimer Deposited 2020-05-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 281–677（397 aa）
Mutation：G106D, A259W, T262R, F279W, T280P NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；296 K；15% PEG 3350 pH 4.4, 0.1M Sodium Acetate Trihydrate + 0.1M Sodium Iodide
Resolution 3.42 Å R-free 0.337
6ZQU Cryo-EM structure of mature Dengue virus 2 at 3.1 angstrom resolution Deposited 2020-07-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 360 PDB declaration: 360-meric
Chain A 281–775（495 aa）
Chain C 281–775（495 aa）
Chain E 281–775（495 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 360 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；PBS buffer
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.10 Å
7K93 DENV2 NS1 in complex with neutralizing 2B7 single chain Fab variable region (scFv) Deposited 2020-09-28 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 × 4 PDB declaration: tetrameric
Chain A 775–1127（353 aa）
Chain B 775–1127（353 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；50 mM Tris pH 8.5, 50 mM (NH4)2SO4, 10% (v/v) glycerol
Resolution 2.89 Å R-free 0.269
7K93 DENV2 NS1 in complex with neutralizing 2B7 single chain Fab variable region (scFv) Deposited 2020-09-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 775–1127（353 aa）
Chain D 775–1127（353 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；50 mM Tris pH 8.5, 50 mM (NH4)2SO4, 10% (v/v) glycerol
Resolution 2.89 Å R-free 0.269

4 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name D0EPS0_9FLAV
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–393； UniProt 281–675 Author chain B； PDBConstruct 1–393； UniProt 281–675 Author chain C； PDBConstruct 1–393； UniProt 281–675

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 3j35

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3j35
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id3j35
Deposition date deposition_date2013-02-24
Structure title titleCryo-EM reconstruction of Dengue virus at 37 C
Keywords keywordsbumpy structure, conformational change, temperature dependent, VIRUS; VIRUS
Experimental Method methodELECTRON MICROSCOPY
▼

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

Radius of gyration Rg (Guinier) rg_guinier73.20 Å
Radius of gyration Rg (electron density) rg_electron74.27 Å
Forward intensity I(0) i0244759000.00
Molecular weight molecular_weight131200.0 kDa
Excluded volume excluded_volume160410 ų
Envelope volume envelope_volume211370 ų
Hydration-shell volume shell_volume26644 ų
Envelope diameter envelope_diameter223.2 Å
Shell Rg shell_rg64.80 Å
Envelope Rg envelope_rg68.68 Å
Shape Rg shape_rg74.33 Å
Total Rg total_rg74.13 Å
Total atoms total_atoms—
Residues n_residues—
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
▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax212.3 Å
Rg (real space) rg_real73.84 Å
Rg uncertainty (real space) rg_real_error1.90 Å
I(0) (real space) i0_real2.4470e+08
I(0) uncertainty (real space) i0_real_error5.3180e+06
Rg (reciprocal space) rg_reciprocal70.31 Å
I(0) (reciprocal space) i0_reciprocal243000000.0000
Solution quality estimate total_estimate0.6276
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary30.3 Å
Skewness Skewness skewness0.282
Kurtosis Kurtosis kurtosis-1.128
Angular range angular_range— – 0.1050 Å−1
Current regularization parameter α current_alpha0.0003
Highest regularization parameter α highest_alpha5563000.0000
Real-space data points n_real_points22
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.341; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.133; Smooth: 0.000
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (1)

▶

8. Citations (1)

▶

9. Files and Curves (10)