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4gt0

Structure of dengue virus serotype 1 sE containing stem to residue 421

Method: X-RAY DIFFRACTION Dmax: 149.9 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Envelope protein E

Dengue virus 1

UniProt P17763

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain A； UniProt 281–701 Fragment：sE(421), UNP residues 281-701 Mutation：W101H NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 CD CADMIUM ION × 6 CL CHLORIDE ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.57 Å R-free 0.210
2 Protein homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain B； UniProt 281–701 Fragment：sE(421), UNP residues 281-701 Mutation：W101H NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 CD CADMIUM ION × 6 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.57 Å R-free 0.210

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 4GT0 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3L6P Crystal Structure of Dengue Virus 1 NS2B/NS3 protease Deposited 2009-12-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1476–1661（186 aa） Fragment：NS2B residues 1394-1440, NS3 PROTEASE residues 1476-1661
Mutation：deletion NS3 PROTEASE, residues 1486-1495 NI NICKEL (II) ION × 6 CD CADMIUM ION × 2 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；293 K；0.1M HEPES pH 7.5, 12% PEG 3350 and 0.005M each of NiCl2, CdCl2, MgCl2 and CoCl2, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.20 Å R-free 0.284
3L6P Crystal Structure of Dengue Virus 1 NS2B/NS3 protease Deposited 2009-12-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1476–1661（186 aa） Fragment：NS2B residues 1394-1440, NS3 PROTEASE residues 1476-1661
Mutation：deletion NS3 PROTEASE, residues 1486-1495 NI NICKEL (II) ION × 12 CD CADMIUM ION × 4 SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；293 K；0.1M HEPES pH 7.5, 12% PEG 3350 and 0.005M each of NiCl2, CdCl2, MgCl2 and CoCl2, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.20 Å R-free 0.284
3LKW Crystal Structure of Dengue Virus 1 NS2B/NS3 protease active site mutant Deposited 2010-01-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1476–1661（186 aa） Fragment：NS2B residues 1394-1440, NS3 PROTEASE residues 1476-1661
Mutation：deletion NS3 PROTEASE, residues 1486-1495 CL CHLORIDE ION × 2 CD CADMIUM ION × 2 SO4 SULFATE ION × 2 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；293 K；0.1M Hepes pH 7.5, 12% PEG 3350, 0.005M each NiCl2, CdCl2, MgCl2, CoCl2, 0.1M Potassium sodium tartrate tetrahydrate, vapor diffusion, temperature 293K
Resolution 2.00 Å R-free 0.249
3LKW Crystal Structure of Dengue Virus 1 NS2B/NS3 protease active site mutant Deposited 2010-01-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1476–1661（186 aa） Fragment：NS2B residues 1394-1440, NS3 PROTEASE residues 1476-1661
Mutation：deletion NS3 PROTEASE, residues 1486-1495 CL CHLORIDE ION × 4 CD CADMIUM ION × 4 SO4 SULFATE ION × 4 GOL GLYCEROL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；293 K；0.1M Hepes pH 7.5, 12% PEG 3350, 0.005M each NiCl2, CdCl2, MgCl2, CoCl2, 0.1M Potassium sodium tartrate tetrahydrate, vapor diffusion, temperature 293K
Resolution 2.00 Å R-free 0.249
4FFZ Crystal Structure of DENV1-E111 fab fragment bound to DENV-1 DIII (Western Pacific-74 strain). Deposited 2012-06-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 573–679（107 aa） Fragment：UNP residues 573-679
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；20% PEG 6000, 0.1M MES, 1% glycerol., pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.80 Å R-free 0.278
4FFZ Crystal Structure of DENV1-E111 fab fragment bound to DENV-1 DIII (Western Pacific-74 strain). Deposited 2012-06-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain X 573–679（107 aa） Fragment：UNP residues 573-679
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；20% PEG 6000, 0.1M MES, 1% glycerol., pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.80 Å R-free 0.278
4GSX High resolution structure of dengue virus serotype 1 sE containing stem Deposited 2012-08-28 Different construct Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 281–691（411 aa） Fragment：UNP residues 281-691
Mutation：W101H NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 CD CADMIUM ION × 6 CL CHLORIDE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.90 Å R-free 0.186
4GSX High resolution structure of dengue virus serotype 1 sE containing stem Deposited 2012-08-28 Different construct Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain B 281–691（411 aa） Fragment：UNP residues 281-691
Mutation：W101H NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 CD CADMIUM ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.90 Å R-free 0.186
4OIG Dengue Virus Non-structural Protein NS1 Deposited 2014-01-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 947–1127（181 aa） Fragment：UNP residues 947-1127
Chain B 947–1127（181 aa） Fragment：UNP residues 947-1127
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；12mg/mL in 20% PEG 4K, 0.2 M magnesium sulfate, 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.69 Å R-free 0.268
4OIG Dengue Virus Non-structural Protein NS1 Deposited 2014-01-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain D 947–1127（181 aa） Fragment：UNP residues 947-1127
Chain E 947–1127（181 aa） Fragment：UNP residues 947-1127
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；12mg/mL in 20% PEG 4K, 0.2 M magnesium sulfate, 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.69 Å R-free 0.268
5VIC Crystal structure of anti-Zika antibody Z004 bound to DENV-1 Envelope protein DIII Deposited 2017-04-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 578–676（99 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；295 K；0.1M sodium acetate trihydrate pH 4.5, 30% w/v PEG 1500
Resolution 3.00 Å R-free 0.286
8VPR Crystal structure of mouse Importin alpha in complex with Dengue 1 NS5 central NLS peptide Deposited 2024-01-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 2875–2890（16 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；296 K；0.75 M sodium citrate, 0.1 M HEPES
Resolution 2.70 Å R-free 0.242

7 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name POLG_DEN1W
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 17–437； UniProt 281–701 Author chain B； PDBConstruct 17–437； UniProt 281–701

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 4gt0

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4gt0
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4gt0
Deposition date deposition_date2012-08-28
Structure title titleStructure of dengue virus serotype 1 sE containing stem to residue 421
Keywords keywordsViral fusion protein, VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier41.62 Å
Radius of gyration Rg (electron density) rg_electron42.07 Å
Forward intensity I(0) i0113470000.00
Molecular weight molecular_weight85732.0 kDa
Excluded volume excluded_volume107190 ų
Envelope volume envelope_volume155460 ų
Hydration-shell volume shell_volume34020 ų
Envelope diameter envelope_diameter153.8 Å
Shell Rg shell_rg41.41 Å
Envelope Rg envelope_rg41.60 Å
Shape Rg shape_rg42.02 Å
Total Rg total_rg42.22 Å
Total atoms total_atoms5977
Residues n_residues780
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 dmax149.9 Å
Rg (real space) rg_real42.11 Å
Rg uncertainty (real space) rg_real_error2.26 Å
I(0) (real space) i0_real1.1350e+08
I(0) uncertainty (real space) i0_real_error2.4160e+06
Rg (reciprocal space) rg_reciprocal41.62 Å
I(0) (reciprocal space) i0_reciprocal113400000.0000
Solution quality estimate total_estimate0.7993
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary35.5 Å
Skewness Skewness skewness0.582
Kurtosis Kurtosis kurtosis-0.324
Angular range angular_range— – 0.1900 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha6687000.0000
Real-space data points n_real_points39
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.660; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.658; Smooth: 0.750
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd4gt0a1
Class classf — Membrane and cell surface proteins and peptides
Fold Fold foldf.10 — Viral glycoprotein, central and dimerisation domains
Superfamily Superfamily superfamilyf.10.1 — Viral glycoprotein, central and dimerisation domains
Family Family familyf.10.1.0 — automated matches
Domain ID domain_idd4gt0a2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.18 — E set domains
Family Family familyb.1.18.0 — automated matches
Domain ID domain_idd4gt0b1
Class classf — Membrane and cell surface proteins and peptides
Fold Fold foldf.10 — Viral glycoprotein, central and dimerisation domains
Superfamily Superfamily superfamilyf.10.1 — Viral glycoprotein, central and dimerisation domains
Family Family familyf.10.1.0 — automated matches
Domain ID domain_idd4gt0b2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.18 — E set domains
Family Family familyb.1.18.0 — automated matches

CATH v4.4 (8 domains)

Domain ID domain_id4gt0A01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology98 — Tick-borne Encephalitis virus Glycoprotein; domain 1
Homologous superfamily homologous superfamily10 — Tick-borne Encephalitis virus Glycoprotein, domain 1
Domain ID domain_id4gt0A02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology67 — Viral Envelope Glycoprotein; domain 2
Homologous superfamily homologous superfamily10 — Viral Envelope Glycoprotein, domain 2
Domain ID domain_id4gt0A03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology387 — Viral Envelope Glycoprotein; domain 3
Homologous superfamily homologous superfamily10 — Viral Envelope Glycoprotein, domain 3
Domain ID domain_id4gt0A04
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily350 —
Domain ID domain_id4gt0B01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology98 — Tick-borne Encephalitis virus Glycoprotein; domain 1
Homologous superfamily homologous superfamily10 — Tick-borne Encephalitis virus Glycoprotein, domain 1
Domain ID domain_id4gt0B02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology67 — Viral Envelope Glycoprotein; domain 2
Homologous superfamily homologous superfamily10 — Viral Envelope Glycoprotein, domain 2
Domain ID domain_id4gt0B03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology387 — Viral Envelope Glycoprotein; domain 3
Homologous superfamily homologous superfamily10 — Viral Envelope Glycoprotein, domain 3
Domain ID domain_id4gt0B04
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily350 —
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8. Citations (1)

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9. Files and Curves (10)