SAXSdb — 2r69

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

Major envelope protein E

Dengue virus 2 Thailand/16681/84

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 478–574	Not recorded	Heavy chain of 1A1D-2 × 1 Light chain of 1A1D-2 × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.8；298 K；12% PEG 3350, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.80 Å R-free 0.363

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 2R69	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2JSF Solution structures of the envelope protein domain III from the dengue-2 virus Deposited 2007-07-03	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 469–577（109 aa） Fragment：Residues 469-577	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.4；298 K；Ionic strength (raw mmCIF value) 0.31；Pressure ambient NMR sample composition 1-5 mM EDTA, 1-5 mM DTT, 1 mM sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2R6P Fit of E protein and Fab 1A1D-2 into 24 angstrom resolution cryoEM map of Fab complexed with dengue 2 virus. Deposited 2007-09-06	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 420 PDB declaration: 420-MERIC	Chain A 181–570（390 aa） Fragment：E protein Chain B 181–570（390 aa） Fragment：E protein Chain C 181–570（390 aa） Fragment：E protein	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE；SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE	Resolution 24.00 Å
2R6P Fit of E protein and Fab 1A1D-2 into 24 angstrom resolution cryoEM map of Fab complexed with dengue 2 virus. Deposited 2007-09-06	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain A 181–570（390 aa） Fragment：E protein Chain B 181–570（390 aa） Fragment：E protein Chain C 181–570（390 aa） Fragment：E protein	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE；SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE	Resolution 24.00 Å
2R6P Fit of E protein and Fab 1A1D-2 into 24 angstrom resolution cryoEM map of Fab complexed with dengue 2 virus. Deposited 2007-09-06	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric	Chain A 181–570（390 aa） Fragment：E protein Chain B 181–570（390 aa） Fragment：E protein Chain C 181–570（390 aa） Fragment：E protein	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE；SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE	Resolution 24.00 Å
2R6P Fit of E protein and Fab 1A1D-2 into 24 angstrom resolution cryoEM map of Fab complexed with dengue 2 virus. Deposited 2007-09-06	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 42 PDB declaration: 42-meric	Chain A 181–570（390 aa） Fragment：E protein Chain B 181–570（390 aa） Fragment：E protein Chain C 181–570（390 aa） Fragment：E protein	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE；SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE	Resolution 24.00 Å
2R6P Fit of E protein and Fab 1A1D-2 into 24 angstrom resolution cryoEM map of Fab complexed with dengue 2 virus. Deposited 2007-09-06	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain A 181–570（390 aa） Fragment：E protein Chain B 181–570（390 aa） Fragment：E protein Chain C 181–570（390 aa） Fragment：E protein	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE；SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE	Resolution 24.00 Å
3C6R Low pH Immature Dengue Virus Deposited 2008-02-05	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 360 PDB declaration: 360-meric	Chain A 181–575（395 aa） Chain B 181–575（395 aa） Chain C 181–575（395 aa） Chain D 15–95（81 aa） Chain E 15–95（81 aa） Chain F 15–95（81 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 6；The virus was mixed in NTE buffer (10 mM Tris, 120 mM NaCl, and 1 mM EDTA at pH 8) with 50 mM MES, 120 mM NaCl at pH 5.6 to yield a final pH of 6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 25.00 Å
3C6R Low pH Immature Dengue Virus Deposited 2008-02-05	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 181–575（395 aa） Chain B 181–575（395 aa） Chain C 181–575（395 aa） Chain D 15–95（81 aa） Chain E 15–95（81 aa） Chain F 15–95（81 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 6；The virus was mixed in NTE buffer (10 mM Tris, 120 mM NaCl, and 1 mM EDTA at pH 8) with 50 mM MES, 120 mM NaCl at pH 5.6 to yield a final pH of 6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 25.00 Å
3C6R Low pH Immature Dengue Virus Deposited 2008-02-05	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 30 PDB declaration: 30-meric	Chain A 181–575（395 aa） Chain B 181–575（395 aa） Chain C 181–575（395 aa） Chain D 15–95（81 aa） Chain E 15–95（81 aa） Chain F 15–95（81 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 6；The virus was mixed in NTE buffer (10 mM Tris, 120 mM NaCl, and 1 mM EDTA at pH 8) with 50 mM MES, 120 mM NaCl at pH 5.6 to yield a final pH of 6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 25.00 Å
3C6R Low pH Immature Dengue Virus Deposited 2008-02-05	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 36 PDB declaration: 36-meric	Chain A 181–575（395 aa） Chain B 181–575（395 aa） Chain C 181–575（395 aa） Chain D 15–95（81 aa） Chain E 15–95（81 aa） Chain F 15–95（81 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 6；The virus was mixed in NTE buffer (10 mM Tris, 120 mM NaCl, and 1 mM EDTA at pH 8) with 50 mM MES, 120 mM NaCl at pH 5.6 to yield a final pH of 6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 25.00 Å
3C6R Low pH Immature Dengue Virus Deposited 2008-02-05	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 181–575（395 aa） Chain B 181–575（395 aa） Chain C 181–575（395 aa） Chain D 15–95（81 aa） Chain E 15–95（81 aa） Chain F 15–95（81 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 6；The virus was mixed in NTE buffer (10 mM Tris, 120 mM NaCl, and 1 mM EDTA at pH 8) with 50 mM MES, 120 mM NaCl at pH 5.6 to yield a final pH of 6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 25.00 Å
3IXY The pseudo-atomic structure of dengue immature virus in complex with Fab fragments of the anti-fusion loop antibody E53 Deposited 2009-02-26	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 600 PDB declaration: 600-MERIC	Chain D 15–95（81 aa） Chain E 15–95（81 aa） Chain F 15–95（81 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6；12 mM Tris-HCl, 120 mM NaCl, 1 mM EDTA cryo-EM vitrification conditions A small vial of ethane is placed inside a larger liquid nitrogen reservoir. The grid holding a few microliters of the sample is held in place at the bottom of a plunger by the means of fine tweezers. Once the ethane in the vial is completely frozen, it needs to be slightly melted. When the liquid ethane is ready, a piece of filter paper is then pressed against the sample to blot of excess buffer, sufficient to leave a thin layer on the grid. After a predetermined time, the filter paper is removed, and the plunger is allowed to drop into the liquid ethane. Once the grid enters the liquid ethane, the sample is rapidly frozen, and the grid is transferred under liquid nitrogen to a storage box immersed liquid nitrogen for later use in the microscope.；Cryogen ETHANE	Resolution 23.00 Å
3IXY The pseudo-atomic structure of dengue immature virus in complex with Fab fragments of the anti-fusion loop antibody E53 Deposited 2009-02-26	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain D 15–95（81 aa） Chain E 15–95（81 aa） Chain F 15–95（81 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6；12 mM Tris-HCl, 120 mM NaCl, 1 mM EDTA cryo-EM vitrification conditions A small vial of ethane is placed inside a larger liquid nitrogen reservoir. The grid holding a few microliters of the sample is held in place at the bottom of a plunger by the means of fine tweezers. Once the ethane in the vial is completely frozen, it needs to be slightly melted. When the liquid ethane is ready, a piece of filter paper is then pressed against the sample to blot of excess buffer, sufficient to leave a thin layer on the grid. After a predetermined time, the filter paper is removed, and the plunger is allowed to drop into the liquid ethane. Once the grid enters the liquid ethane, the sample is rapidly frozen, and the grid is transferred under liquid nitrogen to a storage box immersed liquid nitrogen for later use in the microscope.；Cryogen ETHANE	Resolution 23.00 Å
3IXY The pseudo-atomic structure of dengue immature virus in complex with Fab fragments of the anti-fusion loop antibody E53 Deposited 2009-02-26	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 50 PDB declaration: 50-meric	Chain D 15–95（81 aa） Chain E 15–95（81 aa） Chain F 15–95（81 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6；12 mM Tris-HCl, 120 mM NaCl, 1 mM EDTA cryo-EM vitrification conditions A small vial of ethane is placed inside a larger liquid nitrogen reservoir. The grid holding a few microliters of the sample is held in place at the bottom of a plunger by the means of fine tweezers. Once the ethane in the vial is completely frozen, it needs to be slightly melted. When the liquid ethane is ready, a piece of filter paper is then pressed against the sample to blot of excess buffer, sufficient to leave a thin layer on the grid. After a predetermined time, the filter paper is removed, and the plunger is allowed to drop into the liquid ethane. Once the grid enters the liquid ethane, the sample is rapidly frozen, and the grid is transferred under liquid nitrogen to a storage box immersed liquid nitrogen for later use in the microscope.；Cryogen ETHANE	Resolution 23.00 Å
3IXY The pseudo-atomic structure of dengue immature virus in complex with Fab fragments of the anti-fusion loop antibody E53 Deposited 2009-02-26	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 60 PDB declaration: 60-meric	Chain D 15–95（81 aa） Chain E 15–95（81 aa） Chain F 15–95（81 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6；12 mM Tris-HCl, 120 mM NaCl, 1 mM EDTA cryo-EM vitrification conditions A small vial of ethane is placed inside a larger liquid nitrogen reservoir. The grid holding a few microliters of the sample is held in place at the bottom of a plunger by the means of fine tweezers. Once the ethane in the vial is completely frozen, it needs to be slightly melted. When the liquid ethane is ready, a piece of filter paper is then pressed against the sample to blot of excess buffer, sufficient to leave a thin layer on the grid. After a predetermined time, the filter paper is removed, and the plunger is allowed to drop into the liquid ethane. Once the grid enters the liquid ethane, the sample is rapidly frozen, and the grid is transferred under liquid nitrogen to a storage box immersed liquid nitrogen for later use in the microscope.；Cryogen ETHANE	Resolution 23.00 Å
3IXY The pseudo-atomic structure of dengue immature virus in complex with Fab fragments of the anti-fusion loop antibody E53 Deposited 2009-02-26	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain D 15–95（81 aa） Chain E 15–95（81 aa） Chain F 15–95（81 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6；12 mM Tris-HCl, 120 mM NaCl, 1 mM EDTA cryo-EM vitrification conditions A small vial of ethane is placed inside a larger liquid nitrogen reservoir. The grid holding a few microliters of the sample is held in place at the bottom of a plunger by the means of fine tweezers. Once the ethane in the vial is completely frozen, it needs to be slightly melted. When the liquid ethane is ready, a piece of filter paper is then pressed against the sample to blot of excess buffer, sufficient to leave a thin layer on the grid. After a predetermined time, the filter paper is removed, and the plunger is allowed to drop into the liquid ethane. Once the grid enters the liquid ethane, the sample is rapidly frozen, and the grid is transferred under liquid nitrogen to a storage box immersed liquid nitrogen for later use in the microscope.；Cryogen ETHANE	Resolution 23.00 Å
3IYA Association of the pr peptides with dengue virus blocks membrane fusion at acidic pH Deposited 2009-06-01	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 360 PDB declaration: 360-meric	Chain A 181–575（395 aa） Chain B 181–575（395 aa） Chain C 181–575（395 aa） Chain D 15–95（81 aa） Chain E 15–95（81 aa） Chain F 15–95（81 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 6；6 mM Tris-HCL 25 mM MES 120 mM NaCl 1 mM EDTA cryo-EM vitrification conditions A small vial of ethane is placed inside a larger liquid nitrogen reservoir. The grid holding a few microliters of the sample is held in place at the bottom of a plunger by the means of fine tweezers. Once the ethane in the vial is completely frozen, it needs to be slightly melted. When the liquid ethane is ready, a piece of filter paper is then pressed against the sample to blot of excess buffer, sufficient to leave a thin layer on the grid. After a predetermined time, the filter paper is removed, and the plunger is allowed to drop into the liquid ethane. Once the grid enters the liquid ethane, the sample is rapidly frozen, and the grid is transferred under liquid nitrogen to a storage box immersed liquid nitrogen for later use in the microscope.；Cryogen ETHANE	Resolution 22.00 Å
3IYA Association of the pr peptides with dengue virus blocks membrane fusion at acidic pH Deposited 2009-06-01	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 181–575（395 aa） Chain B 181–575（395 aa） Chain C 181–575（395 aa） Chain D 15–95（81 aa） Chain E 15–95（81 aa） Chain F 15–95（81 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 6；6 mM Tris-HCL 25 mM MES 120 mM NaCl 1 mM EDTA cryo-EM vitrification conditions A small vial of ethane is placed inside a larger liquid nitrogen reservoir. The grid holding a few microliters of the sample is held in place at the bottom of a plunger by the means of fine tweezers. Once the ethane in the vial is completely frozen, it needs to be slightly melted. When the liquid ethane is ready, a piece of filter paper is then pressed against the sample to blot of excess buffer, sufficient to leave a thin layer on the grid. After a predetermined time, the filter paper is removed, and the plunger is allowed to drop into the liquid ethane. Once the grid enters the liquid ethane, the sample is rapidly frozen, and the grid is transferred under liquid nitrogen to a storage box immersed liquid nitrogen for later use in the microscope.；Cryogen ETHANE	Resolution 22.00 Å
3IYA Association of the pr peptides with dengue virus blocks membrane fusion at acidic pH Deposited 2009-06-01	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 30 PDB declaration: 30-meric	Chain A 181–575（395 aa） Chain B 181–575（395 aa） Chain C 181–575（395 aa） Chain D 15–95（81 aa） Chain E 15–95（81 aa） Chain F 15–95（81 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 6；6 mM Tris-HCL 25 mM MES 120 mM NaCl 1 mM EDTA cryo-EM vitrification conditions A small vial of ethane is placed inside a larger liquid nitrogen reservoir. The grid holding a few microliters of the sample is held in place at the bottom of a plunger by the means of fine tweezers. Once the ethane in the vial is completely frozen, it needs to be slightly melted. When the liquid ethane is ready, a piece of filter paper is then pressed against the sample to blot of excess buffer, sufficient to leave a thin layer on the grid. After a predetermined time, the filter paper is removed, and the plunger is allowed to drop into the liquid ethane. Once the grid enters the liquid ethane, the sample is rapidly frozen, and the grid is transferred under liquid nitrogen to a storage box immersed liquid nitrogen for later use in the microscope.；Cryogen ETHANE	Resolution 22.00 Å
3IYA Association of the pr peptides with dengue virus blocks membrane fusion at acidic pH Deposited 2009-06-01	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 36 PDB declaration: 36-meric	Chain A 181–575（395 aa） Chain B 181–575（395 aa） Chain C 181–575（395 aa） Chain D 15–95（81 aa） Chain E 15–95（81 aa） Chain F 15–95（81 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 6；6 mM Tris-HCL 25 mM MES 120 mM NaCl 1 mM EDTA cryo-EM vitrification conditions A small vial of ethane is placed inside a larger liquid nitrogen reservoir. The grid holding a few microliters of the sample is held in place at the bottom of a plunger by the means of fine tweezers. Once the ethane in the vial is completely frozen, it needs to be slightly melted. When the liquid ethane is ready, a piece of filter paper is then pressed against the sample to blot of excess buffer, sufficient to leave a thin layer on the grid. After a predetermined time, the filter paper is removed, and the plunger is allowed to drop into the liquid ethane. Once the grid enters the liquid ethane, the sample is rapidly frozen, and the grid is transferred under liquid nitrogen to a storage box immersed liquid nitrogen for later use in the microscope.；Cryogen ETHANE	Resolution 22.00 Å
3IYA Association of the pr peptides with dengue virus blocks membrane fusion at acidic pH Deposited 2009-06-01	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 181–575（395 aa） Chain B 181–575（395 aa） Chain C 181–575（395 aa） Chain D 15–95（81 aa） Chain E 15–95（81 aa） Chain F 15–95（81 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 6；6 mM Tris-HCL 25 mM MES 120 mM NaCl 1 mM EDTA cryo-EM vitrification conditions A small vial of ethane is placed inside a larger liquid nitrogen reservoir. The grid holding a few microliters of the sample is held in place at the bottom of a plunger by the means of fine tweezers. Once the ethane in the vial is completely frozen, it needs to be slightly melted. When the liquid ethane is ready, a piece of filter paper is then pressed against the sample to blot of excess buffer, sufficient to leave a thin layer on the grid. After a predetermined time, the filter paper is removed, and the plunger is allowed to drop into the liquid ethane. Once the grid enters the liquid ethane, the sample is rapidly frozen, and the grid is transferred under liquid nitrogen to a storage box immersed liquid nitrogen for later use in the microscope.；Cryogen ETHANE	Resolution 22.00 Å

5 other PDB entries and 21 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	POLG_DEN2U
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–97； UniProt 478–574

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	2r69
Deposition date deposition_date	2007-09-05
Structure title title	Crystal structure of Fab 1A1D-2 complexed with E-DIII of Dengue virus at 3.8 angstrom resolution
Keywords keywords	;Fab-antigen complex, Capsid protein, Cleavage on pair of basic residues, Core protein, Envelope protein, Glycoprotein, Membrane, Transmembrane, Virion, viral protein-Immune system COMPLEX ;; viral protein/Immune system
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	27.99 Å
Radius of gyration Rg (electron density) rg_electron	27.53 Å
Forward intensity I(0) i0	49854600.00
Molecular weight molecular_weight	55152.0 kDa
Excluded volume excluded_volume	69051 Å³
Envelope volume envelope_volume	92106 Å³
Hydration-shell volume shell_volume	29097 Å³
Envelope diameter envelope_diameter	99.8 Å
Shell Rg shell_rg	33.62 Å
Envelope Rg envelope_rg	27.53 Å
Shape Rg shape_rg	27.51 Å
Total Rg total_rg	28.25 Å
Total atoms total_atoms	3886
Residues n_residues	504
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	96.0 Å
Rg (real space) rg_real	28.15 Å
Rg uncertainty (real space) rg_real_error	0.76 Å
I(0) (real space) i0_real	4.9850e+07
I(0) uncertainty (real space) i0_real_error	7.7040e+05
Rg (reciprocal space) rg_reciprocal	28.10 Å
I(0) (reciprocal space) i0_reciprocal	49850000.0000
Solution quality estimate total_estimate	0.8598
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	30.3 Å
Skewness Skewness skewness	0.518
Kurtosis Kurtosis kurtosis	-0.094
Angular range angular_range	— – 0.2850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	12520000.0000
Real-space data points n_real_points	58
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.800; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.925; Smooth: 0.847

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Major envelope protein E
Molecular weight formula_weight	10932.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3886

SYSMCTGKFKVVKEIAETQHGTIVIRVQYEGDGSPCKIPFEIMDLEKRHVLGRLITVNPIVTEKDSPVNIEAEPPFGDSYIIIGVEPGQLKLNWFKK

来源 Source

来源生物 organism	Dengue virus 2 Thailand/16681/84
NCBI Class编号 ncbi_taxonomy_id	31634
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Heavy chain of 1A1D-2
Molecular weight formula_weight	22926.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

EVQLQQSGAELVKPGASVKLSCTASGFNIKDTYMHWVKQRPEQGLEWIGRIDPANGYSKYDPKFQGKATITADTSSNAAYLQLSSLTSEDTAVYFCARDYEGFAYWGQGTLVTVSSAKTTPPSVYPLAPGAATSSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQTITCNVAHPASSTKVDKKIEPR

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI Class编号 ncbi_taxonomy_id	10090

Entity 3 Entity 3 polymer

Description description	Light chain of 1A1D-2
Molecular weight formula_weight	23412.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

DIVLTQSPASLAVSLGQRATISCRASESVVRYGNSFMHWYQQKPGQPPKLLIYRASSLESGIPTRFSGSGSRTDFTLTINPVEADDVATYYCQQTNVDPWAFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATSPIVKSFNRNE

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI Class编号 ncbi_taxonomy_id	10090

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d2r69a1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.18 — E set domains
Family Family family	b.1.18.4 — Class II viral fusion proteins C-terminal domain

Domain ID domain_id	d2r69l1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d2r69l2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

CATH v4.4 (5 domains)

Domain ID domain_id	2r69A00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	350 —

Domain ID domain_id	2r69H01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2r69H02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2r69L01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2r69L02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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8. Citations (1)

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Unit-cell length a length_a	164.770 Å
Unit-cell length b length_b	66.888 Å
Unit-cell length c length_c	79.410 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	113.05 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	3.800 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.3130
R_free r_free	0.3630

fit	/app/data/saxs_computation/r6/2r69/2r69.fit
pddf	/app/data/pr_computation/r6/2r69/2r69.pr.out
profile	/app/data/saxs_computation/r6/2r69/2r69.dat

Crystal structure of Fab 1A1D-2 complexed with E-DIII of Dengue virus at 3.8 angstrom resolution

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

Major envelope protein E

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (3 domains)

CATH v4.4 (5 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)