SAXSdb — 3ixy

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

Envelope protein E

Dengue virus 2

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 × 600 PDB declaration: 600-MERIC（600） Consistent with protein copy count	Chain A； UniProt 281–675 Chain B； UniProt 281–675 Chain C； UniProt 281–675	Not recorded	Peptide pr × 180 （P18356） E53 Fab Fragment (chain H) × 120 E53 Fab Fragment (chain L) × 120	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
2	Protein heterocomplex Heteromer Protein × 10 PDB declaration: decameric（10） Consistent with protein copy count	Chain A； UniProt 281–675 Chain B； UniProt 281–675 Chain C； UniProt 281–675	Not recorded	Peptide pr × 3 （P18356） E53 Fab Fragment (chain H) × 2 E53 Fab Fragment (chain L) × 2	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
3	Protein heterocomplex Heteromer Protein × 50 PDB declaration: 50-meric（50） Consistent with protein copy count	Chain A； UniProt 281–675 Chain B； UniProt 281–675 Chain C； UniProt 281–675	Not recorded	Peptide pr × 15 （P18356） E53 Fab Fragment (chain H) × 10 E53 Fab Fragment (chain L) × 10	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
4	Protein heterocomplex Heteromer Protein × 60 PDB declaration: 60-meric（60） Consistent with protein copy count	Chain A； UniProt 281–675 Chain B； UniProt 281–675 Chain C； UniProt 281–675	Not recorded	Peptide pr × 18 （P18356） E53 Fab Fragment (chain H) × 12 E53 Fab Fragment (chain L) × 12	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
5	Protein heterocomplex Heteromer Protein × 10 PDB declaration: decameric（10） Consistent with protein copy count	Chain A； UniProt 281–675 Chain B； UniProt 281–675 Chain C； UniProt 281–675	Not recorded	Peptide pr × 3 （P18356） E53 Fab Fragment (chain H) × 2 E53 Fab Fragment (chain L) × 2	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

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 3IXY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3C6D The pseudo-atomic structure of dengue immature virus Deposited 2008-02-04	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 360 PDB declaration: 360-meric	Chain A 281–675（395 aa） Chain B 281–675（395 aa） Chain C 281–675（395 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 Cryogen ETHANE	Resolution 12.50 Å
3C6D The pseudo-atomic structure of dengue immature virus Deposited 2008-02-04	Different oligomeric state Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 281–675（395 aa） Chain B 281–675（395 aa） Chain C 281–675（395 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 Cryogen ETHANE	Resolution 12.50 Å
3C6D The pseudo-atomic structure of dengue immature virus Deposited 2008-02-04	Different oligomeric state Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric	Chain A 281–675（395 aa） Chain B 281–675（395 aa） Chain C 281–675（395 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 Cryogen ETHANE	Resolution 12.50 Å
3C6D The pseudo-atomic structure of dengue immature virus Deposited 2008-02-04	Different oligomeric state Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric	Chain A 281–675（395 aa） Chain B 281–675（395 aa） Chain C 281–675（395 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 Cryogen ETHANE	Resolution 12.50 Å
3C6D The pseudo-atomic structure of dengue immature virus Deposited 2008-02-04	Different oligomeric state Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 281–675（395 aa） Chain B 281–675（395 aa） Chain C 281–675（395 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 Cryogen ETHANE	Resolution 12.50 Å
3J42 Obstruction of Dengue Virus Maturation by Fab Fragments of the 2H2 Antibody Deposited 2013-06-13	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 720 PDB declaration: 720-meric	Chain A 281–675（395 aa） Fragment：UNP residues 281-675 Chain B 281–675（395 aa） Fragment：UNP residues 281-675 Chain C 281–675（395 aa） Fragment：UNP residues 281-675	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 100 mM phosphate buffer；pH 7；100 mM phosphate buffer cryo-EM vitrification conditions 100 K；Cryogen ETHANE；Plunged into liquid ethane (homemade plunger)	Resolution 21.00 Å
3J42 Obstruction of Dengue Virus Maturation by Fab Fragments of the 2H2 Antibody Deposited 2013-06-13	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 281–675（395 aa） Fragment：UNP residues 281-675 Chain B 281–675（395 aa） Fragment：UNP residues 281-675 Chain C 281–675（395 aa） Fragment：UNP residues 281-675	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 100 mM phosphate buffer；pH 7；100 mM phosphate buffer cryo-EM vitrification conditions 100 K；Cryogen ETHANE；Plunged into liquid ethane (homemade plunger)	Resolution 21.00 Å
3J42 Obstruction of Dengue Virus Maturation by Fab Fragments of the 2H2 Antibody Deposited 2013-06-13	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Insufficient information Heteromer；Protein × 60 PDB declaration: 60-meric	Chain A 281–675（395 aa） Fragment：UNP residues 281-675 Chain B 281–675（395 aa） Fragment：UNP residues 281-675 Chain C 281–675（395 aa） Fragment：UNP residues 281-675	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 100 mM phosphate buffer；pH 7；100 mM phosphate buffer cryo-EM vitrification conditions 100 K；Cryogen ETHANE；Plunged into liquid ethane (homemade plunger)	Resolution 21.00 Å
3J42 Obstruction of Dengue Virus Maturation by Fab Fragments of the 2H2 Antibody Deposited 2013-06-13	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Insufficient information Heteromer；Protein × 72 PDB declaration: 72-meric	Chain A 281–675（395 aa） Fragment：UNP residues 281-675 Chain B 281–675（395 aa） Fragment：UNP residues 281-675 Chain C 281–675（395 aa） Fragment：UNP residues 281-675	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 100 mM phosphate buffer；pH 7；100 mM phosphate buffer cryo-EM vitrification conditions 100 K；Cryogen ETHANE；Plunged into liquid ethane (homemade plunger)	Resolution 21.00 Å
3J42 Obstruction of Dengue Virus Maturation by Fab Fragments of the 2H2 Antibody Deposited 2013-06-13	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 5 Insufficient information Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 281–675（395 aa） Fragment：UNP residues 281-675 Chain B 281–675（395 aa） Fragment：UNP residues 281-675 Chain C 281–675（395 aa） Fragment：UNP residues 281-675	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 100 mM phosphate buffer；pH 7；100 mM phosphate buffer cryo-EM vitrification conditions 100 K；Cryogen ETHANE；Plunged into liquid ethane (homemade plunger)	Resolution 21.00 Å
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 B 206–280（75 aa） Chain D 206–280（75 aa） Chain F 206–280（75 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

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

Peptide pr

Dengue virus 2

UniProt P18356

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 × 600 PDB declaration: 600-MERIC（600） Consistent with protein copy count	Chain D； UniProt 15–95 Chain E； UniProt 15–95 Chain F； UniProt 15–95	Not recorded	Envelope protein E × 180 （O11875） E53 Fab Fragment (chain H) × 120 E53 Fab Fragment (chain L) × 120	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
2	Protein heterocomplex Heteromer Protein × 10 PDB declaration: decameric（10） Consistent with protein copy count	Chain D； UniProt 15–95 Chain E； UniProt 15–95 Chain F； UniProt 15–95	Not recorded	Envelope protein E × 3 （O11875） E53 Fab Fragment (chain H) × 2 E53 Fab Fragment (chain L) × 2	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
3	Protein heterocomplex Heteromer Protein × 50 PDB declaration: 50-meric（50） Consistent with protein copy count	Chain D； UniProt 15–95 Chain E； UniProt 15–95 Chain F； UniProt 15–95	Not recorded	Envelope protein E × 15 （O11875） E53 Fab Fragment (chain H) × 10 E53 Fab Fragment (chain L) × 10	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
4	Protein heterocomplex Heteromer Protein × 60 PDB declaration: 60-meric（60） Consistent with protein copy count	Chain D； UniProt 15–95 Chain E； UniProt 15–95 Chain F； UniProt 15–95	Not recorded	Envelope protein E × 18 （O11875） E53 Fab Fragment (chain H) × 12 E53 Fab Fragment (chain L) × 12	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
5	Protein heterocomplex Heteromer Protein × 10 PDB declaration: decameric（10） Consistent with protein copy count	Chain D； UniProt 15–95 Chain E； UniProt 15–95 Chain F； UniProt 15–95	Not recorded	Envelope protein E × 3 （O11875） E53 Fab Fragment (chain H) × 2 E53 Fab Fragment (chain L) × 2	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

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 3IXY	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 mutation/modification 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
2R69 Crystal structure of Fab 1A1D-2 complexed with E-DIII of Dengue virus at 3.8 angstrom resolution Deposited 2007-09-05	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 478–574（97 aa）	Not recorded	No recorded non-water small molecule	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
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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 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 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 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 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 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
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 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 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 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 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 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 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	POLG_DEN2U
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 1–81； UniProt 15–95 Author chain E； PDBConstruct 1–81； UniProt 15–95 Author chain F； PDBConstruct 1–81； UniProt 15–95

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	3ixy
Deposition date deposition_date	2009-02-26
Structure title title	The pseudo-atomic structure of dengue immature virus in complex with Fab fragments of the anti-fusion loop antibody E53
Keywords keywords	;Dengue Virus, DENV, immature, fusion loop, Fab, E53, ATP-binding, Envelope protein, Helicase, Hydrolase, Membrane, Nucleotide-binding, RNA replication, Transmembrane, Virion, Capsid protein, Cleavage on pair of basic residues, Core protein, Endoplasmic reticulum, Glycoprotein, Secreted, VIRUS ;; VIRUS
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	62.32 Å
Radius of gyration Rg (electron density) rg_electron	62.64 Å
Forward intensity I(0) i0	927034000.00
Molecular weight molecular_weight	251680.0 kDa
Excluded volume excluded_volume	305890 Å³
Envelope volume envelope_volume	358030 Å³
Hydration-shell volume shell_volume	53698 Å³
Envelope diameter envelope_diameter	196.2 Å
Shell Rg shell_rg	53.35 Å
Envelope Rg envelope_rg	59.43 Å
Shape Rg shape_rg	62.90 Å
Total Rg total_rg	62.44 Å
Total atoms total_atoms	—
Residues n_residues	—
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	205.9 Å
Rg (real space) rg_real	62.38 Å
Rg uncertainty (real space) rg_real_error	2.06 Å
I(0) (real space) i0_real	9.2700e+08
I(0) uncertainty (real space) i0_real_error	1.9600e+07
Rg (reciprocal space) rg_reciprocal	62.22 Å
I(0) (reciprocal space) i0_reciprocal	926700000.0000
Solution quality estimate total_estimate	0.8510
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	82.3 Å
Skewness Skewness skewness	0.204
Kurtosis Kurtosis kurtosis	-0.543
Angular range angular_range	— – 0.1250 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	23670000.0000
Real-space data points n_real_points	26
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.922; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.294

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Envelope protein E
Molecular weight formula_weight	43904.4 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	2281

MRCIGISNRDFVEGVSGGSWVDIVLEHGSCVTTMAKNKPTLDFELIKTEAKQPATLRKYCIEAKLTNTTTESRCPTQGEPSLNEEQDKRFVCKHSMVDRGWGNGCGLFGKGGIVTCAMFRCKKNMEGKVVQPENLEYTVVITPHSGEEHAVGNDTGKHGKEVKITPQSSITEAELTGYGTVTMECSPRTGLDFNEMVLLQMENKAWLVHRQWFLDLPLPWLPGADTQGSNWIQKETLVTFKNPHAKKQDVVVLGSQEGAMHTALTGATEIQMSSGNLLFTGHLKCRLRMDKLQLKGMSYSMCTGKFKVVKEIAETQHGTIVIRVQYEGDGSPCKIPFEIMDLEKRHVLGRLITVNPIVTEKDSPVNIEAEPPFGDSYIIIGVEPGQLKLDWFKKG

来源 Source

来源生物 organism	Dengue virus 2
NCBI Class编号 ncbi_taxonomy_id	11060
宿主生物 host_organism	Aedes albopictus

Entity 2 Entity 2 polymer

Description description	Peptide pr
Molecular weight formula_weight	9261.5 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,E,F

FHLTTRNGEPHMIVSRQEKGKSLLFKTEDGVNMCTLMAMDLGELCEDTITYKCPLLRQNEPEDIDCWCNSTSTWVTYGTCT

来源 Source

来源生物 organism	Dengue virus 2
NCBI Class编号 ncbi_taxonomy_id	11060
宿主生物 host_organism	Aedes albopictus

Entity 3 Entity 3 polymer

Description description	E53 Fab Fragment (chain H)
Molecular weight formula_weight	23630.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,I

EVKLVESGGGLVLPGGSLRLSCATSGFTFTDYYMTWVRQPPGKALEWLGFIGNKANDYTTEYSASVKGRFTISRDDSQSILYLQMSTLRAEDRATYYCATVYGNYPYFDVWGAGTTVAVSSAKTTPPSVYPLAPVCGGTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSGLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPR

来源 Source

来源生物 organism	Mus musculus
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	E53 Fab Fragment (chain L)
Molecular weight formula_weight	23588.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H,J

QIVLTQSPAIMSASPGEKVTMTCSASSSVSYMHWYQQKSGTSPKIWIYESSKLASGVPVRFSGSGSGTSYSLTISSMEAEDVATYYCQQWSSHPHPLTFGAGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

来源 Source

来源生物 organism	Mus musculus
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	1

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	23.00 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	2741

fit	/app/data/saxs_computation/ix/3ixy/3ixy.fit
pddf	/app/data/pr_computation/ix/3ixy/3ixy.pr.out
profile	/app/data/saxs_computation/ix/3ixy/3ixy.dat

The pseudo-atomic structure of dengue immature virus in complex with Fab fragments of the anti-fusion loop antibody E53

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

Envelope protein E

State in the Current Structure

Other States of the Same Protein in the Database

Peptide pr

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (4)

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

Entity 4 Entity 4 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)