SAXSdb — 3ixy

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1. 蛋白身份与相关结构 Protein Identity & Related Structures

Envelope protein E

Dengue virus 2

当前结构中的状态

Assembly	聚集状态	构建体	突变与修饰	配体、离子与共同组分	实验方法与环境	结构质量
1	蛋白异源复合物异源复合物蛋白 × 600 PDB 声明：600-MERIC（600）与蛋白拷贝数一致	链 A； UniProt 281–675 链 B； UniProt 281–675 链 C； UniProt 281–675	未记录	Peptide pr × 180 （P18356） E53 Fab Fragment (chain H) × 120 E53 Fab Fragment (chain L) × 120	ELECTRON MICROSCOPY cryo-EM缓冲液：pH 7.6；12 mM Tris-HCl, 120 mM NaCl, 1 mM EDTA cryo-EM玻璃化条件：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.；冷冻剂 ETHANE	分辨率 23.00 Å
2	蛋白异源复合物异源复合物蛋白 × 10 PDB 声明：decameric（10）与蛋白拷贝数一致	链 A； UniProt 281–675 链 B； UniProt 281–675 链 C； UniProt 281–675	未记录	Peptide pr × 3 （P18356） E53 Fab Fragment (chain H) × 2 E53 Fab Fragment (chain L) × 2	ELECTRON MICROSCOPY cryo-EM缓冲液：pH 7.6；12 mM Tris-HCl, 120 mM NaCl, 1 mM EDTA cryo-EM玻璃化条件：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.；冷冻剂 ETHANE	分辨率 23.00 Å
3	蛋白异源复合物异源复合物蛋白 × 50 PDB 声明：50-meric（50）与蛋白拷贝数一致	链 A； UniProt 281–675 链 B； UniProt 281–675 链 C； UniProt 281–675	未记录	Peptide pr × 15 （P18356） E53 Fab Fragment (chain H) × 10 E53 Fab Fragment (chain L) × 10	ELECTRON MICROSCOPY cryo-EM缓冲液：pH 7.6；12 mM Tris-HCl, 120 mM NaCl, 1 mM EDTA cryo-EM玻璃化条件：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.；冷冻剂 ETHANE	分辨率 23.00 Å
4	蛋白异源复合物异源复合物蛋白 × 60 PDB 声明：60-meric（60）与蛋白拷贝数一致	链 A； UniProt 281–675 链 B； UniProt 281–675 链 C； UniProt 281–675	未记录	Peptide pr × 18 （P18356） E53 Fab Fragment (chain H) × 12 E53 Fab Fragment (chain L) × 12	ELECTRON MICROSCOPY cryo-EM缓冲液：pH 7.6；12 mM Tris-HCl, 120 mM NaCl, 1 mM EDTA cryo-EM玻璃化条件：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.；冷冻剂 ETHANE	分辨率 23.00 Å
5	蛋白异源复合物异源复合物蛋白 × 10 PDB 声明：decameric（10）与蛋白拷贝数一致	链 A； UniProt 281–675 链 B； UniProt 281–675 链 C； UniProt 281–675	未记录	Peptide pr × 3 （P18356） E53 Fab Fragment (chain H) × 2 E53 Fab Fragment (chain L) × 2	ELECTRON MICROSCOPY cryo-EM缓冲液：pH 7.6；12 mM Tris-HCl, 120 mM NaCl, 1 mM EDTA cryo-EM玻璃化条件：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.；冷冻剂 ETHANE	分辨率 23.00 Å

数据库中的同蛋白其他状态

以下每一行都是同一 UniProt 蛋白在另一个 PDB 条目中的 biological assembly， “相对当前条目”直接指出证据层面的不同；没有差异标签表示当前已读取字段一致。

其他 PDB	相对当前条目 3IXY	Assembly / 聚集状态	构建体	突变与修饰	配体、离子与非聚合物	实验方法与环境	结构质量
3C6D The pseudo-atomic structure of dengue immature virus 提交 2008-02-04	聚集状态不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 360 PDB 声明：360-meric	链 A 281–675（395 aa）链 B 281–675（395 aa）链 C 281–675（395 aa）	未记录	未记录非水小分子	ELECTRON MICROSCOPY cryo-EM缓冲液 pH 7.6；12 mM Tris-HCl, 120 mM NaCl, 1 mM EDTA cryo-EM玻璃化条件冷冻剂 ETHANE	分辨率 12.50 Å
3C6D The pseudo-atomic structure of dengue immature virus 提交 2008-02-04	聚集状态不同结构质量不同	Assembly 2 蛋白异源复合物异源复合物；蛋白 × 6 PDB 声明：hexameric	链 A 281–675（395 aa）链 B 281–675（395 aa）链 C 281–675（395 aa）	未记录	未记录非水小分子	ELECTRON MICROSCOPY cryo-EM缓冲液 pH 7.6；12 mM Tris-HCl, 120 mM NaCl, 1 mM EDTA cryo-EM玻璃化条件冷冻剂 ETHANE	分辨率 12.50 Å
3C6D The pseudo-atomic structure of dengue immature virus 提交 2008-02-04	聚集状态不同结构质量不同	Assembly 3 蛋白异源复合物异源复合物；蛋白 × 30 PDB 声明：30-meric	链 A 281–675（395 aa）链 B 281–675（395 aa）链 C 281–675（395 aa）	未记录	未记录非水小分子	ELECTRON MICROSCOPY cryo-EM缓冲液 pH 7.6；12 mM Tris-HCl, 120 mM NaCl, 1 mM EDTA cryo-EM玻璃化条件冷冻剂 ETHANE	分辨率 12.50 Å
3C6D The pseudo-atomic structure of dengue immature virus 提交 2008-02-04	聚集状态不同结构质量不同	Assembly 4 蛋白异源复合物异源复合物；蛋白 × 36 PDB 声明：36-meric	链 A 281–675（395 aa）链 B 281–675（395 aa）链 C 281–675（395 aa）	未记录	未记录非水小分子	ELECTRON MICROSCOPY cryo-EM缓冲液 pH 7.6；12 mM Tris-HCl, 120 mM NaCl, 1 mM EDTA cryo-EM玻璃化条件冷冻剂 ETHANE	分辨率 12.50 Å
3C6D The pseudo-atomic structure of dengue immature virus 提交 2008-02-04	聚集状态不同结构质量不同	Assembly 5 蛋白异源复合物异源复合物；蛋白 × 6 PDB 声明：hexameric	链 A 281–675（395 aa）链 B 281–675（395 aa）链 C 281–675（395 aa）	未记录	未记录非水小分子	ELECTRON MICROSCOPY cryo-EM缓冲液 pH 7.6；12 mM Tris-HCl, 120 mM NaCl, 1 mM EDTA cryo-EM玻璃化条件冷冻剂 ETHANE	分辨率 12.50 Å
3J42 Obstruction of Dengue Virus Maturation by Fab Fragments of the 2H2 Antibody 提交 2013-06-13	构建体不同聚集状态不同实验环境不同结构质量不同	Assembly 1 信息不足异源复合物；蛋白 × 720 PDB 声明：720-meric	链 A 281–675（395 aa）片段：UNP residues 281-675 链 B 281–675（395 aa）片段：UNP residues 281-675 链 C 281–675（395 aa）片段：UNP residues 281-675	未记录	未记录非水小分子	ELECTRON MICROSCOPY cryo-EM缓冲液 100 mM phosphate buffer；pH 7；100 mM phosphate buffer cryo-EM玻璃化条件 100 K；冷冻剂 ETHANE；Plunged into liquid ethane (homemade plunger)	分辨率 21.00 Å
3J42 Obstruction of Dengue Virus Maturation by Fab Fragments of the 2H2 Antibody 提交 2013-06-13	构建体不同聚集状态不同实验环境不同结构质量不同	Assembly 2 信息不足异源复合物；蛋白 × 12 PDB 声明：dodecameric	链 A 281–675（395 aa）片段：UNP residues 281-675 链 B 281–675（395 aa）片段：UNP residues 281-675 链 C 281–675（395 aa）片段：UNP residues 281-675	未记录	未记录非水小分子	ELECTRON MICROSCOPY cryo-EM缓冲液 100 mM phosphate buffer；pH 7；100 mM phosphate buffer cryo-EM玻璃化条件 100 K；冷冻剂 ETHANE；Plunged into liquid ethane (homemade plunger)	分辨率 21.00 Å
3J42 Obstruction of Dengue Virus Maturation by Fab Fragments of the 2H2 Antibody 提交 2013-06-13	构建体不同聚集状态不同实验环境不同结构质量不同	Assembly 3 信息不足异源复合物；蛋白 × 60 PDB 声明：60-meric	链 A 281–675（395 aa）片段：UNP residues 281-675 链 B 281–675（395 aa）片段：UNP residues 281-675 链 C 281–675（395 aa）片段：UNP residues 281-675	未记录	未记录非水小分子	ELECTRON MICROSCOPY cryo-EM缓冲液 100 mM phosphate buffer；pH 7；100 mM phosphate buffer cryo-EM玻璃化条件 100 K；冷冻剂 ETHANE；Plunged into liquid ethane (homemade plunger)	分辨率 21.00 Å
3J42 Obstruction of Dengue Virus Maturation by Fab Fragments of the 2H2 Antibody 提交 2013-06-13	构建体不同聚集状态不同实验环境不同结构质量不同	Assembly 4 信息不足异源复合物；蛋白 × 72 PDB 声明：72-meric	链 A 281–675（395 aa）片段：UNP residues 281-675 链 B 281–675（395 aa）片段：UNP residues 281-675 链 C 281–675（395 aa）片段：UNP residues 281-675	未记录	未记录非水小分子	ELECTRON MICROSCOPY cryo-EM缓冲液 100 mM phosphate buffer；pH 7；100 mM phosphate buffer cryo-EM玻璃化条件 100 K；冷冻剂 ETHANE；Plunged into liquid ethane (homemade plunger)	分辨率 21.00 Å
3J42 Obstruction of Dengue Virus Maturation by Fab Fragments of the 2H2 Antibody 提交 2013-06-13	构建体不同聚集状态不同实验环境不同结构质量不同	Assembly 5 信息不足异源复合物；蛋白 × 12 PDB 声明：dodecameric	链 A 281–675（395 aa）片段：UNP residues 281-675 链 B 281–675（395 aa）片段：UNP residues 281-675 链 C 281–675（395 aa）片段：UNP residues 281-675	未记录	未记录非水小分子	ELECTRON MICROSCOPY cryo-EM缓冲液 100 mM phosphate buffer；pH 7；100 mM phosphate buffer cryo-EM玻璃化条件 100 K；冷冻剂 ETHANE；Plunged into liquid ethane (homemade plunger)	分辨率 21.00 Å
6ZQU Cryo-EM structure of mature Dengue virus 2 at 3.1 angstrom resolution 提交 2020-07-10	构建体不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 360 PDB 声明：360-meric	链 B 206–280（75 aa）链 D 206–280（75 aa）链 F 206–280（75 aa）	未记录	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 360	ELECTRON MICROSCOPY cryo-EM缓冲液 pH 7.4；PBS buffer cryo-EM玻璃化条件冷冻剂 ETHANE-PROPANE	分辨率 3.10 Å

共 3 个其他 PDB 条目、11 个 assembly。打开独立比较页并筛选聚集状态

查看构建体与数据证据

UniProt名称	O11875_9FLAV
Isoform	—
PDB实体	1
链与序列区间	作者链 A； PDB构建体 1–395； UniProt 281–675 作者链 B； PDB构建体 1–395； UniProt 281–675 作者链 C； PDB构建体 1–395； UniProt 281–675

Peptide pr

Dengue virus 2

UniProt P18356

当前结构中的状态

Assembly	聚集状态	构建体	突变与修饰	配体、离子与共同组分	实验方法与环境	结构质量
1	蛋白异源复合物异源复合物蛋白 × 600 PDB 声明：600-MERIC（600）与蛋白拷贝数一致	链 D； UniProt 15–95 链 E； UniProt 15–95 链 F； UniProt 15–95	未记录	Envelope protein E × 180 （O11875） E53 Fab Fragment (chain H) × 120 E53 Fab Fragment (chain L) × 120	ELECTRON MICROSCOPY cryo-EM缓冲液：pH 7.6；12 mM Tris-HCl, 120 mM NaCl, 1 mM EDTA cryo-EM玻璃化条件：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.；冷冻剂 ETHANE	分辨率 23.00 Å
2	蛋白异源复合物异源复合物蛋白 × 10 PDB 声明：decameric（10）与蛋白拷贝数一致	链 D； UniProt 15–95 链 E； UniProt 15–95 链 F； UniProt 15–95	未记录	Envelope protein E × 3 （O11875） E53 Fab Fragment (chain H) × 2 E53 Fab Fragment (chain L) × 2	ELECTRON MICROSCOPY cryo-EM缓冲液：pH 7.6；12 mM Tris-HCl, 120 mM NaCl, 1 mM EDTA cryo-EM玻璃化条件：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.；冷冻剂 ETHANE	分辨率 23.00 Å
3	蛋白异源复合物异源复合物蛋白 × 50 PDB 声明：50-meric（50）与蛋白拷贝数一致	链 D； UniProt 15–95 链 E； UniProt 15–95 链 F； UniProt 15–95	未记录	Envelope protein E × 15 （O11875） E53 Fab Fragment (chain H) × 10 E53 Fab Fragment (chain L) × 10	ELECTRON MICROSCOPY cryo-EM缓冲液：pH 7.6；12 mM Tris-HCl, 120 mM NaCl, 1 mM EDTA cryo-EM玻璃化条件：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.；冷冻剂 ETHANE	分辨率 23.00 Å
4	蛋白异源复合物异源复合物蛋白 × 60 PDB 声明：60-meric（60）与蛋白拷贝数一致	链 D； UniProt 15–95 链 E； UniProt 15–95 链 F； UniProt 15–95	未记录	Envelope protein E × 18 （O11875） E53 Fab Fragment (chain H) × 12 E53 Fab Fragment (chain L) × 12	ELECTRON MICROSCOPY cryo-EM缓冲液：pH 7.6；12 mM Tris-HCl, 120 mM NaCl, 1 mM EDTA cryo-EM玻璃化条件：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.；冷冻剂 ETHANE	分辨率 23.00 Å
5	蛋白异源复合物异源复合物蛋白 × 10 PDB 声明：decameric（10）与蛋白拷贝数一致	链 D； UniProt 15–95 链 E； UniProt 15–95 链 F； UniProt 15–95	未记录	Envelope protein E × 3 （O11875） E53 Fab Fragment (chain H) × 2 E53 Fab Fragment (chain L) × 2	ELECTRON MICROSCOPY cryo-EM缓冲液：pH 7.6；12 mM Tris-HCl, 120 mM NaCl, 1 mM EDTA cryo-EM玻璃化条件：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.；冷冻剂 ETHANE	分辨率 23.00 Å

数据库中的同蛋白其他状态

以下每一行都是同一 UniProt 蛋白在另一个 PDB 条目中的 biological assembly， “相对当前条目”直接指出证据层面的不同；没有差异标签表示当前已读取字段一致。

其他 PDB	相对当前条目 3IXY	Assembly / 聚集状态	构建体	突变与修饰	配体、离子与非聚合物	实验方法与环境	结构质量
2JSF Solution structures of the envelope protein domain III from the dengue-2 virus 提交 2007-07-03	构建体不同突变/修饰不同聚集状态不同实验方法不同实验环境不同结构质量不同	Assembly 1 蛋白单体单体；蛋白 × 1 PDB 声明：monomeric	链 A 469–577（109 aa）片段：Residues 469-577	未记录	未记录非水小分子	SOLUTION NMR NMR测量条件 pH 7.4；298 K；离子强度（mmCIF原始值）0.31；压力 ambient NMR样品组成 1-5 mM EDTA, 1-5 mM DTT, 1 mM sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O	分辨率未提供
2R69 Crystal structure of Fab 1A1D-2 complexed with E-DIII of Dengue virus at 3.8 angstrom resolution 提交 2007-09-05	构建体不同突变/修饰不同聚集状态不同实验方法不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 3 PDB 声明：trimeric	链 A 478–574（97 aa）	未记录	未记录非水小分子	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 5.8；298 K；12% PEG 3350, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	分辨率 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. 提交 2007-09-06	构建体不同聚集状态不同实验环境不同结构质量不同	Assembly 1 蛋白异源复合物异源复合物；蛋白 × 420 PDB 声明：420-MERIC	链 A 181–570（390 aa）片段：E protein 链 B 181–570（390 aa）片段：E protein 链 C 181–570（390 aa）片段：E protein	未记录	未记录非水小分子	ELECTRON MICROSCOPY cryo-EM缓冲液 pH 7.6 cryo-EM玻璃化条件冷冻剂 ETHANE；SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE	分辨率 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. 提交 2007-09-06	构建体不同聚集状态不同实验环境不同结构质量不同	Assembly 2 蛋白异源复合物异源复合物；蛋白 × 7 PDB 声明：heptameric	链 A 181–570（390 aa）片段：E protein 链 B 181–570（390 aa）片段：E protein 链 C 181–570（390 aa）片段：E protein	未记录	未记录非水小分子	ELECTRON MICROSCOPY cryo-EM缓冲液 pH 7.6 cryo-EM玻璃化条件冷冻剂 ETHANE；SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE	分辨率 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. 提交 2007-09-06	构建体不同聚集状态不同实验环境不同结构质量不同	Assembly 3 蛋白异源复合物异源复合物；蛋白 × 35 PDB 声明：35-meric	链 A 181–570（390 aa）片段：E protein 链 B 181–570（390 aa）片段：E protein 链 C 181–570（390 aa）片段：E protein	未记录	未记录非水小分子	ELECTRON MICROSCOPY cryo-EM缓冲液 pH 7.6 cryo-EM玻璃化条件冷冻剂 ETHANE；SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE	分辨率 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. 提交 2007-09-06	构建体不同聚集状态不同实验环境不同结构质量不同	Assembly 4 蛋白异源复合物异源复合物；蛋白 × 42 PDB 声明：42-meric	链 A 181–570（390 aa）片段：E protein 链 B 181–570（390 aa）片段：E protein 链 C 181–570（390 aa）片段：E protein	未记录	未记录非水小分子	ELECTRON MICROSCOPY cryo-EM缓冲液 pH 7.6 cryo-EM玻璃化条件冷冻剂 ETHANE；SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE	分辨率 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. 提交 2007-09-06	构建体不同聚集状态不同实验环境不同结构质量不同	Assembly 5 蛋白异源复合物异源复合物；蛋白 × 7 PDB 声明：heptameric	链 A 181–570（390 aa）片段：E protein 链 B 181–570（390 aa）片段：E protein 链 C 181–570（390 aa）片段：E protein	未记录	未记录非水小分子	ELECTRON MICROSCOPY cryo-EM缓冲液 pH 7.6 cryo-EM玻璃化条件冷冻剂 ETHANE；SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE	分辨率 24.00 Å
3C6R Low pH Immature Dengue Virus 提交 2008-02-05	构建体不同突变/修饰不同聚集状态不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 360 PDB 声明：360-meric	链 A 181–575（395 aa）链 B 181–575（395 aa）链 C 181–575（395 aa）链 D 15–95（81 aa）链 E 15–95（81 aa）链 F 15–95（81 aa）	未记录	未记录非水小分子	ELECTRON MICROSCOPY cryo-EM缓冲液 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玻璃化条件冷冻剂 ETHANE	分辨率 25.00 Å
3C6R Low pH Immature Dengue Virus 提交 2008-02-05	构建体不同突变/修饰不同聚集状态不同实验环境不同结构质量不同	Assembly 2 蛋白同源多聚体同源多聚体；蛋白 × 6 PDB 声明：hexameric	链 A 181–575（395 aa）链 B 181–575（395 aa）链 C 181–575（395 aa）链 D 15–95（81 aa）链 E 15–95（81 aa）链 F 15–95（81 aa）	未记录	未记录非水小分子	ELECTRON MICROSCOPY cryo-EM缓冲液 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玻璃化条件冷冻剂 ETHANE	分辨率 25.00 Å
3C6R Low pH Immature Dengue Virus 提交 2008-02-05	构建体不同突变/修饰不同聚集状态不同实验环境不同结构质量不同	Assembly 3 蛋白同源多聚体同源多聚体；蛋白 × 30 PDB 声明：30-meric	链 A 181–575（395 aa）链 B 181–575（395 aa）链 C 181–575（395 aa）链 D 15–95（81 aa）链 E 15–95（81 aa）链 F 15–95（81 aa）	未记录	未记录非水小分子	ELECTRON MICROSCOPY cryo-EM缓冲液 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玻璃化条件冷冻剂 ETHANE	分辨率 25.00 Å
3C6R Low pH Immature Dengue Virus 提交 2008-02-05	构建体不同突变/修饰不同聚集状态不同实验环境不同结构质量不同	Assembly 4 蛋白同源多聚体同源多聚体；蛋白 × 36 PDB 声明：36-meric	链 A 181–575（395 aa）链 B 181–575（395 aa）链 C 181–575（395 aa）链 D 15–95（81 aa）链 E 15–95（81 aa）链 F 15–95（81 aa）	未记录	未记录非水小分子	ELECTRON MICROSCOPY cryo-EM缓冲液 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玻璃化条件冷冻剂 ETHANE	分辨率 25.00 Å
3C6R Low pH Immature Dengue Virus 提交 2008-02-05	构建体不同突变/修饰不同聚集状态不同实验环境不同结构质量不同	Assembly 5 蛋白同源多聚体同源多聚体；蛋白 × 6 PDB 声明：hexameric	链 A 181–575（395 aa）链 B 181–575（395 aa）链 C 181–575（395 aa）链 D 15–95（81 aa）链 E 15–95（81 aa）链 F 15–95（81 aa）	未记录	未记录非水小分子	ELECTRON MICROSCOPY cryo-EM缓冲液 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玻璃化条件冷冻剂 ETHANE	分辨率 25.00 Å
3IYA Association of the pr peptides with dengue virus blocks membrane fusion at acidic pH 提交 2009-06-01	构建体不同突变/修饰不同聚集状态不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 360 PDB 声明：360-meric	链 A 181–575（395 aa）链 B 181–575（395 aa）链 C 181–575（395 aa）链 D 15–95（81 aa）链 E 15–95（81 aa）链 F 15–95（81 aa）	未记录	未记录非水小分子	ELECTRON MICROSCOPY cryo-EM缓冲液 pH 6；6 mM Tris-HCL 25 mM MES 120 mM NaCl 1 mM EDTA cryo-EM玻璃化条件 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.；冷冻剂 ETHANE	分辨率 22.00 Å
3IYA Association of the pr peptides with dengue virus blocks membrane fusion at acidic pH 提交 2009-06-01	构建体不同突变/修饰不同聚集状态不同实验环境不同结构质量不同	Assembly 2 蛋白同源多聚体同源多聚体；蛋白 × 6 PDB 声明：hexameric	链 A 181–575（395 aa）链 B 181–575（395 aa）链 C 181–575（395 aa）链 D 15–95（81 aa）链 E 15–95（81 aa）链 F 15–95（81 aa）	未记录	未记录非水小分子	ELECTRON MICROSCOPY cryo-EM缓冲液 pH 6；6 mM Tris-HCL 25 mM MES 120 mM NaCl 1 mM EDTA cryo-EM玻璃化条件 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.；冷冻剂 ETHANE	分辨率 22.00 Å
3IYA Association of the pr peptides with dengue virus blocks membrane fusion at acidic pH 提交 2009-06-01	构建体不同突变/修饰不同聚集状态不同实验环境不同结构质量不同	Assembly 3 蛋白同源多聚体同源多聚体；蛋白 × 30 PDB 声明：30-meric	链 A 181–575（395 aa）链 B 181–575（395 aa）链 C 181–575（395 aa）链 D 15–95（81 aa）链 E 15–95（81 aa）链 F 15–95（81 aa）	未记录	未记录非水小分子	ELECTRON MICROSCOPY cryo-EM缓冲液 pH 6；6 mM Tris-HCL 25 mM MES 120 mM NaCl 1 mM EDTA cryo-EM玻璃化条件 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.；冷冻剂 ETHANE	分辨率 22.00 Å
3IYA Association of the pr peptides with dengue virus blocks membrane fusion at acidic pH 提交 2009-06-01	构建体不同突变/修饰不同聚集状态不同实验环境不同结构质量不同	Assembly 4 蛋白同源多聚体同源多聚体；蛋白 × 36 PDB 声明：36-meric	链 A 181–575（395 aa）链 B 181–575（395 aa）链 C 181–575（395 aa）链 D 15–95（81 aa）链 E 15–95（81 aa）链 F 15–95（81 aa）	未记录	未记录非水小分子	ELECTRON MICROSCOPY cryo-EM缓冲液 pH 6；6 mM Tris-HCL 25 mM MES 120 mM NaCl 1 mM EDTA cryo-EM玻璃化条件 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.；冷冻剂 ETHANE	分辨率 22.00 Å
3IYA Association of the pr peptides with dengue virus blocks membrane fusion at acidic pH 提交 2009-06-01	构建体不同突变/修饰不同聚集状态不同实验环境不同结构质量不同	Assembly 5 蛋白同源多聚体同源多聚体；蛋白 × 6 PDB 声明：hexameric	链 A 181–575（395 aa）链 B 181–575（395 aa）链 C 181–575（395 aa）链 D 15–95（81 aa）链 E 15–95（81 aa）链 F 15–95（81 aa）	未记录	未记录非水小分子	ELECTRON MICROSCOPY cryo-EM缓冲液 pH 6；6 mM Tris-HCL 25 mM MES 120 mM NaCl 1 mM EDTA cryo-EM玻璃化条件 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.；冷冻剂 ETHANE	分辨率 22.00 Å

共 5 个其他 PDB 条目、17 个 assembly。打开独立比较页并筛选聚集状态

查看构建体与数据证据

UniProt名称	POLG_DEN2U
Isoform	—
PDB实体	2
链与序列区间	作者链 D； PDB构建体 1–81； UniProt 15–95 作者链 E； PDB构建体 1–81； UniProt 15–95 作者链 F； PDB构建体 1–81； UniProt 15–95

页面优先展示蛋白身份、当前 assembly、共同组分、聚集状态和跨 PDB 结构链接。链映射与序列区间收在“数据证据”中；数据库内部编号、导入时间和 assembly 操作表达式仅用于维护，因此不在读者页面展示。

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2. 结构基本信息 2. Structure Basics

条目编号 entry_id	3ixy
沉积日期 deposition_date	2009-02-26
结构标题 title	The pseudo-atomic structure of dengue immature virus in complex with Fab fragments of the anti-fusion loop antibody E53
关键词 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
实验方法 method	ELECTRON MICROSCOPY

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3. SAXS 参数 (CRYSOL 理论计算) 3. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	62.32 Å
回转半径 Rg (电子) rg_electron	62.64 Å
零角强度 I(0) i0	927034000.00
分子量 molecular_weight	251680.0 kDa
排除体积 excluded_volume	305890 Å³
包络体积 envelope_volume	358030 Å³
水化壳体积 shell_volume	53698 Å³
包络直径 envelope_diameter	196.2 Å
壳层 Rg shell_rg	53.35 Å
包络 Rg envelope_rg	59.43 Å
形状 Rg shape_rg	62.90 Å
总 Rg total_rg	62.44 Å
总原子数 total_atoms	—
残基数 n_residues	—
球谐函数阶数 n_harmonics	20
q 范围 q_range	— – 0.5000 Å⁻¹
数据点数 n_points	101
壳层类型 shell_type	directional
溶剂电子密度 solvent_density	0.3340 e/Å³
壳层衬度 contrast_shell	0.0300 e/Å³
CRYSOL 版本 crysol_version	4.1.3

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4. P(r) 距离分布 (GNOM 反演) 4. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	205.9 Å
Rg (实空间) rg_real	62.38 Å
Rg 误差 (实空间) rg_real_error	2.06 Å
I(0) (实空间) i0_real	9.2700e+08
I(0) 误差 (实空间) i0_real_error	1.9600e+07
Rg (倒空间) rg_reciprocal	62.22 Å
I(0) (倒空间) i0_reciprocal	926700000.0000
解质量估计 total_estimate	0.8510
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	82.3 Å
偏度 Skewness skewness	0.204
峰度 Kurtosis kurtosis	-0.543
角度范围 angular_range	— – 0.1250 Å⁻¹
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	23670000.0000
实空间数据点数 n_real_points	26
GNOM 版本 gnom_version	4.1.3
质量判据 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. 晶体学与实验 5. Crystallography & Experiment

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6. 实体与聚合物信息 Entities & Polymers (4)

实体 1 Entity 1 polymer

描述 description	Envelope protein E
分子量 formula_weight	43904.4 kDa
来源方法 src_method	man
拷贝数 entity_count	3

聚合物 Polymer

聚合物类型 type	polypeptide(L)
链编号 strand_id	A,B,C
原子数 atom_count	2281

MRCIGISNRDFVEGVSGGSWVDIVLEHGSCVTTMAKNKPTLDFELIKTEAKQPATLRKYCIEAKLTNTTTESRCPTQGEPSLNEEQDKRFVCKHSMVDRGWGNGCGLFGKGGIVTCAMFRCKKNMEGKVVQPENLEYTVVITPHSGEEHAVGNDTGKHGKEVKITPQSSITEAELTGYGTVTMECSPRTGLDFNEMVLLQMENKAWLVHRQWFLDLPLPWLPGADTQGSNWIQKETLVTFKNPHAKKQDVVVLGSQEGAMHTALTGATEIQMSSGNLLFTGHLKCRLRMDKLQLKGMSYSMCTGKFKVVKEIAETQHGTIVIRVQYEGDGSPCKIPFEIMDLEKRHVLGRLITVNPIVTEKDSPVNIEAEPPFGDSYIIIGVEPGQLKLDWFKKG

来源 Source

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

实体 2 Entity 2 polymer

描述 description	Peptide pr
分子量 formula_weight	9261.5 kDa
来源方法 src_method	man
拷贝数 entity_count	3

聚合物 Polymer

聚合物类型 type	polypeptide(L)
链编号 strand_id	D,E,F

FHLTTRNGEPHMIVSRQEKGKSLLFKTEDGVNMCTLMAMDLGELCEDTITYKCPLLRQNEPEDIDCWCNSTSTWVTYGTCT

来源 Source

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

实体 3 Entity 3 polymer

描述 description	E53 Fab Fragment (chain H)
分子量 formula_weight	23630.5 kDa
来源方法 src_method	man
拷贝数 entity_count	2

聚合物 Polymer

聚合物类型 type	polypeptide(L)
链编号 strand_id	G,I

EVKLVESGGGLVLPGGSLRLSCATSGFTFTDYYMTWVRQPPGKALEWLGFIGNKANDYTTEYSASVKGRFTISRDDSQSILYLQMSTLRAEDRATYYCATVYGNYPYFDVWGAGTTVAVSSAKTTPPSVYPLAPVCGGTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSGLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPR

来源 Source

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

实体 4 Entity 4 polymer

描述 description	E53 Fab Fragment (chain L)
分子量 formula_weight	23588.1 kDa
来源方法 src_method	man
拷贝数 entity_count	2

聚合物 Polymer

聚合物类型 type	polypeptide(L)
链编号 strand_id	H,J

QIVLTQSPAIMSASPGEKVTMTCSASSSVSYMHWYQQKSGTSPKIWIYESSKLASGVPVRFSGSGSGTSYSLTISSMEAEDVATYYCQQWSSHPHPLTFGAGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

来源 Source

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

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8. 引用文献 (1)

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晶胞边长 a length_a	1.000 Å
晶胞边长 b length_b	1.000 Å
晶胞边长 c length_c	1.000 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.00 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	1

空间群 space_group	P 1
空间群编号 int_tables_number	1
晶系 crystal_system	—

分辨率 resolution	23.00 Å
分辨率测定方法 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. 蛋白身份与相关结构 Protein Identity & Related Structures

Envelope protein E

当前结构中的状态

数据库中的同蛋白其他状态

Peptide pr

当前结构中的状态

数据库中的同蛋白其他状态

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

2. 结构基本信息 2. Structure Basics

3. SAXS 参数 (CRYSOL 理论计算) 3. SAXS Parameters (CRYSOL)

4. P(r) 距离分布 (GNOM 反演) 4. P(r) Analysis (GNOM)

5. 晶体学与实验 5. Crystallography & Experiment

晶胞参数 Unit Cell

对称性 Symmetry

冷冻电镜 EM 3D

6. 实体与聚合物信息 Entities & Polymers (4)

实体 1 Entity 1 polymer

聚合物 Polymer

来源 Source

实体 2 Entity 2 polymer

聚合物 Polymer

来源 Source

实体 3 Entity 3 polymer

聚合物 Polymer

来源 Source

实体 4 Entity 4 polymer

聚合物 Polymer

来源 Source

8. 引用文献 (1)

9. 文件与曲线 (10)

Files (7)

Curves (3)