6pdl

Crystal Structure of Hendra Virus Attachment G Glycoprotein in Complex with Receptor Ephrin-B2

Method: X-RAY DIFFRACTION

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

Attachment glycoprotein

Hendra henipavirus

当前结构中的状态

Assembly	物理组成	蛋白状态	分子拷贝数	共同组分	数据核对
1	其他组合	异源复合物	蛋白 2 其他聚合物 3	Ephrin-B2 × 1 （P52799） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 water × 2	与蛋白数一致
2	其他组合	异源复合物	蛋白 2 其他聚合物 3	Ephrin-B2 × 1 （P52799） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ;beta-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 water × 2	与蛋白数一致
3	其他组合	异源复合物	蛋白 2 其他聚合物 3	Ephrin-B2 × 1 （P52799） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 water × 2	与蛋白数一致
4	其他组合	异源复合物	蛋白 2 其他聚合物 3	Ephrin-B2 × 1 （P52799） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 water × 2	与蛋白数一致

数据库中的同蛋白其他状态

查看构建体与数据证据

UniProt名称	F4YH71_9MONO
Isoform	—
PDB实体	1
链与序列区间	作者链 A； PDB构建体 1–434； UniProt 171–604 作者链 C； PDB构建体 1–434； UniProt 171–604 作者链 E； PDB构建体 1–434； UniProt 171–604 作者链 G； PDB构建体 1–434； UniProt 171–604

Ephrin-B2

Homo sapiens

UniProt P52799

当前结构中的状态

Assembly	物理组成	蛋白状态	分子拷贝数	共同组分	数据核对
1	其他组合	异源复合物	蛋白 2 其他聚合物 3	Attachment glycoprotein × 1 （F4YH71） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 water × 2	与蛋白数一致
2	其他组合	异源复合物	蛋白 2 其他聚合物 3	Attachment glycoprotein × 1 （F4YH71） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ;beta-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 water × 2	与蛋白数一致
3	其他组合	异源复合物	蛋白 2 其他聚合物 3	Attachment glycoprotein × 1 （F4YH71） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 water × 2	与蛋白数一致
4	其他组合	异源复合物	蛋白 2 其他聚合物 3	Attachment glycoprotein × 1 （F4YH71） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 water × 2	与蛋白数一致

数据库中的同蛋白其他状态

查看构建体与数据证据

UniProt名称	EFNB2_HUMAN
Isoform	—
PDB实体	2
链与序列区间	作者链 B； PDB构建体 1–141； UniProt 27–167 作者链 D； PDB构建体 1–141； UniProt 27–167 作者链 F； PDB构建体 1–141； UniProt 27–167 作者链 H； PDB构建体 1–141； UniProt 27–167

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	6pdl
沉积日期 deposition_date	2019-06-19
结构标题 title	Crystal Structure of Hendra Virus Attachment G Glycoprotein in Complex with Receptor Ephrin-B2
关键词 keywords	attachment, glycoprotein, G protein, VIRAL PROTEIN, receptor, VIRAL PROTEIN-SIGNALING PROTEIN complex; VIRAL PROTEIN/SIGNALING PROTEIN
实验方法 method	X-RAY DIFFRACTION

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3. Official assembly/model 理论 SAXS Official SAXS Profiles

页面只读取最新 assembly 计算结果。每一条曲线都对应明确的 PDB、official biological assembly 和 coordinate model。

6pdl__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

下载该曲线 .dat

6pdl__assembly_3__model_1 | I(q)

100 个绘图点；横轴和纵轴均采用对数尺度。

6pdl__assembly_3__model_1 | P(r) · Pending

P(r) 将按相同 assembly/model 分别计算和展示。

Rg（Guinier）	25.37 Å
Rg（电子密度）	24.28 Å
总 Rg	25.27 Å
原子数	4547
残基数	554
排除体积	81293 Å³
最大 q	0.500 Å⁻¹

Assembly	Model	结构单元	聚集说明	状态	CRYSOL	操作
1	1	`6pdl__assembly_1__model_1`	dimeric （2）	成功	4.1.3-1-20251215 (887e7ef)	查看下载
2	1	`6pdl__assembly_2__model_1`	dimeric （2）	成功	4.1.3-1-20251215 (887e7ef)	查看下载
3	1	`6pdl__assembly_3__model_1`	dimeric （2）	成功	4.1.3-1-20251215 (887e7ef)	查看下载
4	1	`6pdl__assembly_4__model_1`	dimeric （2）	成功	4.1.3-1-20251215 (887e7ef)	查看下载

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4. 晶体学与实验 4. Crystallography & Experiment

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5. 实体与聚合物信息 Entities & Polymers (9)

实体 1 Entity 1 polymer

描述 description	Attachment glycoprotein
分子量 formula_weight	49431.1 kDa
来源方法 src_method	man
拷贝数 entity_count	4

聚合物 Polymer

聚合物类型 type	polypeptide(L)
链编号 strand_id	A,C,E,G
原子数 atom_count	18707

YRPISQGVSDLVGLPNQICLQKTTSTILKPRLISYTLPINTREGVCITDPLLAVDNGFFAYSHLEKIGSCTRGIAKQRIIGVGEVLDRGDKVPSMFMTNVWTPPNPSTIHHCSSTYHEDFYYTLCAVSHVGDPILNSTSWTESLSLIRLAVRPKSDSGDYNQKYIAITKVERGKYDKVMPYGPSGIKQGDTLYFPAVGFLPRTEFQYNDSNCPIIHCKYSKAENCRLSMGVNSKSHYILRSGLLKYNLSLGGDIILQFIEIADNRLTIGSPSKIYNSLGQPVFYQASYSWDTMIKLGDVDTVDPLRVQWRNNSVISRPGQSQCPRFNVCPEVCWEGTYNDAFLIDRLNWVSAGVYLNSNQTAENPVFAVFKDNEILYQVPLAEDDTNAQKTITDCFLLENVIWCISLVEIYDTGDSVIRPKLFAVKIPAQCSESGRGLVPR

来源 Source

来源生物 organism	Hendra henipavirus
NCBI 分类编号 ncbi_taxonomy_id	63330
宿主生物 host_organism	Insect cell expression vector pTIE1

实体 2 Entity 2 polymer

描述 description	Ephrin-B2
分子量 formula_weight	16103.4 kDa
来源方法 src_method	man
拷贝数 entity_count	4

聚合物 Polymer

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

SIVLEPIYWNSSNSKFLPGQGLVLYPQIGDKLDIICPKVDSKTVGQYEYYKVYMVDKDQADRCTIKKENTPLLNCAKPDQDIKFTIKFQEFSPNLWGLEFQKNKDYYIISTSNGSLEGLDNQEGGVCQTRAMKILMKVGQD

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Insect cell expression vector pTIE1

实体 3 Entity 3 branched

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	424.4 kDa
来源方法 src_method	man
拷贝数 entity_count	6

实体 4 Entity 4 branched

描述 description	;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	1203.1 kDa
来源方法 src_method	man
拷贝数 entity_count	2

实体 5 Entity 5 branched

描述 description	;beta-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	1203.1 kDa
来源方法 src_method	man
拷贝数 entity_count	1

实体 6 Entity 6 branched

描述 description	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	586.5 kDa
来源方法 src_method	man
拷贝数 entity_count	2

实体 7 Entity 7 branched

描述 description	;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	878.8 kDa
来源方法 src_method	man
拷贝数 entity_count	1

实体 8 Entity 8 non-polymer

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	221.2 kDa
来源方法 src_method	man
拷贝数 entity_count	13

实体 9 Entity 9 water

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	425

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6. 折叠分类 (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d6pdlb_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.6 — Cupredoxin-like
超家族 Superfamily superfamily	b.6.1 — Cupredoxins
家族 Family family	b.6.1.5 — Ephrin ectodomain

结构域编号 domain_id	d6pdld_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.6 — Cupredoxin-like
超家族 Superfamily superfamily	b.6.1 — Cupredoxins
家族 Family family	b.6.1.5 — Ephrin ectodomain

结构域编号 domain_id	d6pdlf_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.6 — Cupredoxin-like
超家族 Superfamily superfamily	b.6.1 — Cupredoxins
家族 Family family	b.6.1.5 — Ephrin ectodomain

结构域编号 domain_id	d6pdlh_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.6 — Cupredoxin-like
超家族 Superfamily superfamily	b.6.1 — Cupredoxins
家族 Family family	b.6.1.5 — Ephrin ectodomain

CATH v4.4 (8 domains)

结构域编号 domain_id	6pdlA00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	120 — 6 Propeller
拓扑 Topology topology	10 — Neuraminidase
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	6pdlB00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

结构域编号 domain_id	6pdlC00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	120 — 6 Propeller
拓扑 Topology topology	10 — Neuraminidase
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	6pdlD00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

结构域编号 domain_id	6pdlE00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	120 — 6 Propeller
拓扑 Topology topology	10 — Neuraminidase
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	6pdlF00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

结构域编号 domain_id	6pdlG00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	120 — 6 Propeller
拓扑 Topology topology	10 — Neuraminidase
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	6pdlH00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

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晶胞边长 a length_a	75.764 Å
晶胞边长 b length_b	94.642 Å
晶胞边长 c length_c	102.522 Å
晶胞夹角 α angle_alpha	112.86 °
晶胞夹角 β angle_beta	97.44 °
晶胞夹角 γ angle_gamma	97.56 °
晶胞分子数 Z z_pdb	4

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

分辨率 resolution	2.700 Å
最低分辨率 resolution_low	37.561 Å
R 因子 r_factor	0.1746
R_work r_work	0.1719
R_free r_free	0.2269

Crystal Structure of Hendra Virus Attachment G Glycoprotein in Complex with Receptor Ephrin-B2

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

Attachment glycoprotein

当前结构中的状态

数据库中的同蛋白其他状态

Ephrin-B2

当前结构中的状态

数据库中的同蛋白其他状态

2. 结构基本信息 2. Structure Basics

3. Official assembly/model 理论 SAXS Official SAXS Profiles

6pdl__assembly_3__model_1

6pdl__assembly_3__model_1 | I(q)

6pdl__assembly_3__model_1 | P(r) · Pending

4. 晶体学与实验 4. Crystallography & Experiment

晶胞参数 Unit Cell

对称性 Symmetry

精修参数 Refinement

衍射实验 Diffraction

5. 实体与聚合物信息 Entities & Polymers (9)

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 branched

实体 4 Entity 4 branched

实体 5 Entity 5 branched

实体 6 Entity 6 branched

实体 7 Entity 7 branched

实体 8 Entity 8 non-polymer

实体 9 Entity 9 water

6. 折叠分类 (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. 引用文献 (2)

Crystal Structure of Hendra Virus Attachment G Glycoprotein in Complex with Receptor Ephrin-B2

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

Attachment glycoprotein

当前结构中的状态

数据库中的同蛋白其他状态

单体

同源二聚体

同源四聚体

其他同源多聚体

异源或核酸复合物

Ephrin-B2

当前结构中的状态

数据库中的同蛋白其他状态

单体

同源二聚体

同源四聚体

其他同源多聚体

异源或核酸复合物

2. 结构基本信息 2. Structure Basics

3. Official assembly/model 理论 SAXS Official SAXS Profiles

6pdl__assembly_3__model_1

6pdl__assembly_3__model_1 | I(q)

6pdl__assembly_3__model_1 | P(r) · Pending

4. 晶体学与实验 4. Crystallography & Experiment

晶胞参数 Unit Cell

对称性 Symmetry

精修参数 Refinement

衍射实验 Diffraction

5. 实体与聚合物信息 Entities & Polymers (9)

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 branched

实体 4 Entity 4 branched

实体 5 Entity 5 branched

实体 6 Entity 6 branched

实体 7 Entity 7 branched

实体 8 Entity 8 non-polymer

实体 9 Entity 9 water

6. 折叠分类 (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. 引用文献 (2)