2gjw

RNA Recognition and Cleavage by an Splicing Endonuclease

Method: X-RAY DIFFRACTION

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

tRNA-splicing endonuclease

Archaeoglobus fulgidus

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	蛋白–RNA	同源多聚体	蛋白 2 RNA 3	5'-R(GPCPGPAPCPCPGPAPCPCPAP(DU)PAPGPCPUPGPCPA)-3' × 1 5'-R(UPGPCPAPGPCPGPGPUPCPAP(A23))-3' × 1 5'-R(APGPGPUPCPGPC)-3' × 1	与全部聚合物一致
2	蛋白–RNA	同源多聚体	蛋白 2 RNA 3	5'-R(GPCPGPAPCPCPGPAPCPCPAP(DU)PAPGPCPUPGPCPA)-3' × 1 5'-R(UPGPCPAPGPCPGPGPUPCPAP(A23))-3' × 1 5'-R(APGPGPUPCPGPC)-3' × 1	与全部聚合物一致

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	ENDA_ARCFU
Isoform	—
PDB实体	4
链与序列区间	作者链 A； PDB构建体 10–313； UniProt 2–305 作者链 B； PDB构建体 10–313； UniProt 2–305 作者链 C； PDB构建体 10–313； UniProt 2–305 作者链 D； PDB构建体 10–313； UniProt 2–305

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	2gjw
沉积日期 deposition_date	2006-03-31
结构标题 title	RNA Recognition and Cleavage by an Splicing Endonuclease
关键词 keywords	Bulge-Helix-Bulge RNA-protein complex, Splicing Endonuclease Af, Hydrolase-RNA COMPLEX; Hydrolase/RNA
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。

2gjw__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

下载该曲线 .dat

2gjw__assembly_2__model_1 | I(q)

100 个绘图点；横轴和纵轴均采用对数尺度。

2gjw__assembly_2__model_1 | P(r) · Pending

P(r) 将按相同 assembly/model 分别计算和展示。

Rg（Guinier）	28.98 Å
Rg（电子密度）	28.89 Å
总 Rg	29.47 Å
原子数	5895
残基数	647
排除体积	102380 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	`2gjw__assembly_1__model_1`	pentameric （5）	成功	4.1.3-1-20251215 (887e7ef)	查看下载
2	1	`2gjw__assembly_2__model_1`	pentameric （5）	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 (4)

实体 1 Entity 1 polymer

描述 description	5'-R(GPCPGPAPCPCPGPAPCPCPAP(DU)PAPGPCPUPGPCP*A)-3'
分子量 formula_weight	6059.7 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

聚合物 Polymer

聚合物类型 type	polyribonucleotide
链编号 strand_id	E,I
原子数 atom_count	11778

GCGACCGACCAUAGCUGCA

实体 2 Entity 2 polymer

描述 description	5'-R(UPGPCPAPGPCPGPGPUPCPAP(A23))-3'
分子量 formula_weight	3913.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

聚合物 Polymer

聚合物类型 type	polyribonucleotide
链编号 strand_id	F,J

UGCAGCGGUCAA

实体 3 Entity 3 polymer

描述 description	5'-R(APGPGPUPCPGP*C)-3'
分子量 formula_weight	2236.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

聚合物 Polymer

聚合物类型 type	polyribonucleotide
链编号 strand_id	H,L

AGGUCGC

实体 4 Entity 4 polymer

描述 description	tRNA-splicing endonuclease
分子量 formula_weight	37105.4 kDa
EC 编号 ec_number	3.1.27.9
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,B,C,D

MHHHHHHHHIGGDFAVVKAKKSLERRGFGVKRGDKIYLHPLEVVYLQIKGIESFGELEDVLSWAESRMEDFSTYYFVYEDLRDRGNKVKIQGEFLLTKKPYLPISERKTIRMEEIAEKARNFDELRLAVVDEESEITYFRVYEPDMMGEQKEELPEIAGVLSDEYVITKQTEIFSRYFYGSEKGDLVTLSLIESLYLLDLGKLNLLNADREELVKRAREVERNFDRRYEVYRNLKERGFVVKTGFKFGSEFRVYRKVESVDDLPHSEYLVDIADSREIRLIDLARAVRLAQNVRKRMVFAYGKNYLCFERVKV

来源 Source

来源生物 organism	Archaeoglobus fulgidus
NCBI 分类编号 ncbi_taxonomy_id	2234
宿主生物 host_organism	Escherichia coli

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6. 折叠分类 (SCOP + CATH) 31 domains

SCOP 2.08 (19 domains)

结构域编号 domain_id	d2gjwa1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.52 — Restriction endonuclease-like
超家族 Superfamily superfamily	c.52.2 — tRNA-intron endonuclease catalytic domain-like
家族 Family family	c.52.2.1 — tRNA-intron endonuclease catalytic domain-like

结构域编号 domain_id	d2gjwa2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.52 — Restriction endonuclease-like
超家族 Superfamily superfamily	c.52.2 — tRNA-intron endonuclease catalytic domain-like
家族 Family family	c.52.2.1 — tRNA-intron endonuclease catalytic domain-like

结构域编号 domain_id	d2gjwa3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.75 — MutS N-terminal domain-like
超家族 Superfamily superfamily	d.75.1 — tRNA-intron endonuclease N-terminal domain-like
家族 Family family	d.75.1.1 — tRNA-intron endonuclease N-terminal domain-like

结构域编号 domain_id	d2gjwa4
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.75 — MutS N-terminal domain-like
超家族 Superfamily superfamily	d.75.1 — tRNA-intron endonuclease N-terminal domain-like
家族 Family family	d.75.1.1 — tRNA-intron endonuclease N-terminal domain-like

结构域编号 domain_id	d2gjwa5
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d2gjwb1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.52 — Restriction endonuclease-like
超家族 Superfamily superfamily	c.52.2 — tRNA-intron endonuclease catalytic domain-like
家族 Family family	c.52.2.1 — tRNA-intron endonuclease catalytic domain-like

结构域编号 domain_id	d2gjwb2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.52 — Restriction endonuclease-like
超家族 Superfamily superfamily	c.52.2 — tRNA-intron endonuclease catalytic domain-like
家族 Family family	c.52.2.1 — tRNA-intron endonuclease catalytic domain-like

结构域编号 domain_id	d2gjwb3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.75 — MutS N-terminal domain-like
超家族 Superfamily superfamily	d.75.1 — tRNA-intron endonuclease N-terminal domain-like
家族 Family family	d.75.1.1 — tRNA-intron endonuclease N-terminal domain-like

结构域编号 domain_id	d2gjwb4
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.75 — MutS N-terminal domain-like
超家族 Superfamily superfamily	d.75.1 — tRNA-intron endonuclease N-terminal domain-like
家族 Family family	d.75.1.1 — tRNA-intron endonuclease N-terminal domain-like

结构域编号 domain_id	d2gjwb5
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d2gjwc1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.52 — Restriction endonuclease-like
超家族 Superfamily superfamily	c.52.2 — tRNA-intron endonuclease catalytic domain-like
家族 Family family	c.52.2.1 — tRNA-intron endonuclease catalytic domain-like

结构域编号 domain_id	d2gjwc2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.52 — Restriction endonuclease-like
超家族 Superfamily superfamily	c.52.2 — tRNA-intron endonuclease catalytic domain-like
家族 Family family	c.52.2.1 — tRNA-intron endonuclease catalytic domain-like

结构域编号 domain_id	d2gjwc3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.75 — MutS N-terminal domain-like
超家族 Superfamily superfamily	d.75.1 — tRNA-intron endonuclease N-terminal domain-like
家族 Family family	d.75.1.1 — tRNA-intron endonuclease N-terminal domain-like

结构域编号 domain_id	d2gjwc4
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.75 — MutS N-terminal domain-like
超家族 Superfamily superfamily	d.75.1 — tRNA-intron endonuclease N-terminal domain-like
家族 Family family	d.75.1.1 — tRNA-intron endonuclease N-terminal domain-like

结构域编号 domain_id	d2gjwc5
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d2gjwd1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.52 — Restriction endonuclease-like
超家族 Superfamily superfamily	c.52.2 — tRNA-intron endonuclease catalytic domain-like
家族 Family family	c.52.2.1 — tRNA-intron endonuclease catalytic domain-like

结构域编号 domain_id	d2gjwd2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.52 — Restriction endonuclease-like
超家族 Superfamily superfamily	c.52.2 — tRNA-intron endonuclease catalytic domain-like
家族 Family family	c.52.2.1 — tRNA-intron endonuclease catalytic domain-like

结构域编号 domain_id	d2gjwd3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.75 — MutS N-terminal domain-like
超家族 Superfamily superfamily	d.75.1 — tRNA-intron endonuclease N-terminal domain-like
家族 Family family	d.75.1.1 — tRNA-intron endonuclease N-terminal domain-like

结构域编号 domain_id	d2gjwd4
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.75 — MutS N-terminal domain-like
超家族 Superfamily superfamily	d.75.1 — tRNA-intron endonuclease N-terminal domain-like
家族 Family family	d.75.1.1 — tRNA-intron endonuclease N-terminal domain-like

CATH v4.4 (12 domains)

结构域编号 domain_id	2gjwA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1350 — Trna Endonuclease; Chain: A, domain 1
同源超家族 H-superfamily homologous superfamily	150 —

结构域编号 domain_id	2gjwA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1170 — MutS, DNA mismatch repair protein, domain I
同源超家族 H-superfamily homologous superfamily	20 — tRNA intron endonuclease, N-terminal domain

结构域编号 domain_id	2gjwA03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1350 — Trna Endonuclease; Chain: A, domain 1
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	2gjwB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1350 — Trna Endonuclease; Chain: A, domain 1
同源超家族 H-superfamily homologous superfamily	150 —

结构域编号 domain_id	2gjwB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1170 — MutS, DNA mismatch repair protein, domain I
同源超家族 H-superfamily homologous superfamily	20 — tRNA intron endonuclease, N-terminal domain

结构域编号 domain_id	2gjwB03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1350 — Trna Endonuclease; Chain: A, domain 1
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	2gjwC01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1350 — Trna Endonuclease; Chain: A, domain 1
同源超家族 H-superfamily homologous superfamily	150 —

结构域编号 domain_id	2gjwC02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1170 — MutS, DNA mismatch repair protein, domain I
同源超家族 H-superfamily homologous superfamily	20 — tRNA intron endonuclease, N-terminal domain

结构域编号 domain_id	2gjwC03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1350 — Trna Endonuclease; Chain: A, domain 1
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	2gjwD01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1350 — Trna Endonuclease; Chain: A, domain 1
同源超家族 H-superfamily homologous superfamily	150 —

结构域编号 domain_id	2gjwD02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1170 — MutS, DNA mismatch repair protein, domain I
同源超家族 H-superfamily homologous superfamily	20 — tRNA intron endonuclease, N-terminal domain

结构域编号 domain_id	2gjwD03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1350 — Trna Endonuclease; Chain: A, domain 1
同源超家族 H-superfamily homologous superfamily	10 —

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晶胞边长 a length_a	90.073 Å
晶胞边长 b length_b	140.357 Å
晶胞边长 c length_c	82.048 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	111.69 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	—

分辨率 resolution	2.850 Å
最低分辨率 resolution_low	35.090 Å
R 因子 r_factor	0.2499
R_work r_work	0.2474
R_free r_free	0.2965

RNA Recognition and Cleavage by an Splicing Endonuclease

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

tRNA-splicing endonuclease

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

2gjw__assembly_2__model_1

2gjw__assembly_2__model_1 | I(q)

2gjw__assembly_2__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 (4)

实体 1 Entity 1 polymer

聚合物 Polymer

实体 2 Entity 2 polymer

聚合物 Polymer

实体 3 Entity 3 polymer

聚合物 Polymer

实体 4 Entity 4 polymer

聚合物 Polymer

来源 Source

6. 折叠分类 (SCOP + CATH) 31 domains

SCOP 2.08 (19 domains)

CATH v4.4 (12 domains)

7. 引用文献 (1)

RNA Recognition and Cleavage by an Splicing Endonuclease

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

tRNA-splicing endonuclease

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

2gjw__assembly_2__model_1

2gjw__assembly_2__model_1 | I(q)

2gjw__assembly_2__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 (4)

实体 1 Entity 1 polymer

聚合物 Polymer

实体 2 Entity 2 polymer

聚合物 Polymer

实体 3 Entity 3 polymer

聚合物 Polymer

实体 4 Entity 4 polymer

聚合物 Polymer

来源 Source

6. 折叠分类 (SCOP + CATH) 31 domains

SCOP 2.08 (19 domains)

CATH v4.4 (12 domains)

7. 引用文献 (1)