1s3s

Crystal structure of AAA ATPase p97/VCP ND1 in complex with p47 C

Method: X-RAY DIFFRACTION D_max: 192.2 Å Quality: GOOD

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

下载 Download SAXS (.dat) P(r) (.pr.out) CIF

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1s3s
沉积日期 deposition_date	2004-01-14
结构标题 title	Crystal structure of AAA ATPase p97/VCP ND1 in complex with p47 C
关键词 keywords	AAA ATPase, p97, p47, protein-protein complex, UBX domain, PROTEIN BINDING; PROTEIN BINDING
实验方法 method	X-RAY DIFFRACTION

▼

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	55.78 Å
回转半径 Rg (电子) rg_electron	55.93 Å
零角强度 I(0) i0	1474060000.00
分子量 molecular_weight	317930.0 kDa
排除体积 excluded_volume	396990 Å³
包络体积 envelope_volume	571220 Å³
水化壳体积 shell_volume	84347 Å³
包络直径 envelope_diameter	203.9 Å
壳层 Rg shell_rg	57.97 Å
包络 Rg envelope_rg	55.80 Å
形状 Rg shape_rg	55.96 Å
总 Rg total_rg	55.89 Å
总原子数 total_atoms	22304
残基数 n_residues	2871
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

▼

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	192.2 Å
Rg (实空间) rg_real	55.81 Å
Rg 误差 (实空间) rg_real_error	1.70 Å
I(0) (实空间) i0_real	1.4740e+09
I(0) 误差 (实空间) i0_real_error	2.9110e+07
Rg (倒空间) rg_reciprocal	55.72 Å
I(0) (倒空间) i0_reciprocal	1474000000.0000
解质量估计 total_estimate	0.8830
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	68.7 Å
偏度 Skewness skewness	0.269
峰度 Kurtosis kurtosis	-0.534
角度范围 angular_range	— – 0.1400 Å⁻¹
当前正则化参数 α current_alpha	0.0002
最高正则化参数 α highest_alpha	113400000.0000
实空间数据点数 n_real_points	29
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.877; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; Smooth: 0.861

▶

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

▶

5. 实体与聚合体信息 (4)

Entity 1 polymer

描述 description	;Transitional endoplasmic reticulum ATPase (TER ATPase) (15S Mg(2+)- ATPase p97 subunit) (Valosin containing protein) (VCP) [Contains: Valosin] ;
分子量 formula_weight	51027.5 kDa
来源方法 src_method	man
拷贝数 entity_count	6

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F
原子数 atom_count	22367

MASGADSKGDDLSTAILKQKNRPNRLIVDEAINEDNSVVSLSQPKMDELQLFRGDTVLLKGKKRREAVCIVLSDDTCSDEKIRMNRVVRNNLRVRLGDVISIQPCPDVKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVETDPSPYCIVAPDTVIHCEGEPIKREDEEESLNEVGYDDVGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHGHVGADLAALCSEAALQAIRKKMDLIDLEDETIDAEVMNSLAVTMDDFRWALSQ

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI 分类编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

Entity 2 polymer

描述 description	p47 protein
分子量 formula_weight	13775.6 kDa
来源方法 src_method	man
拷贝数 entity_count	3

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	G,H,I

VKPKGAFKAFTGEGQKLGSTAPQVLNTSSPAQQAENEAKASSSILINEAEPTTNIQIRLADGGRLVQKFNHSHRISDIRLFIVDARPAMAATSFVLMTTFPNKELADENQTLKEANLLNAVIVQRLT

来源 Source

来源生物 organism	Rattus norvegicus
通用名 common_name	Norway rat
NCBI 分类编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Escherichia coli

Entity 3 non-polymer

描述 description	ADENOSINE-5'-DIPHOSPHATE
分子量 formula_weight	427.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

Entity 4 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	63

▼

6. 折叠分类 (SCOP + CATH) 47 domains

SCOP 2.08 (21 domains)

结构域编号 domain_id	d1s3sa1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.52 — Double psi beta-barrel
超家族 Superfamily superfamily	b.52.2 — ADC-like
家族 Family family	b.52.2.3 — Cdc48 N-terminal domain-like

结构域编号 domain_id	d1s3sa2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family family	c.37.1.20 — Extended AAA-ATPase domain

结构域编号 domain_id	d1s3sa3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.31 — Cdc48 domain 2-like
超家族 Superfamily superfamily	d.31.1 — Cdc48 domain 2-like
家族 Family family	d.31.1.1 — Cdc48 domain 2-like

结构域编号 domain_id	d1s3sb1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.52 — Double psi beta-barrel
超家族 Superfamily superfamily	b.52.2 — ADC-like
家族 Family family	b.52.2.3 — Cdc48 N-terminal domain-like

结构域编号 domain_id	d1s3sb2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family family	c.37.1.20 — Extended AAA-ATPase domain

结构域编号 domain_id	d1s3sb3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.31 — Cdc48 domain 2-like
超家族 Superfamily superfamily	d.31.1 — Cdc48 domain 2-like
家族 Family family	d.31.1.1 — Cdc48 domain 2-like

结构域编号 domain_id	d1s3sc1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.52 — Double psi beta-barrel
超家族 Superfamily superfamily	b.52.2 — ADC-like
家族 Family family	b.52.2.3 — Cdc48 N-terminal domain-like

结构域编号 domain_id	d1s3sc2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family family	c.37.1.20 — Extended AAA-ATPase domain

结构域编号 domain_id	d1s3sc3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.31 — Cdc48 domain 2-like
超家族 Superfamily superfamily	d.31.1 — Cdc48 domain 2-like
家族 Family family	d.31.1.1 — Cdc48 domain 2-like

结构域编号 domain_id	d1s3sd1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.52 — Double psi beta-barrel
超家族 Superfamily superfamily	b.52.2 — ADC-like
家族 Family family	b.52.2.3 — Cdc48 N-terminal domain-like

结构域编号 domain_id	d1s3sd2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family family	c.37.1.20 — Extended AAA-ATPase domain

结构域编号 domain_id	d1s3sd3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.31 — Cdc48 domain 2-like
超家族 Superfamily superfamily	d.31.1 — Cdc48 domain 2-like
家族 Family family	d.31.1.1 — Cdc48 domain 2-like

结构域编号 domain_id	d1s3se1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.52 — Double psi beta-barrel
超家族 Superfamily superfamily	b.52.2 — ADC-like
家族 Family family	b.52.2.3 — Cdc48 N-terminal domain-like

结构域编号 domain_id	d1s3se2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family family	c.37.1.20 — Extended AAA-ATPase domain

结构域编号 domain_id	d1s3se3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.31 — Cdc48 domain 2-like
超家族 Superfamily superfamily	d.31.1 — Cdc48 domain 2-like
家族 Family family	d.31.1.1 — Cdc48 domain 2-like

结构域编号 domain_id	d1s3sf1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.52 — Double psi beta-barrel
超家族 Superfamily superfamily	b.52.2 — ADC-like
家族 Family family	b.52.2.3 — Cdc48 N-terminal domain-like

结构域编号 domain_id	d1s3sf2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family family	c.37.1.20 — Extended AAA-ATPase domain

结构域编号 domain_id	d1s3sf3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.31 — Cdc48 domain 2-like
超家族 Superfamily superfamily	d.31.1 — Cdc48 domain 2-like
家族 Family family	d.31.1.1 — Cdc48 domain 2-like

结构域编号 domain_id	d1s3sg_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.15 — beta-Grasp (ubiquitin-like)
超家族 Superfamily superfamily	d.15.1 — Ubiquitin-like
家族 Family family	d.15.1.2 — UBX domain

结构域编号 domain_id	d1s3sh_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.15 — beta-Grasp (ubiquitin-like)
超家族 Superfamily superfamily	d.15.1 — Ubiquitin-like
家族 Family family	d.15.1.2 — UBX domain

结构域编号 domain_id	d1s3si_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.15 — beta-Grasp (ubiquitin-like)
超家族 Superfamily superfamily	d.15.1 — Ubiquitin-like
家族 Family family	d.15.1.2 — UBX domain

CATH v4.4 (26 domains)

结构域编号 domain_id	1s3sA01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	40 — Barwin-like endoglucanases
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	1s3sA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

结构域编号 domain_id	1s3sA03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	330 — Vcp-like ATPase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1s3sA04
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	8 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily	60 —

结构域编号 domain_id	1s3sB01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	40 — Barwin-like endoglucanases
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	1s3sB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

结构域编号 domain_id	1s3sB03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	330 — Vcp-like ATPase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1s3sB04
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	8 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily	60 —

结构域编号 domain_id	1s3sC01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	40 — Barwin-like endoglucanases
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	1s3sC02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

结构域编号 domain_id	1s3sC03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	330 — Vcp-like ATPase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1s3sC04
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	8 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily	60 —

结构域编号 domain_id	1s3sD01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	40 — Barwin-like endoglucanases
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	1s3sD02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

结构域编号 domain_id	1s3sD03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	330 — Vcp-like ATPase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1s3sD04
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	8 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily	60 —

结构域编号 domain_id	1s3sE01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	40 — Barwin-like endoglucanases
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	1s3sE02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

结构域编号 domain_id	1s3sE03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	330 — Vcp-like ATPase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1s3sE04
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	8 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily	60 —

结构域编号 domain_id	1s3sF01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	40 — Barwin-like endoglucanases
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	1s3sF02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

结构域编号 domain_id	1s3sF03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	330 — Vcp-like ATPase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1s3sF04
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	8 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily	60 —

结构域编号 domain_id	1s3sG00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	20 — Ubiquitin-like (UB roll)
同源超家族 H-superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

结构域编号 domain_id	1s3sH00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	20 — Ubiquitin-like (UB roll)
同源超家族 H-superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	157.719 Å
晶胞边长 b length_b	157.719 Å
晶胞边长 c length_c	243.195 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	120.00 °
晶胞分子数 Z z_pdb	36

空间群 space_group	P 65
空间群编号 int_tables_number	170
晶系 crystal_system	—

分辨率 resolution	2.900 Å
最低分辨率 resolution_low	39.700 Å
R 因子 r_factor	—
R_work r_work	0.2480
R_free r_free	0.2940

Crystal structure of AAA ATPase p97/VCP ND1 in complex with p47 C

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

1. 结构基本信息 1. Structure Basics

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

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. 实体与聚合体信息 (4)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 non-polymer

Entity 4 water

6. 折叠分类 (SCOP + CATH) 47 domains

SCOP 2.08 (21 domains)

CATH v4.4 (26 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)

fit	/app/data/saxs_computation/s3/1s3s/1s3s.fit
pddf	/app/data/pr_computation/s3/1s3s/1s3s.pr.out
profile	/app/data/saxs_computation/s3/1s3s/1s3s.dat