SAXSdb — 6f8d

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

Serrate RNA effector molecule homolog

Homo sapiens

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	蛋白同源多聚体同源多聚体蛋白 × 2 PDB 声明：dimeric（2）与蛋白拷贝数一致	链 A； UniProt 171–270 链 C； UniProt 408–763	未记录	无其他共同聚合物	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION, HANGING DROP；pH 10.5；277 K；Crystals of ARS2 were obtained at 4 C in 2 microlitre hanging drops with a 1:1 ratio of protein solution (6 mg/ml in 20 mM HEPES, 300 mM NaCl, 2 mM tris(2-carboxyethyl)phosphine pH 7.8) to crystallisation solution. The crystallisation solution was 1.2 M sodium dihydrogen phosphate, 0.8 M dipotassium hydrogen phosphate, 0.2 M lithium sulphate, 0.1 M CAPS pH 10.5	分辨率 3.48 Å R-free 0.292
2	蛋白同源多聚体同源多聚体蛋白 × 2 PDB 声明：dimeric（2）与蛋白拷贝数一致	链 B； UniProt 171–270 链 D； UniProt 408–763	未记录	无其他共同聚合物	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION, HANGING DROP；pH 10.5；277 K；Crystals of ARS2 were obtained at 4 C in 2 microlitre hanging drops with a 1:1 ratio of protein solution (6 mg/ml in 20 mM HEPES, 300 mM NaCl, 2 mM tris(2-carboxyethyl)phosphine pH 7.8) to crystallisation solution. The crystallisation solution was 1.2 M sodium dihydrogen phosphate, 0.8 M dipotassium hydrogen phosphate, 0.2 M lithium sulphate, 0.1 M CAPS pH 10.5	分辨率 3.48 Å R-free 0.292

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 6F8D	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
5OO6 Complex of human nuclear cap-binding complex with ARS2 C-terminal peptide 提交 2017-08-06	构建体不同突变/修饰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 × 3 PDB 声明：trimeric	链 C 827–871（45 aa）	未记录	MGT 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；CBC was mixed with an access of ARS2(827-871) in the presence of 1 mM m7GTP and subjected to gel filtration (120 mM NaCl, 5 mM beta-mercaptoethanol, 20 mM HEPES pH 7.8). The complex was concentrated to 8 mg/ml. Crystals were obtained in mother liquor containing 0.1 M sodium acetate pH 5, 8% (v/v) MPD and 0.1 M guanidine hydrochloride at 20 C.	分辨率 2.80 Å R-free 0.268
5OO6 Complex of human nuclear cap-binding complex with ARS2 C-terminal peptide 提交 2017-08-06	构建体不同突变/修饰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 2 蛋白异源复合物异源复合物；蛋白 × 3 PDB 声明：trimeric	链 F 827–871（45 aa）	未记录	MGT 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；CBC was mixed with an access of ARS2(827-871) in the presence of 1 mM m7GTP and subjected to gel filtration (120 mM NaCl, 5 mM beta-mercaptoethanol, 20 mM HEPES pH 7.8). The complex was concentrated to 8 mg/ml. Crystals were obtained in mother liquor containing 0.1 M sodium acetate pH 5, 8% (v/v) MPD and 0.1 M guanidine hydrochloride at 20 C.	分辨率 2.80 Å R-free 0.268
5OO6 Complex of human nuclear cap-binding complex with ARS2 C-terminal peptide 提交 2017-08-06	构建体不同突变/修饰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 3 蛋白异源复合物异源复合物；蛋白 × 3 PDB 声明：trimeric	链 I 827–871（45 aa）	未记录	MGT 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；CBC was mixed with an access of ARS2(827-871) in the presence of 1 mM m7GTP and subjected to gel filtration (120 mM NaCl, 5 mM beta-mercaptoethanol, 20 mM HEPES pH 7.8). The complex was concentrated to 8 mg/ml. Crystals were obtained in mother liquor containing 0.1 M sodium acetate pH 5, 8% (v/v) MPD and 0.1 M guanidine hydrochloride at 20 C.	分辨率 2.80 Å R-free 0.268
5OO6 Complex of human nuclear cap-binding complex with ARS2 C-terminal peptide 提交 2017-08-06	构建体不同突变/修饰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 4 蛋白异源复合物异源复合物；蛋白 × 3 PDB 声明：trimeric	链 L 827–871（45 aa）	未记录	MGT 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；CBC was mixed with an access of ARS2(827-871) in the presence of 1 mM m7GTP and subjected to gel filtration (120 mM NaCl, 5 mM beta-mercaptoethanol, 20 mM HEPES pH 7.8). The complex was concentrated to 8 mg/ml. Crystals were obtained in mother liquor containing 0.1 M sodium acetate pH 5, 8% (v/v) MPD and 0.1 M guanidine hydrochloride at 20 C.	分辨率 2.80 Å R-free 0.268
5OO6 Complex of human nuclear cap-binding complex with ARS2 C-terminal peptide 提交 2017-08-06	构建体不同突变/修饰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 5 蛋白异源复合物异源复合物；蛋白 × 3 PDB 声明：trimeric	链 O 827–871（45 aa）	未记录	MGT 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；CBC was mixed with an access of ARS2(827-871) in the presence of 1 mM m7GTP and subjected to gel filtration (120 mM NaCl, 5 mM beta-mercaptoethanol, 20 mM HEPES pH 7.8). The complex was concentrated to 8 mg/ml. Crystals were obtained in mother liquor containing 0.1 M sodium acetate pH 5, 8% (v/v) MPD and 0.1 M guanidine hydrochloride at 20 C.	分辨率 2.80 Å R-free 0.268
5OO6 Complex of human nuclear cap-binding complex with ARS2 C-terminal peptide 提交 2017-08-06	构建体不同突变/修饰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 6 蛋白异源复合物异源复合物；蛋白 × 3 PDB 声明：trimeric	链 R 827–871（45 aa）	未记录	MGT 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；CBC was mixed with an access of ARS2(827-871) in the presence of 1 mM m7GTP and subjected to gel filtration (120 mM NaCl, 5 mM beta-mercaptoethanol, 20 mM HEPES pH 7.8). The complex was concentrated to 8 mg/ml. Crystals were obtained in mother liquor containing 0.1 M sodium acetate pH 5, 8% (v/v) MPD and 0.1 M guanidine hydrochloride at 20 C.	分辨率 2.80 Å R-free 0.268
5OO6 Complex of human nuclear cap-binding complex with ARS2 C-terminal peptide 提交 2017-08-06	构建体不同突变/修饰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 7 蛋白异源复合物异源复合物；蛋白 × 3 PDB 声明：trimeric	链 U 827–871（45 aa）	未记录	MGT 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；CBC was mixed with an access of ARS2(827-871) in the presence of 1 mM m7GTP and subjected to gel filtration (120 mM NaCl, 5 mM beta-mercaptoethanol, 20 mM HEPES pH 7.8). The complex was concentrated to 8 mg/ml. Crystals were obtained in mother liquor containing 0.1 M sodium acetate pH 5, 8% (v/v) MPD and 0.1 M guanidine hydrochloride at 20 C.	分辨率 2.80 Å R-free 0.268
5OO6 Complex of human nuclear cap-binding complex with ARS2 C-terminal peptide 提交 2017-08-06	构建体不同突变/修饰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 8 蛋白异源复合物异源复合物；蛋白 × 3 PDB 声明：trimeric	链 X 827–871（45 aa）	未记录	MGT 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；CBC was mixed with an access of ARS2(827-871) in the presence of 1 mM m7GTP and subjected to gel filtration (120 mM NaCl, 5 mM beta-mercaptoethanol, 20 mM HEPES pH 7.8). The complex was concentrated to 8 mg/ml. Crystals were obtained in mother liquor containing 0.1 M sodium acetate pH 5, 8% (v/v) MPD and 0.1 M guanidine hydrochloride at 20 C.	分辨率 2.80 Å R-free 0.268
6F7J Crystal structure of Human ARS2 residues 171-270 + 408-763 提交 2017-12-10	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 × 2 PDB 声明：dimeric	链 A 171–270（100 aa）链 B 408–763（356 aa）	未记录	未记录非水小分子	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 10.5；281 K；Protein solution at 6 mg per ml in 20 mM HEPES, 300 mM NaCl, 2 mM tris(2-carboxyethyl)phosphine pH 7.8, mixed 1:1 with reservoir solution containing 1.2 M sodium dihydrogen phosphate, 0.8 M dipotassium hydrogen phosphate, 0.2 M lithium sulphate and 0.1 M CAPS pH 10.5.	分辨率 3.22 Å R-free 0.322
6F7P Crystal structure of Human ARS2 residues 147-270 + 408-763 提交 2017-12-11	构建体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 × 2 PDB 声明：dimeric	链 A 147–270（124 aa）链 C 408–763（356 aa）	未记录	未记录非水小分子	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 7.8；281 K；Crystals were obtained at 4 C in 2 microlitre hanging drops with a 1:1 ratio of protein solution at 6 mg per ml in 20 mM HEPES, 300 mM NaCl, 2 mM tris(2-carboxyethyl)phosphine pH 7.8) to crystallisation solution. The crystallisation solution was 0.2 M lithium sulphate and 20% (w/v) PEG 3550.	分辨率 3.70 Å R-free 0.309
6F7P Crystal structure of Human ARS2 residues 147-270 + 408-763 提交 2017-12-11	构建体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 × 2 PDB 声明：dimeric	链 B 147–270（124 aa）链 D 408–763（356 aa）	未记录	未记录非水小分子	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 7.8；281 K；Crystals were obtained at 4 C in 2 microlitre hanging drops with a 1:1 ratio of protein solution at 6 mg per ml in 20 mM HEPES, 300 mM NaCl, 2 mM tris(2-carboxyethyl)phosphine pH 7.8) to crystallisation solution. The crystallisation solution was 0.2 M lithium sulphate and 20% (w/v) PEG 3550.	分辨率 3.70 Å R-free 0.309
6F7S Crystal structure of Human ARS2 residues 147-270 + 408-763 with deletion of loop B 提交 2017-12-11	构建体不同突变/修饰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 × 2 PDB 声明：dimeric	链 A 147–270（124 aa）片段：UNP residues 147-270 链 C 408–567（160 aa）片段：UNP residues 408-567,UNP residues 599-763 链 C 599–763（165 aa）片段：UNP residues 408-567,UNP residues 599-763	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 8.3；281 K；Crystals of human ARS2 were obtained at 4 C in 2 microliter hanging drops with a 1:1 ratio of protein solution (6 mg per ml in 20 mM HEPES, 300 mM NaCl, 2 mM tris(2-carboxyethyl)phosphine, pH 7.8) to crystallisation solution. The crystallisation solution was 0.2 M potassium citrate tribasic monohydrate, 20 % (w/v) PEG 3350.	分辨率 3.37 Å R-free 0.303
6F7S Crystal structure of Human ARS2 residues 147-270 + 408-763 with deletion of loop B 提交 2017-12-11	构建体不同突变/修饰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 × 2 PDB 声明：dimeric	链 B 147–270（124 aa）片段：UNP residues 147-270 链 D 408–567（160 aa）片段：UNP residues 408-567,UNP residues 599-763 链 D 599–763（165 aa）片段：UNP residues 408-567,UNP residues 599-763	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 8.3；281 K；Crystals of human ARS2 were obtained at 4 C in 2 microliter hanging drops with a 1:1 ratio of protein solution (6 mg per ml in 20 mM HEPES, 300 mM NaCl, 2 mM tris(2-carboxyethyl)phosphine, pH 7.8) to crystallisation solution. The crystallisation solution was 0.2 M potassium citrate tribasic monohydrate, 20 % (w/v) PEG 3350.	分辨率 3.37 Å R-free 0.303
8PMP Structure of the human nuclear cap-binding complex bound to ARS2[147-871] and m7GTP 提交 2023-06-29	构建体不同突变/修饰不同聚集状态不同配体/离子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 D 148–876（729 aa）	未记录	MGT 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM缓冲液 pH 8 cryo-EM玻璃化条件冷冻剂 ETHANE	分辨率 3.43 Å

共 5 个其他 PDB 条目、14 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	SRRT_HUMAN
Isoform	Q9BXP5-4
PDB实体	1, 2
链与序列区间	作者链 A； PDB构建体 1–100； UniProt 171–270 作者链 B； PDB构建体 1–100； UniProt 171–270 作者链 C； PDB构建体 1–356； UniProt 408–763 作者链 D； PDB构建体 1–356； UniProt 408–763

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	6f8d
沉积日期 deposition_date	2017-12-13
结构标题 title	Crystal structure of Human ARS2 residues 171-270 + 408-763 (P65 form)
关键词 keywords	RNA BINDING PROTEIN; RNA BINDING PROTEIN
实验方法 method	X-RAY DIFFRACTION

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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	34.11 Å
回转半径 Rg (电子) rg_electron	33.83 Å
零角强度 I(0) i0	136905000.00
分子量 molecular_weight	92434.0 kDa
排除体积 excluded_volume	115750 Å³
包络体积 envelope_volume	165610 Å³
水化壳体积 shell_volume	41714 Å³
包络直径 envelope_diameter	150.1 Å
壳层 Rg shell_rg	39.13 Å
包络 Rg envelope_rg	34.21 Å
形状 Rg shape_rg	33.83 Å
总 Rg total_rg	34.27 Å
总原子数 total_atoms	6504
残基数 n_residues	782
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	143.7 Å
Rg (实空间) rg_real	34.19 Å
Rg 误差 (实空间) rg_real_error	2.07 Å
I(0) (实空间) i0_real	1.3690e+08
I(0) 误差 (实空间) i0_real_error	2.4680e+06
Rg (倒空间) rg_reciprocal	34.14 Å
I(0) (倒空间) i0_reciprocal	136900000.0000
解质量估计 total_estimate	0.7612
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	43.7 Å
偏度 Skewness skewness	0.516
峰度 Kurtosis kurtosis	0.376
角度范围 angular_range	— – 0.2300 Å⁻¹
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	24360000.0000
实空间数据点数 n_real_points	47
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.359; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.816; Smooth: 0.999

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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 (2)

实体 1 Entity 1 polymer

描述 description	Serrate RNA effector molecule homolog
分子量 formula_weight	12027.7 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	A,B
原子数 atom_count	6504

RYNDYKLDFRRQQMQDFFLAHKDEEWFRSKYHPDEVGKRRQEARGALQNRLRVFLSLMETGWFDNLLLDIDKADAIVKMLDAAVIKMEGGTENDLRILEQ

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	Escherichia coli BL21(DE3)

实体 2 Entity 2 polymer

描述 description	Serrate RNA effector molecule homolog
分子量 formula_weight	41169.2 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	C,D

GLECKPRPLHKTCSLFMRNIAPNISRAEIISLCKRYPGFMRVALSEPQPERRFFRRGWVTFDRSVNIKEICWNLQNIRLRECELSPGVNRDLTRRVRNINGITQHKQIVRNDIKLAAKLIHTLDDRTQLWASEPGTPPLPTSLPSQNPILKNITDYLIEEVSAEEEELLGSSGGAPPEEPPKEGNPAEINVERDEKLIKVLDKLLLYLRIVHSLDYYNTCEYPNEDEMPNRCGIIHVRGPMPPNRISHGEVLEWQKTFEEKLTPLLSVRESLSEEEAQKMGRKDPEQEVEKFVTSNTQELGKDKWLCPLSGKKFKGPEFVRKHIFNKHAEKIEEVKKEVAFFNNFLTDAKRPALPE

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	Escherichia coli BL21(DE3)

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8. 引用文献 (1)

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晶胞边长 a length_a	105.210 Å
晶胞边长 b length_b	105.210 Å
晶胞边长 c length_c	267.040 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	12

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

分辨率 resolution	3.480 Å
最低分辨率 resolution_low	91.110 Å
R 因子 r_factor	0.2654
R_work r_work	0.2641
R_free r_free	0.2922

fit	/app/data/saxs_computation/f8/6f8d/6f8d.fit
pddf	/app/data/pr_computation/f8/6f8d/6f8d.pr.out
profile	/app/data/saxs_computation/f8/6f8d/6f8d.dat

Crystal structure of Human ARS2 residues 171-270 + 408-763 (P65 form)

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

Serrate RNA effector molecule homolog

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

精修参数 Refinement

衍射实验 Diffraction

6. 实体与聚合物信息 Entities & Polymers (2)

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

8. 引用文献 (1)

9. 文件与曲线 (10)

Files (7)

Curves (3)