9yai

KIF1A R350W bound to microtubules in two-heads-bound state with AMP-PNP

Method: ELECTRON MICROSCOPY Dmax: 188.3 Å Quality: GOOD

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

Kinesin-like protein KIF1A

Homo sapiens

UniProt Q12756

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 × 6 PDB 声明:hexameric(6) 与蛋白拷贝数一致 链 K; UniProt 1–393 链 N; UniProt 1–393 突变:R350W Tubulin alpha-1B chain × 2 (Q2XVP4) Tubulin beta-2B chain × 2 (A0A287AGU7) MG MAGNESIUM ION × 3 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 2 TA1 TAXOL × 2 ELECTRON MICROSCOPY cryo-EM缓冲液:pH 6.8;BRB80 buffer composed of 80 mM PIPES, 2 mM MgCl2, 1 mM EGTA, PH 6.8 cryo-EM玻璃化条件:冷冻剂 ETHANE;4uL of a 6uM MT solution in BRB80 (80mM PIPES, 2mM MgCl2, 1mM EGTA pH 6.8) along with 20uM paclitaxel was added onto a plasma-cleaned grid. The MTs were incubated for 1 minute at room temperature, and then the excess liquid was removed from the grid using Whatman #1 paper. Next, 4uL of a solution containing 17.5uM KIF1A-R350W in BRB80 supplemented with 20uM paclitaxel and 5mM AMP-PNP was added to the grid. The grid with the MT and kinesin mixture was then mounted into a Vitrobot, incubated for 1 minute at room temperature, and plunge-frozen into liquid nitrogen-cooled ethane. 分辨率 3.12 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。

共 20 个其他 PDB 条目、24 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 KIF1A_HUMAN
Isoform
PDB实体 1
链与序列区间 作者链 K; PDB构建体 1–393; UniProt 1–393 作者链 N; PDB构建体 1–393; UniProt 1–393

Tubulin alpha-1B chain

物种未注明

UniProt Q2XVP4

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 × 6 PDB 声明:hexameric(6) 与蛋白拷贝数一致 链 A; UniProt 1–451 链 E; UniProt 1–451 未记录 Kinesin-like protein KIF1A × 2 (Q12756) Tubulin beta-2B chain × 2 (A0A287AGU7) MG MAGNESIUM ION × 3 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 2 TA1 TAXOL × 2 ELECTRON MICROSCOPY cryo-EM缓冲液:pH 6.8;BRB80 buffer composed of 80 mM PIPES, 2 mM MgCl2, 1 mM EGTA, PH 6.8 cryo-EM玻璃化条件:冷冻剂 ETHANE;4uL of a 6uM MT solution in BRB80 (80mM PIPES, 2mM MgCl2, 1mM EGTA pH 6.8) along with 20uM paclitaxel was added onto a plasma-cleaned grid. The MTs were incubated for 1 minute at room temperature, and then the excess liquid was removed from the grid using Whatman #1 paper. Next, 4uL of a solution containing 17.5uM KIF1A-R350W in BRB80 supplemented with 20uM paclitaxel and 5mM AMP-PNP was added to the grid. The grid with the MT and kinesin mixture was then mounted into a Vitrobot, incubated for 1 minute at room temperature, and plunge-frozen into liquid nitrogen-cooled ethane. 分辨率 3.12 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。

共 230 个其他 PDB 条目、243 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 TBA1B_PIG
Isoform
PDB实体 2
链与序列区间 作者链 A; PDB构建体 1–451; UniProt 1–451 作者链 E; PDB构建体 1–451; UniProt 1–451

Tubulin beta-2B chain

物种未注明

UniProt A0A287AGU7

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 × 6 PDB 声明:hexameric(6) 与蛋白拷贝数一致 链 B; UniProt 1–445 链 I; UniProt 1–445 未记录 Kinesin-like protein KIF1A × 2 (Q12756) Tubulin alpha-1B chain × 2 (Q2XVP4) MG MAGNESIUM ION × 3 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 2 TA1 TAXOL × 2 ELECTRON MICROSCOPY cryo-EM缓冲液:pH 6.8;BRB80 buffer composed of 80 mM PIPES, 2 mM MgCl2, 1 mM EGTA, PH 6.8 cryo-EM玻璃化条件:冷冻剂 ETHANE;4uL of a 6uM MT solution in BRB80 (80mM PIPES, 2mM MgCl2, 1mM EGTA pH 6.8) along with 20uM paclitaxel was added onto a plasma-cleaned grid. The MTs were incubated for 1 minute at room temperature, and then the excess liquid was removed from the grid using Whatman #1 paper. Next, 4uL of a solution containing 17.5uM KIF1A-R350W in BRB80 supplemented with 20uM paclitaxel and 5mM AMP-PNP was added to the grid. The grid with the MT and kinesin mixture was then mounted into a Vitrobot, incubated for 1 minute at room temperature, and plunge-frozen into liquid nitrogen-cooled ethane. 分辨率 3.12 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。

共 98 个其他 PDB 条目、98 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 A0A287AGU7_PIG
Isoform
PDB实体 3
链与序列区间 作者链 B; PDB构建体 1–445; UniProt 1–445 作者链 I; PDB构建体 1–445; UniProt 1–445

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。

SAXS 散射曲线 SAXS Profile

SAXS profile for 9yai

P(r) 距离分布 P(r) Distribution

P(r) distribution for 9yai
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2. 结构基本信息 2. Structure Basics

条目编号 entry_id9yai
沉积日期 deposition_date2025-09-16
结构标题 titleKIF1A R350W bound to microtubules in two-heads-bound state with AMP-PNP
关键词 keywordsKIF1A, Kinesin-3 superfamily, KIF1A R350W mutant, motor domain, AMP-PNP bound, cargo transport, MOTOR PROTEIN; MOTOR PROTEIN
实验方法 methodELECTRON MICROSCOPY

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

回转半径 Rg (Guinier) rg_guinier52.47
回转半径 Rg (电子) rg_electron52.78
零角强度 I(0) i01220180000.00
分子量 molecular_weight281670.0 kDa
排除体积 excluded_volume348290 ų
包络体积 envelope_volume465500 ų
水化壳体积 shell_volume76374 ų
包络直径 envelope_diameter194.0
壳层 Rg shell_rg52.32
包络 Rg envelope_rg52.44
形状 Rg shape_rg52.78
总 Rg total_rg52.74
总原子数 total_atoms19749
残基数 n_residues2478
球谐函数阶数 n_harmonics20
q 范围 q_range— – 0.5000 −1
数据点数 n_points101
壳层类型 shell_typedirectional
溶剂电子密度 solvent_density0.3340 e/ų
壳层衬度 contrast_shell0.0300 e/ų
CRYSOL 版本 crysol_version4.1.3

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

最大尺寸 Dmax dmax188.3
Rg (实空间) rg_real52.82
Rg 误差 (实空间) rg_real_error2.70
I(0) (实空间) i0_real1.2200e+09
I(0) 误差 (实空间) i0_real_error2.7060e+07
Rg (倒空间) rg_reciprocal52.17
I(0) (倒空间) i0_reciprocal1219000000.0000
解质量估计 total_estimate0.8252
解质量评级 solution_quality GOOD a GOOD solution
P(r) 峰数 n_peaks2
主峰位置 r_peak_primary50.2
偏度 Skewness skewness0.505
峰度 Kurtosis kurtosis-0.414
角度范围 angular_range— – 0.1500 −1
当前正则化参数 α current_alpha0.0000
最高正则化参数 α highest_alpha154600000.0000
实空间数据点数 n_real_points31
GNOM 版本 gnom_version4.1.3
质量判据 quality_criteria AN1: 0.000; Oscil: 0.679; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.904; Smooth: 0.783

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

6. 实体与聚合物信息 Entities & Polymers (8)

8. 引用文献 (1)

9. 文件与曲线 (10)