9go0

Cryo-EM structure of ShCas12k in complex with a sgRNA and a dsDNA target

Method: ELECTRON MICROSCOPY D_max: 109.5 Å Quality: EXCELLENT

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

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	9go0
沉积日期 deposition_date	2024-09-04
最后修订 last_revision	2025-09-17
结构标题 title	Cryo-EM structure of ShCas12k in complex with a sgRNA and a dsDNA target
关键词 keywords	Cas12k, sgRNA, target DNA, Protein-RNA-DNA complex, Tn7, DNA Binding Protein, Transposition, CRISPR; DNA BINDING PROTEIN
实验方法 method	ELECTRON MICROSCOPY

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

回转半径 Rg (Guinier) rg_guinier	34.93 Å
回转半径 Rg (电子) rg_electron	33.95 Å
零角强度 I(0) i0	572845000.00
分子量 molecular_weight	133180.0 kDa
排除体积 excluded_volume	140760 Å³
包络体积 envelope_volume	211450 Å³
水化壳体积 shell_volume	51468 Å³
包络直径 envelope_diameter	113.2 Å
壳层 Rg shell_rg	40.96 Å
包络 Rg envelope_rg	33.36 Å
形状 Rg shape_rg	33.86 Å
总 Rg total_rg	34.48 Å
总原子数 total_atoms	9014
残基数 n_residues	696
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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3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	109.5 Å
Rg (实空间) rg_real	34.78 Å
Rg 误差 (实空间) rg_real_error	0.62 Å
I(0) (实空间) i0_real	5.7280e+08
I(0) 误差 (实空间) i0_real_error	9.0140e+06
Rg (倒空间) rg_reciprocal	34.88 Å
I(0) (倒空间) i0_reciprocal	572900000.0000
解质量估计 total_estimate	0.9001
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	43.8 Å
偏度 Skewness skewness	0.178
峰度 Kurtosis kurtosis	-0.473
角度范围 angular_range	— – 0.2250 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	24350000.0000
实空间数据点数 n_real_points	46
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.933; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.910

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

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5. 实体与聚合体信息 (4)

Entity 1 polymer

描述 description	Cas12k
分子量 formula_weight	73421.8 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	9014

SNASQITIQARLISFESNRQQLWKLMADLNTPLINELLCQLGQHPDFEKWQQKGKLPSTVVSQLCQPLKTDPRFAGQPSRLYMSAIHIVDYIYKSWLAIQKRLQQQLDGKTRWLEMLNSDAELVELSGDTLEAIRVKAAEILAIAMPASESDSASPKGKKGKKEKKPSSSSPKRSLSKTLFDAYQETEDIKSRSAISYLLKNGCKLTDKEEDSEKFAKRRRQVEIQIQRLTEKLISRMPKGRDLTNAKWLETLLTATTTVAEDNAQAKRWQDILLTRSSSLPFPLVFETNEDMVWSKNQKGRLCVHFNGLSDLIFEVYCGNRQLHWFQRFLEDQQTKRKSKNQHSSGLFTLRNGHLVWLEGEGKGEPWNLHHLTLYCCVDNRLWTEEGTEIVRQEKADEITKFITNMKKKSDLSDTQQALIQRKQSTLTRINNSFERPSQPLYQGQSHILVGVSLGLEKPATVAVVDAIANKVLAYRSIKQLLGDNYELLNRQRRQQQYLSHERHKAQKNFSPNQFGASELGQHIDRLLAKAIVALARTYKAGSIVLPKLGDMREVVQSEIQAIAEQKFPGYIEGQQKYAKQYRVNVHRWSYGRLIQSIQSKAAQTGIVIEEGKQPIRGSPHDKAKELALSAYNLRLTRRS

来源 Source

来源生物 organism	Scytonema hofmannii
NCBI 分类编号 ncbi_taxonomy_id	34078
宿主生物 host_organism	Escherichia coli

Entity 2 polymer

描述 description	sgRNA
分子量 formula_weight	82376.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polyribonucleotide
链编号 strand_id	B

GGAUAUUAAUAGCGCCGCAAUUCAUGCUGCUUGCAGCCUCUGAAUUUUGUUAAAUGAGGGUUAGUUUGACUGUAUAAAUACAGUCUUGCUUUCUGACCCUGGUAGCUGCUCACCCUGAUGCUGCUGUCAAUAGACAGGAUAGGUGCGCUCCCAGCAAUAAGGGCGCGGAUGUACUGCUGUAGUGGCUACUGAAUCACCCCCGAUCAAGGGGGAACCCUAAAUGGGUUGAAAGGAGAAGUCAUUUAAUAAGGCCACU

Entity 3 polymer

描述 description	DNA target strand
分子量 formula_weight	15301.8 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polydeoxyribonucleotide
链编号 strand_id	C

GTTTAACAGTGGCCTTATTAAATGACTTCTCAACCTCCTACGTATCGTAG

Entity 4 polymer

描述 description	DNA non-target strand
分子量 formula_weight	15498.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polydeoxyribonucleotide
链编号 strand_id	D

CTACGATACGTAGGAGGTTGAGAAGTCATTTAATAAGGCCACTGTTAAAC

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7. 引用文献 (1)

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分辨率 resolution	3.04 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	138000

fit	/app/data/saxs_computation/go/9go0/9go0.fit
pddf	/app/data/pr_computation/go/9go0/9go0.pr.out
profile	/app/data/saxs_computation/go/9go0/9go0.dat

Cryo-EM structure of ShCas12k in complex with a sgRNA and a dsDNA target

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

冷冻电镜 EM 3D

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

Entity 3 polymer

聚合体 Polymer

Entity 4 polymer

聚合体 Polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)