8s9v

CRISPR-Cas type III-D effector complex bound to a self-target RNA in the pre-cleavage state

Method: ELECTRON MICROSCOPY D_max: 185.2 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

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8s9v
沉积日期 deposition_date	2023-03-30
结构标题 title	CRISPR-Cas type III-D effector complex bound to a self-target RNA in the pre-cleavage state
关键词 keywords	CRISPR, CRISPR-Cas, type III, complex, RNA, crRNA, RNA BINDING PROTEIN, RNA BINDING PROTEIN-RNA complex; RNA BINDING PROTEIN/RNA
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	52.55 Å
回转半径 Rg (电子) rg_electron	52.89 Å
零角强度 I(0) i0	1652370000.00
分子量 molecular_weight	322020.0 kDa
排除体积 excluded_volume	395810 Å³
包络体积 envelope_volume	532000 Å³
水化壳体积 shell_volume	86060 Å³
包络直径 envelope_diameter	187.2 Å
壳层 Rg shell_rg	53.40 Å
包络 Rg envelope_rg	52.58 Å
形状 Rg shape_rg	52.93 Å
总 Rg total_rg	52.77 Å
总原子数 total_atoms	22616
残基数 n_residues	2755
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	185.2 Å
Rg (实空间) rg_real	52.84 Å
Rg 误差 (实空间) rg_real_error	2.01 Å
I(0) (实空间) i0_real	1.6520e+09
I(0) 误差 (实空间) i0_real_error	3.5190e+07
Rg (倒空间) rg_reciprocal	52.29 Å
I(0) (倒空间) i0_reciprocal	1651000000.0000
解质量估计 total_estimate	0.8339
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	49.4 Å
偏度 Skewness skewness	0.480
峰度 Kurtosis kurtosis	-0.490
角度范围 angular_range	— – 0.1500 Å⁻¹
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	230400000.0000
实空间数据点数 n_real_points	31
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.693; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.950; Smooth: 0.808

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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 (9)

Entity 1 polymer

描述 description	Cas7-Cas5-Cas11
分子量 formula_weight	87558.9 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	22673

MRGIEITITMQSDWHVGTGMGRGELDSVVQRDGDNLPYIPGKTLTGILRDSCEQVALGLDNGQTRGLWHGWINFIFGDQPALAQGAIEPEPRPALIAIGSAHLDPKLKAAFQGKKQLQEAIAFMKPGVAIDAITGTAKKDFLRFEEVVRLGAKLTAEVELNLPDNLSETNKKVIAGILASGAKLTERLGGKRRRGNGRCELKFSGYSDQQIQWLKDNYQSVDQPPKYQQNKLQSAGDNPEQQPPWHIIPLTIKTLSPVVLPARTVGNVVECLDYIPGRYLLGYIHKTLGEYFDVSQAIAAGDLIITNATIKIDGKAGRATPFCLFGEKLDGGLGKGKGVYNRFQESEPDGIQLKGERGGYVGQFEQEQRNLPNTGKINSELFTHNTIQDDVQRPTSDVGGVYSYEAIIAGQTFVAELRLPDSLVKQITSKNKNWQAQLKATIRIGQSKKDQYGKIEVTSGNSADLPKPTGNNKTLSIWFLSDILLRGDRLNFNATPDDLKKYLENALDIKLKERSDNDLICIALRSQRTESWQVRWGLPRPSLVGWQAGSCLIYDIESGTVNAEKLQELMITGIGDRCTEGYGQIGFNDPLLSASLGKLTAKPKASNNQSQNSQSNPLPTNHPTQDYARLIEKAAWREAIQNKALALASSRAKREEILGIKIMGKDSQPTMTQLGGFRSVLKRLHSRNNRDIVTGYLTALEQVSNRKEKWSNTSQGLTKIRNLVTQENLIWNHLDIDFSPLTITQNGVNQLKSELWAEAVRTLVDAIIRGHKRDLEKAQENESNQQSQGAA

来源 Source

来源生物 organism	Synechocystis sp. PCC 6803
NCBI 分类编号 ncbi_taxonomy_id	1148
宿主生物 host_organism	Escherichia coli

Entity 2 polymer

描述 description	TIGR03984 family CRISPR-associated protein
分子量 formula_weight	21899.8 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	B

MPAGGRLMKNLYHYHQYEITLESAVDSCKNHLQAAIGLLYSPQKCELVKLDNSGKLVDSYNRLKFNNLGVFEARFFNLNCELRWVNESNGNGTAVLLSESDITLTGFEKGLQEFITAIDQQYLLWGEPAKHPPNADGWQRLAEARIGKLDIPLDNPLKPKDRVFLTSEEYIAEVDDFGNCAVIDERLIKLEVK

来源 Source

来源生物 organism	Synechocystis sp. PCC 6803
NCBI 分类编号 ncbi_taxonomy_id	1148
宿主生物 host_organism	Escherichia coli

Entity 3 polymer

描述 description	Cas10
分子量 formula_weight	64335.3 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	C

MAHHHHHHVGTENLYFQGFLVLIETSGNQHFIFSTNKLRENIGASELTYLATTEILFQGVDRVFQTNYYDQWSDTNSLNFLADSKLNPAIDDPKNNADIEILLATSGKAIALVKEEGKAKQLIKEVTKQALINAPGLEIGGIYVNCNWQDKLGVAKAVKEAHKQFEVNRAKRAGANGRFLRLPIAAGCSVSELPASDFDYNADGDKIPVSTVSKVKRETAKSAKKRLRSVDGRLVNDLAQLEKSFDELDWLAVVHADGNGLGQILLSLEKYIGEQTNRNYIDKYRRLSLALDNCTINAFKMAIAVFKEDSKKIDLPIVPLILGGDDLTVICRGDYALEFTREFLEAFEGQTETHDDIKVIAQKAFGVDRLSACAGISIIKPHFPFSVAYTLAERLIKSAKEVKQKVTVTNSSPITPFPCSAIDFHILYDSSGIDFDRIREKLRPEDNTELYNRPYVVTAAENLSQAQGYEWSQAHSLQTLADRVSYLRSEDGEGKSALPSSQSHALRTALYLEKNEADAQYSLISQRYKILKNFAEDGENKSLFHLENGKYVTRFLDALDAKDFFANANHKNQGE

来源 Source

来源生物 organism	Synechocystis sp. PCC 6803
NCBI 分类编号 ncbi_taxonomy_id	1148
宿主生物 host_organism	Escherichia coli

Entity 4 polymer

描述 description	Cas7-2x
分子量 formula_weight	56820.8 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	D

MARKVTTRWKITGTLIAETPLHIGGVGGDADTDLALAVNGAGEYYVPGTSLAGALRGWMTQLLNNDESQIKDLWGDHLDAKRGASFVIVDDAVIHIPNNADVEIREGVGIDRHFGTAANGFKYSRAVIPKGSKFKLPLTFDSQDDGLPNALIQLLCALEAGDIRLGAAKTRGLGRIKLDDLKLKSFALDKPEGIFSALLDQGKKLDWNQLKANVTYQSPPYLGISITWNPKDPVMVKAEGDGLAIDILPLVSQVGSDVRFVIPGSSIKGILRTQAERIIRTICQSNGSEKNFLEQLRINLVNELFGSASLSQKQNGKDIDLGKIGALAVNDCFSSLSMTPDQWKAVENATEMTGNLQPALKQATGYPNNISQAYKVLQPAMHVAVDRWTGGAAEGMLYSVLEPIGVTWEPIQVHLDIARLKNYYHGKEEKLKPAIALLLLVLRDLANKKIPVGYGTNRGMGTITVSQITLNGKALPTELEPLNKTMTCPNLTDLDEAFRQDLSTAWKEWIADPIDLCQQEAA

来源 Source

来源生物 organism	Synechocystis sp. PCC 6803
NCBI 分类编号 ncbi_taxonomy_id	1148
宿主生物 host_organism	Escherichia coli

Entity 5 polymer

描述 description	TIGR03986 family CRISPR-associated RAMP protein
分子量 formula_weight	90335.0 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	E

MTVGTLGVVGSAKNLKLQLSFINTRQQYVQITLFERNSFKVAEEEFSTELVEIIKTALPTLKNKKVEFEEDGDQIKQIREKGQAWVGAAEQIAPYVLPSGNITETPRNVNASNFHNPYNFVPALPRDGITGDLGDCAPAGHSYYHGDKYSGRIAVKLTTVTPLLIPDASKEEINNNHKTYPVRIGKDGKPYLPPTSIKGMLRSAYEAVTNSRLAVFEDHDSRLAYRMPATMGLQMVPARIEGDNIVLYPGTSRIGNNGRPANNDPMYAAWLPYYQNRIAYDGSRDYQMAEHGDHVRFWAERYTRGNFCYWRVRQIARHNQNLGNRPERGRNYGQHHSTGVIEQFEGFVYKTNKNIGNKHDERVFIIDRESIEIPLSRDLRRKWRELITSYQEIHKKEVDRGDTGPSAVNGAVWSRQIIADESERNLSDGTLCYAHVKKEDGQYKILNLYPVMITRGLYEIAPVDLLDETLKPATDKKQLSPADRVFGWVNQRGNGCYKGQLRIHSVTCQHDDAIDDFGNQNFSVPLAILGQPKPEQARFYCADDRKGIPLEDGYDRDDGYSDSEQGLRGRKVYPHHKGLPNGYWSNPTEDRSQQAIQGHYQEYRRPKKDGLEQRDDQNRSVKGWVKPLTEFTFEIDVTNLSEVELGALLWLLTLPDLHFHRLGGGKPLGFGSVRLDIDPDKTDLRNGAGWRDYYGSLLETSQPDFTTLISQWINAFQTAVKEEYGSSSFDQVTFIKASGQSLQGFHDNASIHYPRSTPEPKPDGEAFKWFVANEKGRRLALPALEKSQSFPIKPS

来源 Source

来源生物 organism	Synechocystis sp. PCC 6803
NCBI 分类编号 ncbi_taxonomy_id	1148
宿主生物 host_organism	Escherichia coli

Entity 6 polymer

描述 description	CRISPR RNA
分子量 formula_weight	11927.2 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polyribonucleotide
链编号 strand_id	F

ACUGAAACUGUAGUAGAACCAAUCGGGGUCGUCAAUA

来源 Source

来源生物 organism	Synechocystis sp. PCC 6803
NCBI 分类编号 ncbi_taxonomy_id	1148
宿主生物 host_organism	Escherichia coli

Entity 7 polymer

描述 description	Self-target RNA
分子量 formula_weight	19170.3 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	G

CAUGACGGAUCGCGGGAGUUAUUGACGACCCCGAUUGGUUCUACUACAGUUUCAGUCCCC

Entity 8 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	5

Entity 9 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	19

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7. 引用文献 (1)

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晶胞边长 a length_a	1.000 Å
晶胞边长 b length_b	1.000 Å
晶胞边长 c length_c	1.000 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	90.00 °
晶胞分子数 Z z_pdb	—

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

分辨率 resolution	3.00 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	181656

fit	/app/data/saxs_computation/s9/8s9v/8s9v.fit
pddf	/app/data/pr_computation/s9/8s9v/8s9v.pr.out
profile	/app/data/saxs_computation/s9/8s9v/8s9v.dat

CRISPR-Cas type III-D effector complex bound to a self-target RNA in the pre-cleavage state

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

冷冻电镜 EM 3D

5. 实体与聚合体信息 (9)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 polymer

聚合体 Polymer

来源 Source

Entity 4 polymer

聚合体 Polymer

来源 Source

Entity 5 polymer

聚合体 Polymer

来源 Source

Entity 6 polymer

聚合体 Polymer

来源 Source

Entity 7 polymer

聚合体 Polymer

Entity 8 non-polymer

Entity 9 water

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)