9n9q

Cryo-EM structure of the RNA-guided transcription complex

Method: ELECTRON MICROSCOPY D_max: 210.5 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	9n9q
沉积日期 deposition_date	2025-02-11
结构标题 title	Cryo-EM structure of the RNA-guided transcription complex
关键词 keywords	dCas12f, partial R-Loop, RNA BINDING PROTEIN, RNA BINDING PROTEIN-DNA-RNA complex; RNA BINDING PROTEIN/DNA/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	61.09 Å
回转半径 Rg (电子) rg_electron	60.27 Å
零角强度 I(0) i0	4747730000.00
分子量 molecular_weight	544310.0 kDa
排除体积 excluded_volume	666750 Å³
包络体积 envelope_volume	1040500 Å³
水化壳体积 shell_volume	141030 Å³
包络直径 envelope_diameter	209.5 Å
壳层 Rg shell_rg	63.87 Å
包络 Rg envelope_rg	59.53 Å
形状 Rg shape_rg	60.23 Å
总 Rg total_rg	60.48 Å
总原子数 total_atoms	38028
残基数 n_residues	4446
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	210.5 Å
Rg (实空间) rg_real	61.05 Å
Rg 误差 (实空间) rg_real_error	1.65 Å
I(0) (实空间) i0_real	4.7480e+09
I(0) 误差 (实空间) i0_real_error	1.0600e+08
Rg (倒空间) rg_reciprocal	61.10 Å
I(0) (倒空间) i0_reciprocal	4748000000.0000
解质量估计 total_estimate	0.8729
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	64.8 Å
偏度 Skewness skewness	0.288
峰度 Kurtosis kurtosis	-0.516
角度范围 angular_range	— – 0.1300 Å⁻¹
当前正则化参数 α current_alpha	0.0009
最高正则化参数 α highest_alpha	780200000.0000
实空间数据点数 n_real_points	27
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.836; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.853

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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 (11)

Entity 1 polymer

描述 description	Nuclease-deactivated Cas12f
分子量 formula_weight	42913.3 kDa
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	38028

MGKSTLKHTRKIQILIDLPTKDEKKEVMDMMYQWRDRCFRAANIIVTHLYVQEMIKDFFYLSEGIKYKLADEKKDEKGILQRSRMNTTYRVVSDRFKGEMPTNILSTLNHGLISSFNKNRVQYWKGERSLPNFKKDMAFPFGLQGISRLVYDEEKKAFCFRLYRVPFKTYLGKDFTDKRMLLERLVKGDVKLCASNIQLNGGKIFWLAVFEIEKEKHSLKPEVIAEASLSLEYPIVVKTGKNRLTIGTKEEFLYRRLAIQAARRRTQVGATYSRSGKGKKRKLKAVDKYHKTESNYVAHRIHVYSRKLIDFCIKHQAGTLILMNQEDKVGIAKEEEFVLRNWSYYELMTKIKYKAEKAGIELIIG

来源 Source

来源生物 organism	Flagellimonas taeanensis
NCBI 分类编号 ncbi_taxonomy_id	1005926
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

描述 description	RpoE
分子量 formula_weight	31011.5 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

MLYSDFELLKIGDTSALDHIHAKYFRSILWIGRQWLNDDFLIESLVQDTFLKLWVNRDKLESPEHIFYFLRFVMKRECISYYRKPKYKFHKKVNSLEDYDNYQDYMVGYDPVNDSENLDEQESTQKSFDHIKSILPLLNADKRHLIELCLKYGFQYKAISKVMGKGIHETSREIKEAIEDIKTIVHKGNELGSNDTMTNEIKFSGELSEEQAKVLKMRCDLKYSFSEIAKELELSEKEVHQEFMKAYKLMKANHQLQLQSA

来源 Source

来源生物 organism	Flagellimonas taeanensis
NCBI 分类编号 ncbi_taxonomy_id	1005926
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 3 polymer

描述 description	DNA-directed RNA polymerase subunit alpha
分子量 formula_weight	37228.6 kDa
EC 编号 ec_number	2.7.7.6
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	D,E

MALLNFQKPDKVIMIDSTDFEGKFEFRPLEPGYGLTVGNALRRVLLSSLEGFAITSVRIDGVEHEFSVVPGVVEDVTEIILNLKQVRFKRQIDDVESETVSISVSGKEQLTAGDFQKFISGYQVLNPDLVICNMGPKVSINMEIVIEKGRGYVPAEENKKSNAPLGSIAVDSVYTPVKNVKYSIENYRVEQKTDYEKLVFEIITDGSIHPKDALTEAAKVLIHHFMLFSDERITLEADEIAQTETYDEESLHMRQLLKTKLVDMDLSVRALNCLKAAEVDTLGDLVSFNKNDLMKFRNFGKKSLTELEELVINKGLQFGMDLSKYKLDKD

来源 Source

来源生物 organism	Flagellimonas taeanensis
NCBI 分类编号 ncbi_taxonomy_id	1005926
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 4 polymer

描述 description	DNA-directed RNA polymerase subunit beta
分子量 formula_weight	142961.4 kDa
EC 编号 ec_number	2.7.7.6
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	F

MFTNTIERVNFASAKNIPEYPDFLDIQIKSFQDFFQLETKSDERGNEGLYNTFMENFPITDTRNQFVLEFLDYFIDPPRYSIQECIERGLTYSVPLKARLKLYCTDPEHEDFETIVQDVYLGTIPYMTPSGTFVINGAERVVVSQLHRSPGVFFGQSFHANGTKLYSARVIPFKGSWIEFATDINGVMYAYIDRKKKLPVTTLFRAIGFERDKDILEIFDLSEEVKVSKAGLKKVLGRKLAARVLNTWHEDFVDEDTGEVVSIERNEIILDRDTILEKEHIDEIIDADVKTILLHKENNAQSDYAIIHNTLQKDPTNSEKEAVEHIYRQLRNAEPPDEETARGIIEKLFFSDQRYSLGEVGRYRMNKKLGLDIGMDKEVLTKEDIITIIKYLIELINSKAEIDDIDHLSNRRVRTVGEQLSQQFGVGLARMARTIRERMNVRDNEVFTPIDLINAKTLSSVINSFFGTNQLSQFMDQTNPLAEITHKRRLSALGPGGLSRERAGFEVRDVHYTHYGRLCPIETPEGPNIGLISSLSVFAKVNSMGFLETPYRKVVDGKVDVKEHIYLSAEEEEGMKIAQANIPLKDDGTIDREKVIARDEGDFPVVDPVEINYTDVAPNQIASISASLIPFLEHDDANRALMGSNMMRQAVPLLRPESPIVGTGLERQVATDSRVLINAEGDGVVEYVDAQKITIKYDRTEEERLVSFEEDSKTYELVKFRKTNQGTSINLKPIVRKGDKVKKGQVLCEGYATEKGELALGRNMKVAFMPWKGYNFEDAIVISEKVVREDIFTSVHIDEYALEVRDTKLGAEELTNDIPNVSEEATRDLDEYGMIRIGAEVKPGDILIGKITPKGESDPTPEEKLLRAIFGDKAGDVKDASLKASPSLRGVVIDKKLFSRSIKDKRKRSEDKEAISRLEMDYEVKFQQLKDVLIEKLFGLVNGKTSQGVINDLGEEVLPKGKKYTIKMLNAVDDFAHLVGGSWTTDEDTNALVADLLHNYKIKLNDIQGNLRRDKFTISVGDELPAGIMKLAKVYIAKKRKLKVGDKMAGRHGNKGIVARIVRQEDMPFLEDGTPVDIVLNPLGVPSRMNIGQIYETVLGWAGLKLGQKYGTPIFDGATLDDINELTDKAGVPRFGHTYLYDGGTGQRFDQAATVGVIYMLKLGHMVDDKMHARSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGASATLREILTVKSDDVIGRAKTYESIVKGETMPEPGLPESFNVLMHELKGLGLDIRLEE

来源 Source

来源生物 organism	Flagellimonas taeanensis
NCBI 分类编号 ncbi_taxonomy_id	1005926
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 5 polymer

描述 description	;DNA-directed RNA polymerase subunit beta' ;
分子量 formula_weight	160063.4 kDa
EC 编号 ec_number	2.7.7.6
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	G

MARIKDNNAPKRFNKISIGLASPESILAESRGEVLKPETINYRTHKPERDGLFCERIFGPVKDYECACGKYKRIRYRGIVCDRCGVEVTEKKVRRDRVGHINLVVPVAHIWYFRSLPNKIGYLLGLPSKKLDMIIYYERYVVIQPGIAKGPEGEEIHKLDFLTEEEYLNILESLPSENQYLEENDPNKFIAKMGAECLIDLLARIDLEQLSYELRHKANTETSKQRKTEALKRLQVVEALRESQDNRENNPEWMIMKVIPVIPPELRPLVPLDGGRFATSDLNDLYRRVIIRNNRLKRLMEIKAPEVILRNEKRMLQEAVDSLFDNTRKASAVKTESNRPLKSLSDSLKGKQGRFRQNLLGKRVDYSARSVIVVGPEMKLYECGLPKDMAAELYKPFIIRKLIERGIVKTVKSAKKIIDKKEPVVWDILENVLKGHPVLLNRAPTLHRLGIQAFQPKLIEGKAIRLHPLACTAFNADFDGDQMAVHLPLGPEAILEAQLLMLASQNILNPANGSPITVPSQDMVLGLYYMTKEKRSTPEEPVIGEGLTFYSSEEVEIAFNERKVALNAIIKVRTKDFNEAGELVNKIIETTVGRVLFNTVVPEQAGYINTVLNKKSLRNIIGDILAVTDVPTTADFLDKIKTMGYEFAFKGGLSFSLGDIIIPKEKHEMIAEANEQVDGIMMNYNMGLITFNERYNQVIDVWTSTNAMLTELAMKRIREDKQGFNSVYMMLDSGARGSKEQIRQLTGMRGLMAKPKKSTAGGGEIIENPILSNFKEGLSILEYFISTHGARKGLADTALKTADAGYLTRRLVDVSQDVIINTEDCGTLRGIEVEALKKNEEVVETLGERILGRVSLHDVYNPLTEELILKAGQEISEADVKKVEAAPIEKVEVRSPLTCEAAQGICAKCYGRNLATNKMVQRGEAVGVVAAQSIGEPGTQLTLRTFHVGGIAGNISEDSKLEAKFDGIAEIEDLRVVEGVDNGGGKSDIVISRTSEIKIVDAKTGITLSTNNIPYGSQLFVKNGEKITKGTVICQWDPYNGVIVSEFTGQIAYENIEQGMTYQVEIDEQTGFQEKVISESRNKRLIPTLLIKDGKGETIRSYNLPVGSHLMVDNGEKIKEGKILVKIPRKSAKAGDITGGLPRVTELFEARNPSNPAVVTEIDGVVSFGKIKRGNREIIIESKAGEVKKYLVKLSNQILVQENDYVRAGMALSDGSITPEDILAIKGPSAVQQYLVNEVQEVYRLQGVKINDKHFEVVVRQMMRKVQIQDSGDTTFLENQLVHKDDFINENDEIFGKKVVEDAGDSERLKPGQIVTARQLRDENSILRREDKTLVTARDAVAATATPILQGITRASLQTKSFISAASFQETTKVLNEAAVNGKVDTLEGLKENVIVGHKIPAGTGMRDYDSIIVGSKEEYDEIMARKEEFKF

来源 Source

来源生物 organism	Flagellimonas taeanensis
NCBI 分类编号 ncbi_taxonomy_id	1005926
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 6 polymer

描述 description	RNA polymerase Rpb6
分子量 formula_weight	12565.0 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	H

MQDLKNTKAPVSTATLNRNEFDSKTGNIYEAISIASKRAVQINSDIKKELLEKLEEFATYSDSLEEVFENKEQIEVSKFYEKLPKPHALAVQEWLEDKIYYRNTEKDA

来源 Source

来源生物 organism	Flagellimonas taeanensis
NCBI 分类编号 ncbi_taxonomy_id	1005926
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 7 polymer

描述 description	DNA non-template strand
分子量 formula_weight	30316.4 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	a

CTAGCGTTGTGGGATACCCGTTACACTAATTTTTCGGTTCACGATATCCTTTAGTCCCACAACTAACGACTACACTTTTTGGGTGACCGACCCAACACG

Entity 8 polymer

描述 description	DNA template strand
分子量 formula_weight	30761.7 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	b

CGTGTTGGGTCGGTCACCCAAAAAGTGTAGTCGTTAGTTGTGGGACTAAAGGATATCGTGAACCGAAAAATTAGTGTAACGGGTATCCCACAACGCTAG

Entity 9 polymer

描述 description	gRNA (85-MER)
分子量 formula_weight	29922.8 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polyribonucleotide
链编号 strand_id	c

AUUUUGAGGGUGCUUGUACACCCAUAGGGUGAGGUUAAGAAUUACACUCACUAAGUGUGAACAACACAUACAACUUGUGGGAUAUACGCUAAC

来源 Source

来源生物 organism	Flagellimonas taeanensis
NCBI 分类编号 ncbi_taxonomy_id	1005926
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 10 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	1

Entity 11 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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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	2.880 Å
最低分辨率 resolution_low	— Å
R 因子 r_factor	—
R_work r_work	—
R_free r_free	—

分辨率 resolution	2.88 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	54193

fit	/app/data/saxs_computation/n9/9n9q/9n9q.fit
pddf	/app/data/pr_computation/n9/9n9q/9n9q.pr.out
profile	/app/data/saxs_computation/n9/9n9q/9n9q.dat

Cryo-EM structure of the RNA-guided transcription complex

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

冷冻电镜 EM 3D

5. 实体与聚合体信息 (11)

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 polymer

聚合体 Polymer

Entity 9 polymer

聚合体 Polymer

来源 Source

Entity 10 non-polymer

Entity 11 non-polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)