8fnc

Cryo-EM structure of RNase-treated RESC-C in trypanosomal RNA editing

Method: ELECTRON MICROSCOPY D_max: 127.8 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	8fnc
沉积日期 deposition_date	2022-12-27
结构标题 title	Cryo-EM structure of RNase-treated RESC-C in trypanosomal RNA editing
关键词 keywords	HEAT repeat, trypanosoma, RNA editing substrate binding complex, gRNA, 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	40.91 Å
回转半径 Rg (电子) rg_electron	40.48 Å
零角强度 I(0) i0	928160000.00
分子量 molecular_weight	243060.0 kDa
排除体积 excluded_volume	301050 Å³
包络体积 envelope_volume	404860 Å³
水化壳体积 shell_volume	79652 Å³
包络直径 envelope_diameter	136.4 Å
壳层 Rg shell_rg	48.96 Å
包络 Rg envelope_rg	39.90 Å
形状 Rg shape_rg	40.52 Å
总 Rg total_rg	40.76 Å
总原子数 total_atoms	17017
残基数 n_residues	2098
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	127.8 Å
Rg (实空间) rg_real	40.71 Å
Rg 误差 (实空间) rg_real_error	1.07 Å
I(0) (实空间) i0_real	9.2820e+08
I(0) 误差 (实空间) i0_real_error	1.7330e+07
Rg (倒空间) rg_reciprocal	40.90 Å
I(0) (倒空间) i0_reciprocal	928300000.0000
解质量估计 total_estimate	0.8940
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	52.5 Å
偏度 Skewness skewness	0.158
峰度 Kurtosis kurtosis	-0.448
角度范围 angular_range	— – 0.1950 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	130100000.0000
实空间数据点数 n_real_points	40
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.900; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.940

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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 (8)

Entity 1 polymer

描述 description	mRNA
分子量 formula_weight	5507.4 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polyribonucleotide
链编号 strand_id	m
原子数 atom_count	17017

UAAUAGAAUAAGAUAAG

Entity 2 polymer

描述 description	gRNA
分子量 formula_weight	4968.9 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polyribonucleotide
链编号 strand_id	g

UUUUUUUAAAUAAUUU

Entity 3 polymer

描述 description	Mitochondrial RNA binding protein
分子量 formula_weight	34727.5 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	5

MLRHTSRNNALHAFVRSPHYRTIPSAGPNGIVVNRDMLVHQFRDFYKTLQHCSLVDKVHLMSERPSVEALRVADQMVSIGATFLEMPLTGMEHRATEFMESMRYVRGAGGPSTLASYLQDTENCRCNSGDVVCLPNGIAVGHGPRTNAVAHTTLKQLFEVKDDQFSFDVFTLEQEGDAPPLGDYFGFAGSNVLLTWKDEHGLLAVDQYQQKQPHTEMNVVYLEPGCHFLSFYGVDHTIDVLVQKGYERSMDSIAAAGLNPIPVQWSEMDKLGISMRAAVLPLKFFKANVGGMLSRNKSRGARWQTHQLQK

Entity 4 polymer

描述 description	RAP domain-containing protein
分子量 formula_weight	57823.5 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	6

MRSALRRCILRHQGCLRMKQSLSAFPTVVTGMTRHQGNSLIGTTHGAELSLAGDPQSVSHLSARNIATEALQMKKLHQERGGNPMLAQQARRVLFATSIAGQNLDARSVALLLNTAVYFGMESDAKLVRECIDYCLKNDKLITVDVLPIVVTACATLKSRDAREVIEMQAQKAARNAKFLDAKDVTNIISAFSKTGINHEKLFAFLSRRVQTLARVGEFEAAHLVILANAFSRLRYRDKFLFGAIARRAMSLRERVTVNELVPLIVAFSKIGLKDPKLSKRFATKAMEYVDQMNAEQVASMFMAFAYFGIRYDQLFGVLTNRAVELIDEFNAQYISTTLNAFQRIGINNPELFDNLAERALAVVQDHDARDISKTVTALAHFGLKDEELFKRLASHAASIADQFDAMGLVNTAHAFARTNFLQQDMAVALSERSVYVCRLLDAGETRRLLWALAKFQVRDPKILTPVFNRCLALHYDFFADPTGSEEIEEIFDFYGPNFCPPLYQLYISRGSTPQA

Entity 5 polymer

描述 description	RxLR effector protein
分子量 formula_weight	18669.7 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	7

MRSSRGILFLSGAFAIRGMSAYHSYQRLDTVSHTSKVYSLQMQRQTVHFTPITRLGVEATANPTTATNATGQTGDGDGATALDVAMRVNKLKRLHQTGGGPSGKKQVELDAWRDLNNLTEAQINSAEGKAVSLLLNSWAYFAKYWEKGAEGPSASLSEVTPSNDSSSAGEHGTQ

Entity 6 polymer

描述 description	Mitochondrial RNA binding complex 1 subunit
分子量 formula_weight	61109.8 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	8

MLNVLSSTASAALATVVVARPSALHLIFERCKLNLVEFTAQDVYQICTTAYNMDTLGMLQDPDFMRGLHDAFRRSDQTVISPFQANLIADTFRKVGINSMPKEVSVPEEDAISPESLILVLRNMNITKQRDERKINEVLKLMFPILDEFSPTQLSLTVTELARLKSTNADFVGKLAKRIMEYNDDLSALDISSAAVSLAYCPGISHNILYRMMQIVEERMGEFQPEDYINVLHALNTLGPKFVNTFRKIVECGLQHVENMDAVTLTNYMVCFSTMDYKQREHIDIYADALVEVATDLSEKDLVMAFIALQRLRLLSDTMFGTMASCVIRYAAKMDPRNIAPIMDICSTVPHASDHLMKVLMDRAVECTRILTANQLGDILDILGLYPPAREHPLVQLFGKQARLRLDLMGPDALANATRGLANLGYADPEYYAQAAETGFRYGFKDWTLLEPMLMGLSITGQCPPTMVRVLGSHIAPMARSMSLMEIERANRYLRRLGCEDDFVYKAMASRVLQFVKEVTPEMPEDLQVLLQRGAVEPGAAPGVM

Entity 7 polymer

描述 description	RAP domain-containing protein
分子量 formula_weight	60563.7 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	10

MRRRVVLCCQDVGSLLSSKHSVHSGIGYHERVFSRNLLYRRYPVVTVLPKAGFTVLDTKRWIASSGPPVTGSPLSPVTNPSLNVGTGGGEAVAMEGPLPVSYSPGSGVNGSLPVTSTAITAHCDVLSECVAKADELAVQLKAQNALSASAEILTQEGMEEFVEELKTSATNEMTALVKQMQTTPLLQRAGMHELRRTLYYTTSLKERDWLEEKQYTAAMRMLTVEVLRRDGDGVLSADDVLYVTTHVVTANFYNRHLWNRMEKSLLKFSNYENIDMSSVKAFSTRLFKTRRGCAKETLDIRRKVLLAMSRRVGVLANDFDLPSLLGVLQCYTVHDLTPFHLEPLAIRATNHVGDFTPHECATLAHVLRKWRTMRLEVCERLVERICTSDQLTHHMANAAMIAIRTCFNQVSDGGRNAMNAEPTRQKLRAMGEQIGCRLDEVEYPALPVILSILDVVVTLKIYVPKKCLQVIFSQANDMVAIVMEQKDDLVDPKTGKRVRPITAEEGRQLQALLSHYGNDLAPELSQRMKEAFREGVLPDEASL

Entity 8 polymer

描述 description	Phytanoyl-CoA dioxygenase family protein
分子量 formula_weight	41293.1 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	14

MRSGRKLGCFTNRLRLPFFSPCSQITALTASHRCKSYVLKFLRGQLPEDLKDVNGALGCLYGTLPDVDEFGQFVISPDVVNSFHQFGYVKMPIPVLDHQQIDKLADEVNELANNVEHHPKTERLYATSLADLTGGPLFFCQGQWRAAWGMHDLIYLPTITVAASQILNNSLVRLWYDEVFMKAARTGPCVPWQQNYARWQHTKPVNHVTVMIALDTMNKDRGAPCLVPGSHRWREGGLLPPVSYDPTKDEAHQLNTIWEIINEEEGEMLMDTPPVTVDLRRGEALLIHPLTLFATHGNRSLDAVRCCFIHYMGEKTYAVQNGPLLPHTTKFQADAMIQGPFYPVVFDPAMTEELTMLPTAPSEEEA

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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	3.30 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	414524

fit	/app/data/saxs_computation/fn/8fnc/8fnc.fit
pddf	/app/data/pr_computation/fn/8fnc/8fnc.pr.out
profile	/app/data/saxs_computation/fn/8fnc/8fnc.dat

Cryo-EM structure of RNase-treated RESC-C in trypanosomal RNA editing

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 (8)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

Entity 3 polymer

聚合体 Polymer

Entity 4 polymer

聚合体 Polymer

Entity 5 polymer

聚合体 Polymer

Entity 6 polymer

聚合体 Polymer

Entity 7 polymer

聚合体 Polymer

Entity 8 polymer

聚合体 Polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)