8fn6

Cryo-EM structure of RNase-untreated RESC-A in trypanosomal RNA editing

Method: ELECTRON MICROSCOPY D_max: 202.0 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	8fn6
沉积日期 deposition_date	2022-12-27
结构标题 title	Cryo-EM structure of RNase-untreated RESC-A 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	55.16 Å
回转半径 Rg (电子) rg_electron	54.44 Å
零角强度 I(0) i0	1571730000.00
分子量 molecular_weight	320100.0 kDa
排除体积 excluded_volume	396410 Å³
包络体积 envelope_volume	614390 Å³
水化壳体积 shell_volume	95819 Å³
包络直径 envelope_diameter	214.4 Å
壳层 Rg shell_rg	56.23 Å
包络 Rg envelope_rg	53.43 Å
形状 Rg shape_rg	54.37 Å
总 Rg total_rg	54.72 Å
总原子数 total_atoms	22421
残基数 n_residues	2775
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	202.0 Å
Rg (实空间) rg_real	55.34 Å
Rg 误差 (实空间) rg_real_error	2.44 Å
I(0) (实空间) i0_real	1.5720e+09
I(0) 误差 (实空间) i0_real_error	3.2270e+07
Rg (倒空间) rg_reciprocal	54.99 Å
I(0) (倒空间) i0_reciprocal	1571000000.0000
解质量估计 total_estimate	0.8492
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	62.7 Å
偏度 Skewness skewness	0.494
峰度 Kurtosis kurtosis	-0.057
角度范围 angular_range	— – 0.1450 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	140800000.0000
实空间数据点数 n_real_points	30
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.701; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.938

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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	gRNA
分子量 formula_weight	14499.5 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polyribonucleotide
链编号 strand_id	g
原子数 atom_count	22421

UAUAUUUUUUUUUUUUUUUUUUUAAAAAAAAAAAAAAAAAAUUUUU

Entity 2 polymer

描述 description	RNA-editing substrate-binding complex protein 1 (RESC1)
分子量 formula_weight	52608.7 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	1

MLRLLRRSIVGSTFNIMVRRQNQGSVSQGALNMRDQQAAAAENVTPERVWALWNEGNLFSLSLAQLQGFLSRCGVRTDPAAKKAAVVRQVEEYLHSKDTTVKGGGQGAASPQQHQQHGQQGGYGRWNQASVMQPETLLDLSQAGFYEGAANMVPKAFQLLVSDTAPDVVVSRVNTTAFPGFPSNTECYTLGASEKDVAIRSRYSKVLQWCCLNMSNLQMDGELYVDFGKLLLKPSVMRKNRRIVSSYTLQQRLQVNHPYTWVPTLPESCLSKIQEQFLQPEGFAPIGKGVQLTYSGTIKRSKDQLHVDLDNKGKVLAVNSAWVNLQTAWCTHAKGPDVRLLLRSRPPIRRQDVELFASTPIIKLADDDVADVLPPEHGQLVYLSEDETRLFERVSDRGVTITVREVKRQPLIILRDEEEDPRVEYSLSAHIPANAAKATDVRAVGLTAFELAGRLAGLVAEDFVREYGCEAKL

Entity 3 polymer

描述 description	RNA-editing substrate-binding complex protein 2 (RESC2)
分子量 formula_weight	55526.1 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	2

MLRARLKIFSALNGATSAFSRAVAPLQIATRQQSFSAAAPAASGDFSHITRNTVWGLWNEGNLFSLSVPELAFFLQEHCRVANVDPRAKKSALVRQVEEILSAEQQASATVPQEDNPHAIVVTDYDRAEDALEEADEYGDWGAEPGFEDRRELDFMELSPGRMGERYDPLSPRAFQLLHSETATDVGIASIDPSKLPGQSKVKNALAAIHVAPNDANKMRFRMAFEWCLMNIWNMNMPGELNIGAGKALYYRSVAKQNRNVMPLWTVQKHLYAQHPYAWFAIASESNVAAMESLAAALNMSIQQERTTSYKVTIRRMAEFFDCELNGQLKCTMMNKPWDRFFVSHYIRSKMPDLRYVVRARHPIKKRIADAYLEADILRSTRDSVQSVLSPELGDVVYCCERVVRKWAKKTATGVTLQLVETKRTPLIITKAGDEGERLEYEWIVPLPQQAERIDIAALTDELWEYGNKLAAALEEGMEELMVHTMTAVSAY

Entity 4 polymer

描述 description	RNA-editing substrate-binding complex protein 3 (RESC3)
分子量 formula_weight	53146.6 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	3

MSNPFEKVARGIAFKMRSKVHKQGYSNTVMAQQARRLSPTGLLAMERLTELTALQQRHQCTFDPALRSKATQILRTLPLLSIDEDPYFTHTQRALRLAAYFGAVDLPVTYALINQHTKNAFMLDAFSMASFFYTLAKLKHPQTKEIVGILLPRLREVAPELIAREAVHILRLLCSIQMADAQLVKVVTETVVATAADVPLRDARQCAFILSETFPEEAQRILGAVEHRLCDDIDMNADANEVKTTILDVCRVVSATCKGPRRLLNSVARRSMELLPQLTPLDVAFVLKAFHLSSYRHLRLLRVLSSSLAASFPTSNVTKEHGLAASIVVQSLAHFYLSGCEEVVVTLVNASVNVLEGLNLALTLLACVRLRCVSPGVDPAVDALCSGAPMRRYVHNAHSMQVTSRILYGLAHAGRCRSDEEVAIVLPLLKSVVRTPGALRDDCRGFLLDAVTALGADGECSNDALQEQVRKVYERLSQDGGK

Entity 5 polymer

描述 description	RNA-editing substrate-binding complex protein 4 (RESC4)
分子量 formula_weight	120847.9 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	4

MNGRLYCLIRRITSPPVATRLIKEELCLSMAAIARLPLRRDQLAHVTNTEAITTRAQRISHLCTPTELGMIAEGAEALSCNRFDLADALIDGAYESVRRAASSTRLSHVSAIARYSASIKTYGNETITTLLKAGASLLQKNDSVPVLKSFLGVAQSHLTDGEMRVLIDEMCAKATEEQRLCINSIGTQSLAKDAAKCGEETLTKGNEDGDETAVDDEETQAWDMLRARQWMLQLVRCGKPPTAAEAVQAMELYAHFAVRDFVLHEKIEDLVLLVLPTGNKFHLNEMHKIVLRSPNLFPRVRNTLGQDHSGVSDVHRADRGVEWSDDPASSLTTTYTTSRAYSMLLLGQRLSEDIMFDVVQEQSETIPVDVAAQAACLFAEKGDIPEGVILRLSAELEHISPQGVTAFVRAARRDSSGALLPHYAAVLNRFTERDLCDTPLETLLQMCEVFALPAPRGTSEGDNDSINESQSKFQKALIVRLFSVIQGSRDVPFLCKVAKAVRAFDANDELIQFVCSSICAQGALSECEALIAFDMIRCCDFVYEPLLDAMEPVFRRLVESVSAMLEGKSTINDVEVRRCACFATLQSEFDCPDFETLASLLVHTVEKNVTGCPVELIPSVGLLCVRTRRTSALYIVGNKLEGNMQQLSDDAIGELARLLVGTENLATKELAVEFQSVVVSRLLRQQSLPPDVVALSAVVWLRQGDKVGTIDERSVDYIIKWMYAIGSSVYTDLCLAVHLSASVESLSNALIDDLPRRLELLTTNEMANAIFGLGEVSDMGARLSHQLVAERCSDYVVDHSQEFWSGKVIARLLYGFSRMHCTKRSLYNVFATRLAHRPVFSLLDQEAISFAIAAFGRVKYLDKKLFDRFTRWILDHSKDLNAAELLLTIRGVSRVMLLNDQLYDDLGSKAAEKVKEFPIESQCVLLSSFGSLGVEHERLASRMVSSIAENREELTDATKAVDVITSLWSMNYDVEDDKHVAQLADWVVQRAEELTDESIGKLCLVLSDTNWRHVPLVRAIAEQSVRLQGQQSISPKCCREVLDVLGTFMIHHQGARENLSALGRSISKERIQLSEEEEQHLQLLLRR

Entity 6 polymer

描述 description	RNA-editing substrate-binding complex protein 5 (RESC5)
分子量 formula_weight	43469.5 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

MLRHTSRNNALHAFVRSPHYRTIPSAGPNGIVVNRDMLVHQFRDFYKTLQHCSLVDKVHLMSERPSVEALRVADQMVSIGATFLEMPLTGMEHRATEFMESMRYVRGAGGPSTLASYLQDTENCRCNSGDVVCLPNGIAVGHGPRTNAVAHTTLKQLFEVKDDQFSFDVFTLEQEGDAPPLGDYFGFAGSNVLLTWKDEHGLLAVDQYQQKQPHTEMNVVYLEPGCHFLSFYGVDHTIDVLVQKGYERSMDSIAAAGLNPIPVQWSEMDKLGISMRAAVLPLKFFKANVGGMLSRNKSRGARWQTHQLQKGSGSGSASSGASAAGSSGASASSGASAAGSSGASAGHHHHHHHHHHSGSEDQVDPRLIDGKASAWSHPQFEKGGGSGGGSGGSAWSHPQFEK

Entity 7 polymer

描述 description	RNA-editing substrate-binding complex protein 6 (RESC6)
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 8 non-polymer

描述 description	ADENOSINE-5'-TRIPHOSPHATE
分子量 formula_weight	507.2 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	3.70 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	108821

fit	/app/data/saxs_computation/fn/8fn6/8fn6.fit
pddf	/app/data/pr_computation/fn/8fn6/8fn6.pr.out
profile	/app/data/saxs_computation/fn/8fn6/8fn6.dat

Cryo-EM structure of RNase-untreated RESC-A 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 non-polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)