SAXSdb — 8jsm

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8jsm
沉积日期 deposition_date	2023-06-20
结构标题 title	The structure of EBOV L-VP35-RNA complex (conformation 1)
关键词 keywords	EBOV, Polymerase, Replication, cryo-EM, VIRAL PROTEIN/RNA, VIRAL PROTEIN-RNA complex; VIRAL 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	44.03 Å
回转半径 Rg (电子) rg_electron	44.42 Å
零角强度 I(0) i0	658009000.00
分子量 molecular_weight	211210.0 kDa
排除体积 excluded_volume	264790 Å³
包络体积 envelope_volume	369660 Å³
水化壳体积 shell_volume	72953 Å³
包络直径 envelope_diameter	178.3 Å
壳层 Rg shell_rg	47.10 Å
包络 Rg envelope_rg	45.14 Å
形状 Rg shape_rg	44.43 Å
总 Rg total_rg	44.54 Å
总原子数 total_atoms	14850
残基数 n_residues	1866
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	166.5 Å
Rg (实空间) rg_real	44.53 Å
Rg 误差 (实空间) rg_real_error	1.96 Å
I(0) (实空间) i0_real	6.5800e+08
I(0) 误差 (实空间) i0_real_error	1.1990e+07
Rg (倒空间) rg_reciprocal	44.04 Å
I(0) (倒空间) i0_reciprocal	657600000.0000
解质量估计 total_estimate	0.7657
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	50.9 Å
偏度 Skewness skewness	0.851
峰度 Kurtosis kurtosis	0.850
角度范围 angular_range	— – 0.1800 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	82080000.0000
实空间数据点数 n_real_points	37
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.412; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.920; Smooth: 0.793

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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	RNA-directed RNA polymerase L
分子量 formula_weight	252863.7 kDa
EC 编号 ec_number	2.7.7.48,3.6.1.-,2.7.7.88,2.1.1.-
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	14856

MATQHTQYPDARLSSPIVLDQCDLVTRACGLYSSYSLNPQLRNCKLPKHIYRLKYDVTVTKFLSDVPVATLPIDFIVPILLKALSGNGFCPVEPRCQQFLDEIIKYTMQDALFLKYYLKNVGAQEDCVDDHFQEKILSSIQGNEFLHQMFFWYDLAILTRRGRLNRGNSRSTWFVHDDLIDILGYGDYVFWKIPISLLPLNTQGIPHAAMDWYQTSVFKEAVQGHTHIVSVSTADVLIMCKDLITCRFNTTLISKIAEVEDPVCSDYPNFKIVSMLYQSGDYLLSILGSDGYKIIKFLEPLCLAKIQLCSKYTERKGRFLTQMHLAVNHTLEEITEIRALKPSQAHKIREFHRTLIRLEMTPQQLCELFSIQKHWGHPVLHSETAIQKVKKHATVLKALRPIVIFETYCVFKYSIAKHYFDSQGSWYSVTSDRNLTPGLNSYIKRNQFPPLPMIKELLWEFYHLDHPPLFSTKIISDLSIFIKDRATAVERTCWDAVFEPNVLGYNPPHKFSTKRVPEQFLEQENFSIENVLSYAQKLEYLLPQYRNFSFSLKEKELNVGRTFGKLPYPTRNVQTLCEALLADGLAKAFPSNMMVVTEREQKESLLHQASWHHTSDDFGEHATVRGSSFVTDLEKYNLAFRYEFTAPFIEYCNRCYGVKNVFNWMHYTIPQCYMHVSDYYNPPHNLTLENRNNPPEGPSSYRGHMGGIEGLQQKLWTSISCAQISLVEIKTGFKLRSAVMGDNQCITVLSVFPLETDADEQEQSAEDNAARVAASLAKVTSACGIFLKPDETFVHSGFIYFGKKQYLNGVQLPQSLKTATRMAPLSDAIFDDLQGTLASIGTAFERSISETRHIFPCRITAAFHTFFSVRILQYHHLGFNKGFDLGQLTLGKPLDFGTISLALAVPQVLGGLSFLNPEKCFYRNLGDPVTSGLFQLKTYLRMIEMDDLFLPLIAKNPGNCTAIDFVLNPSGLNVPGSQDLTSFLRQIVRRTITLSAKNKLINTLFHASADFEDEMVCKWLLSSTPVMSRFAADIFSRTPSGKRLQILGYLEGTRTLLASKIINNNTETPVLDRLRKITLQRWSLWFSYLDHCDNILAEALTQITCTVDLAQILREYSWAHILEGRPLIGATLPCMIEQFKVVWLKPYEQCPQCSNAKQPGGKPFVSVAVKKHIVSAWPNASRISWTIGDGIPYIGSRTEDKIGQPAIKPKCPSAALREAIELASRLTWVTQGSSNSDLLIKPFLEARVNLSVQEILQMTPSHYSGNIVHRYNDQYSPHSFMANRMSNSATRLIVSTNTLGEFSGGGQSARDSNIIFQNVINYAVALFDIKFRNTEATDIQYNRAHLHLTKCCTREVPAQYLTYTSTLDLDLTRYRENELIYDNNPLKGGLNCNISFDNPFFQGKQLNIIEDDLIRLPHLSGWELAKTIMQSIISDSNNSSTDPISSGETRSFTTHFLTYPKIGLLYSFGAFVSYYLGNTILRTKKLTLDNFLYYLTTQIHNLPHRSLRILKPTFKHASVMSRLMSIDPHFSIYIGGAAGDRGLSDAARLFLRTSISSFLTFVKEWIINRGTIVPLWIVYPLEGQNPTPVNNFLHQIVELLVHDSSRHQAFKTTINDHVHPHDNLVYTCKSTASNFFHASLAYWRSRHRNSNRKDLTRNSSTGSSTNNSDGHIKRSQEQTTRDPHDGTERSLVLQMSHEIKRTTIPQENTHQGPSFQSFLSDSACGTANPKLNFDRSRHNVKSQDHNSASKREGHQIISHRLVLPFFTLSQGTRQLTSSNESQTQDEISKYLRQLRSVIDTTVYCRFTGIVSSMHYKLDEVLWEIENFKSAVTLAEGEGAGALLLIQKYQVKTLFFNTLATESSIESEIVSGMTTPRMLLPVMSKFHNDQIEIILNNSASQITDITNPTWFKDQRARLPRQVEVITMDAETTENINRSKLYEAVHKLILHHVDPSVLKAVVLKVFLSDTEGMLWLNDNLAPFFATGYLIKPITSSARSSEWYLCLTNFLSTTRKMPHQNHLSCKQVILTALQLQIQRSPYWLSHLTQYADCDLHLSYIRLGFPSLEKVLYHRYNLVDSKRGPLVSVTQHLAHLRAEIRELTNDYNQQRQSRTQTYHFIRTAKGRITKLVNDYLKFFLIVQALKHNGTWQAEFKKLPELISVCNRFYHIRDCNCEERFLVQTLYLHRMQDSEVKLIERLTGLLSLFPDGLYRFD

来源 Source

来源生物 organism	Ebola virus
NCBI 分类编号 ncbi_taxonomy_id	1570291
宿主生物 host_organism	Spodoptera

Entity 2 polymer

描述 description	Polymerase cofactor VP35
分子量 formula_weight	37489.4 kDa
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

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

MTTRTKGRGHTVATTQNDRMPGPELSGWISEQLMTGRIPVNDIFCDIENNPGLCYASQMQQTKPNPKMRNSQTQTDPICNHSFEEVVQTLASLATVVQQQTIASESLEQRITSLENGLKPVYDMAKTISSLNRVCAEMVAKYDLLVMTTGRATATAAATEAYWAEHGQPPPGPSLYEESAIRGKIESRDETVPQSVREAFNNLDSTTSLTEENFGKPDISAKDLRNIMYDHLPGFGTAFHQLVQVICKLGKDSNSLDIIHAEFQASLAEGDSPQCALIQITKRVPIFQDAAPPVIHIRSRGDIPRACQKSLRPVPPSPKIDRGWVCVFQLQDGKTLGLKI

来源 Source

来源生物 organism	Ebola virus
NCBI 分类编号 ncbi_taxonomy_id	1570291
宿主生物 host_organism	Spodoptera

Entity 3 polymer

描述 description	The leader sequence of EBOV genome.
分子量 formula_weight	5619.2 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

UUUCUUUUUGUGUGUCCG

Entity 4 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	3.30 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	197788

fit	/app/data/saxs_computation/js/8jsm/8jsm.fit
pddf	/app/data/pr_computation/js/8jsm/8jsm.pr.out
profile	/app/data/saxs_computation/js/8jsm/8jsm.dat

The structure of EBOV L-VP35-RNA complex (conformation 1)

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 (4)

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

Entity 4 non-polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)