8duj

Global map in C1 of RyR1 particles in complex with ImperaCalcin

Method: ELECTRON MICROSCOPY D_max: 257.8 Å Quality: EXCELLENT

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	8duj
沉积日期 deposition_date	2022-07-27
结构标题 title	Global map in C1 of RyR1 particles in complex with ImperaCalcin
关键词 keywords	ryanodine receptor, ion channel, snake toxin, calcin, complex, membrane protein, toxin; MEMBRANE PROTEIN
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	— Å
回转半径 Rg (电子) rg_electron	99.85 Å
零角强度 I(0) i0	32694800000.00
分子量 molecular_weight	1493600.0 kDa
排除体积 excluded_volume	1840900 Å³
包络体积 envelope_volume	4062100 Å³
水化壳体积 shell_volume	329550 Å³
包络直径 envelope_diameter	362.0 Å
壳层 Rg shell_rg	100.90 Å
包络 Rg envelope_rg	97.60 Å
形状 Rg shape_rg	100.10 Å
总 Rg total_rg	99.11 Å
总原子数 total_atoms	105895
残基数 n_residues	16523
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	257.8 Å
Rg (实空间) rg_real	97.59 Å
Rg 误差 (实空间) rg_real_error	0.62 Å
I(0) (实空间) i0_real	3.1340e+10
I(0) 误差 (实空间) i0_real_error	5.7660e+08
Rg (倒空间) rg_reciprocal	102.00 Å
I(0) (倒空间) i0_reciprocal	32740000000.0000
解质量估计 total_estimate	0.9161
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	112.8 Å
偏度 Skewness skewness	0.111
峰度 Kurtosis kurtosis	-0.669
角度范围 angular_range	— – 0.0800 Å⁻¹
当前正则化参数 α current_alpha	0.4353
最高正则化参数 α highest_alpha	4206000000.0000
实空间数据点数 n_real_points	17
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.001; Oscil: 1.000; Stabil: 0.972; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.000

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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	Imperacalcin
分子量 formula_weight	3776.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	M
原子数 atom_count	106156

GDCLPHLKRCKADNDCCGKKCKRRGTNAEKRCR

Entity 2 polymer

描述 description	Ryanodine receptor 1
分子量 formula_weight	565908.6 kDa
来源方法 src_method	nat
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	G,A,D,J

MGDGGEGEDEVQFLRTDDEVVLQCSATVLKEQLKLCLAAEGFGNRLCFLEPTSNAQNVPPDLAICCFTLEQSLSVRALQEMLANTVEAGVESSQGGGHRTLLYGHAILLRHAHSRMYLSCLTTSRSMTDKLAFDVGLQEDATGEACWWTMHPASKQRSEGEKVRVGDDLILVSVSSERYLHLSTASGELQVDASFMQTLWNMNPICSCCEEGYVTGGHVLRLFHGHMDECLTISAADSDDQRRLVYYEGGAVCTHARSLWRLEPLRISWSGSHLRWGQPLRIRHVTTGRYLALTEDQGLVVVDACKAHTKATSFCFRVSKEKLDTAPKRDVEGMGPPEIKYGESLCFVQHVASGLWLTYAAPDPKALRLGVLKKKAILHQEGHMDDALFLTRCQQEESQAARMIHSTAGLYNQFIKGLDSFSGKPRGSGPPAGPALPIEAVILSLQDLIGYFEPPSEELQHEEKQSKLRSLRNRQSLFQEEGMLSLVLNCIDRLNVYTTAAHFAEYAGEEAAESWKEIVNLLYELLASLIRGNRANCALFSTNLDWVVSKLDRLEASSGILEVLYCVLIESPEVLNIIQENHIKSIISLLDKHGRNHKVLDVLCSLCVCNGVAVRSNQDLITENLLPGRELLLQTNLINYVTSIRPNIFVGRAEGSTQYGKWYFEVMVDEVVPFLTAQATHLRVGWALTEGYSPYPGGGEGWGGNGVGDDLYSYGFDGLHLWTGHVARPVTSPGQHLLAPEDVVSCCLDLSVPSISFRINGCPVQGVFEAFNLDGLFFPVVSFSAGVKVRFLLGGRHGEFKFLPPPGYAPCHEAVLPRERLRLEPIKEYRREGPRGPHLVGPSRCLSHTDFVPCPVDTVQIVLPPHLERIREKLAENIHELWALTRIEQGWTYGPVRDDNKRLHPCLVNFHSLPEPERNYNLQMSGETLKTLLALGCHVGMADEKAEDNLKKTKLPKTYMMSNGYKPAPLDLSHVRLTPAQTTLVDRLAENGHNVWARDRVAQGWSYSAVQDIPARRNPRLVPYRLLDEATKRSNRDSLCQAVRTLLGYGYNIEPPDQEPSQVENQSRWDRVRIFRAEKSYTVQSGRWYFEFEAVTTGEMRVGWARPELRPDVELGADELAYVFNGHRGQRWHLGSEPFGRPWQSGDVVGCMIDLTENTIIFTLNGEVLMSDSGSETAFREIEIGDGFLPVCSLGPGQVGHLNLGQDVSSLRFFAICGLQEGFEPFAINMQRPVTTWFSKSLPQFEPVPPEHPHYEVARMDGTVDTPPCLRLAHRTWGSQNSLVEMLFLRLSLPVQFHQHFRCTAGATPLAPPGLQPPAEDEARAAEPDPDYENLRRSAGGWGEAEGGKEGTAKEGTPGGTPQPGVEAQPVRAENEKDATTEKNKKRGFLFKAKKAAMMTQPPATPALPRLPHDVVPADNRDDPEIILNTTTYYYSVRVFAGQEPSCVWVGWVTPDYHQHDMNFDLSKVRAVTVTMGDEQGNVHSSLKCSNCYMVWGGDFVSPGQQGRISHTDLVIGCLVDLATGLMTFTANGKESNTFFQVEPNTKLFPAVFVLPTHQNVIQFELGKQKNIMPLSAAMFLSERKNPAPQCPPRLEVQMLMPVSWSRMPNHFLQVETRRAGERLGWAVQCQDPLTMMALHIPEENRCMDILELSERLDLQRFHSHTLRLYRAVCALGNNRVAHALCSHVDQAQLLHALEDAHLPGPLRAGYYDLLISIHLESACRSRRSMLSEYIVPLTPETRAITLFPPGRKGGNARRHGLPGVGVTTSLRPPHHFSPPCFVAALPAAGVAEAPARLSPAIPLEALRDKALRMLGEAVRDGGQHARDPVGGSVEFQFVPVLKLVSTLLVMGIFGDEDVKQILKMIEPEVFTEEEEEEEEEEEEEEEEEEDEEEKEEDEEEEEKEDAEKEEEEAPEGEKEDLEEGLLQMKLPESVKLQMCNLLEYFCDQELQHRVESLAAFAERYVDKLQANQRSRYALLMRAFTMSAAETARRTREFRSPPQEQINMLLHFKDEADEEDCPLPEDIRQDLQDFHQDLLAHCGIQLEGEEEEPEEETSLSSRLRSLLETVRLVKKKEEKPEEELPAEEKKPQSLQELVSHMVVRWAQEDYVQSPELVRAMFSLLHRQYDGLGELLRALPRAYTISPSSVEDTMSLLECLGQIRSLLIVQMGPQEENLMIQSIGNIMNNKVFYQHPNLMRALGMHETVMEVMVNVLGGGETKEIRFPKMVTSCCRFLCYFCRISRQNQRSMFDHLSYLLENSGIGLGMQGSTPLDVAAASVIDNNELALALQEQDLEKVVSYLAGCGLQSCPMLLAKGYPDIGWNPCGGERYLDFLRFAVFVNGESVEENANVVVRLLIRKPECFGPALRGEGGSGLLAAIEEAIRISEDPARDGPGVRRDRRREHFGEEPPEENRVHLGHAIMSFYAALIDLLGRCAPEMHLIQAGKGEALRIRAILRSLVPLDDLVGIISLPLQIPTLGKDGALVQPKMSASFVPDHKASMVLFLDRVYGIENQDFLLHVLDVGFLPDMRAAASLDTATFSTTEMALALNRYLCLAVLPLITKCAPLFAGTEHRAIMVDSMLHTVYRLSRGRSLTKAQRDVIEDCLMALCRYIRPSMLQHLLRRLVFDVPILNEFAKMPLKLLTNHYERCWKYYCLPTGWANFGVTSEEELHLTRKLFWGIFDSLAHKKYDQELYRMAMPCLCAIAGALPPDYVDASYSSKAEKKATVDAEGNFDPRPVETLNVIIPEKLDSFINKFAEYTHEKWAFDKIQNNWSYGENVDEELKTHPMLRPYKTFSEKDKEIYRWPIKESLKAMIAWEWTIEKAREGEEERTEKKKTRKISQTAQTYDPREGYNPQPPDLSGVTLSRELQAMAEQLAENYHNTWGRKKKQELEAKGGGTHPLLVPYDTLTAKEKARDREKAQELLKFLQMNGYAVTRGLKDMELDTSSIEKRFAFGFLQQLLRWMDISQEFIAHLEAVVSSGRVEKSPHEQEIKFFAKILLPLINQYFTNHCLYFLSTPAKVLGSGGHASNKEKEMITSLFCKLAALVRHRVSLFGTDAPAVVNCLHILARSLDARTVMKSGPEIVKAGLRSFFESASEDIEKMVENLRLGKVSQARTQVKGVGQNLTYTTVALLPVLTTLFQHIAQHQFGDDVILDDVQVSCYRTLCSIYSLGTTKNTYVEKLRPALGECLARLAAAMPVAFLEPQLNEYNACSVYTTKSPRERAILGLPNSVEEMCPDIPVLDRLMADIGGLAESGARYTEMPHVIEITLPMLCSYLPRWWERGPEAPPPALPAGAPPPCTAVTSDHLNSLLGNILRIIVNNLGIDEATWMKRLAVFAQPIVSRARPELLHSHFIPTIGRLRKRAGKVVAEEEQLRLEAKAEAEEGELLVRDEFSVLCRDLYALYPLLIRYVDNNRAHWLTEPNANAEELFRMVGEIFIYWSKSHNFKREEQNFVVQNEINNMSFLTADSKSKMAKAGDAQSGGSDQERTKKKRRGDRYSVQTSLIVATLKKMLPIGLNMCAPTDQDLIMLAKTRYALKDTDEEVREFLQNNLHLQGKVEGSPSLRWQMALYRGLPGREEDADDPEKIVRRVQEVSAVLYHLEQTEHPYKSKKAVWHKLLSKQRRRAVVACFRMTPLYNLPTHRACNMFLESYKAAWILTEDHSFEDRMIDDLSKAGEQEEEEEEVEEKKPDPLHQLVLHFSRTALTEKSKLDEDYLYMAYADIMAKSCHLEEGGENGEAEEEEVEVSFEEKEMEKQRLLYQQSRLHTRGAAEMVLQMISACKGETGAMVSSTLKLGISILNGGNAEVQQKMLDYLKDKKEVGFFQSIQALMQTCSVLDLNAFERQNKAEGLGMVNEDGTVINRQNGEKVMADDEFTQDLFRFLQLLCEGHNNDFQNYLRTQTGNTTTINIIICTVDYLLRLQESISDFYWYYSGKDVIEEQGKRNFSKAMSVAKQVFNSLTEYIQGPCTGNQQSLAHSRLWDAVVGFLHVFAHMMMKLAQDSSQIELLKELLDLQKDMVVMLLSLLEGNVVNGMIARQMVDMLVESSSNVEMILKFFDMFLKLKDIVGSEAFQDYVTDPRGLISKKDFQKAMDSQKQFTGPEIQFLLSCSEADENEMINFEEFANRFQEPARDIGFNVAVLLTNLSEHVPHDPRLRNFLELAESILEYFRPYLGRIEIMGASRRIERIYFEISETNRAQWEMPQVKESKRQFIFDVVNEGGEAEKMELFVSFCEDTIFEMQIAAQISEPEGEPEADEDEGMGEAAAEGAEEGAAGAEGAAGTVAAGATARLAAAAARALRGLSYRSLRRRVRRLRRLTAREAATALAALLWAVVARAGAAGAGAAAGALRLLWGSLFGGGLVEGAKKVTVTELLAGMPDPTSDEVHGEQPAGPGGDADGAGEGEGEGDAAEGDGDEEVAGHEAGPGGAEGVVAVADGGPFRPEGAGGLGDMGDTTPAEPPTPEGSPILKRKLGVDGEEEELVPEPEPEPEPEPEKADEENGEKEEVPEAPPEPPKKAPPSPPAKKEEAGGAGMEFWGELEVQRVKFLNYLSRNFYTLRFLALFLAFAINFILLFYKVSDSPPGEDDMEGSAAGDLAGAGSGGGSGWGSGAGEEAEGDEDENMVYYFLEESTGYMEPALWCLSLLHTLVAFLCIIGYNCLKVPLVIFKREKELARKLEFDGLYITEQPGDDDVKGQWDRLVLNTPSFPSNYWDKFVKRKVLDKHGDIFGRERIAELLGMDLASLEITAHNERKPDPPPGLLTWLMSIDVKYQIWKFGVIFTDNSFLYLGWYMVMSLLGHYNNFFFAAHLLDIAMGVKTLRTILSSVTHNGKQLVMTVGLLAVVVYLYTVVAFNFFRKFYNKSEDEDEPDMKCDDMMTCYLFHMYVGVRAGGGIGDEIEDPAGDEYELYRVVFDITFFFFVIVILLAIIQGLIIDAFGELRDQQEQVKEDMETKCFICGIGSDYFDTTPHGFETHTLEEHNLANYMFFLMYLINKDETEHTGQESYVWKMYQERCWDFFPAGDCFRKQYEDQLS

Entity 3 polymer

描述 description	Peptidyl-prolyl cis-trans isomerase FKBP1B
分子量 formula_weight	11667.3 kDa
EC 编号 ec_number	5.2.1.8
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	H,B,E,K

GVEIETISPGDGRTFPKKGQTCVVHYTGMLQNGKKFDSSRDRNKPFKFRIGKQEVIKGFEEGAAQMSLGQRAKLTCTPDVAYGATGHPGVIPPNATLIFDVELLNLE

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 4 polymer

描述 description	Calmodulin-1
分子量 formula_weight	16620.4 kDa
突变 mutation	E32A, E68A, E105A, E141A
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	I,C,F,L

MADQLTEEQIAEFKEAFSLFDKDGDGTITTKALGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPAFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAALRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEAFVQMMTAK

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 5 non-polymer

描述 description	CAFFEINE
分子量 formula_weight	194.2 kDa
来源方法 src_method	nat
拷贝数 entity_count	4

Entity 6 non-polymer

描述 description	CALCIUM ION
分子量 formula_weight	40.1 kDa
来源方法 src_method	nat
拷贝数 entity_count	4

Entity 7 non-polymer

描述 description	ADENOSINE-5'-TRIPHOSPHATE
分子量 formula_weight	507.2 kDa
来源方法 src_method	nat
拷贝数 entity_count	4

Entity 8 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	nat
拷贝数 entity_count	4

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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	144529

fit	/app/data/saxs_computation/du/8duj/8duj.fit
pddf	/app/data/pr_computation/du/8duj/8duj.pr.out
profile	/app/data/saxs_computation/du/8duj/8duj.dat

Global map in C1 of RyR1 particles in complex with ImperaCalcin

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

来源 Source

Entity 4 polymer

聚合体 Polymer

来源 Source

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 non-polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)