8sri

Cryo-EM structure of TRPM2 chanzyme (E1114A) in the presence of Magnesium and ADP-ribose, closed state

Method: ELECTRON MICROSCOPY D_max: 196.4 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	8sri
沉积日期 deposition_date	2023-05-05
结构标题 title	Cryo-EM structure of TRPM2 chanzyme (E1114A) in the presence of Magnesium and ADP-ribose, closed state
关键词 keywords	TRPM2 Chanzyme, Channel-enzyme, MEMBRANE PROTEIN; 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	59.47 Å
回转半径 Rg (电子) rg_electron	59.22 Å
零角强度 I(0) i0	4456760000.00
分子量 molecular_weight	575690.0 kDa
排除体积 excluded_volume	724660 Å³
包络体积 envelope_volume	1130600 Å³
水化壳体积 shell_volume	154690 Å³
包络直径 envelope_diameter	192.9 Å
壳层 Rg shell_rg	65.64 Å
包络 Rg envelope_rg	57.09 Å
形状 Rg shape_rg	59.29 Å
总 Rg total_rg	59.13 Å
总原子数 total_atoms	40636
残基数 n_residues	5472
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	196.4 Å
Rg (实空间) rg_real	59.17 Å
Rg 误差 (实空间) rg_real_error	1.17 Å
I(0) (实空间) i0_real	4.4570e+09
I(0) 误差 (实空间) i0_real_error	8.9150e+07
Rg (倒空间) rg_reciprocal	59.70 Å
I(0) (倒空间) i0_reciprocal	4460000000.0000
解质量估计 total_estimate	0.7951
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	75.6 Å
偏度 Skewness skewness	0.212
峰度 Kurtosis kurtosis	-0.304
角度范围 angular_range	— – 0.1300 Å⁻¹
当前正则化参数 α current_alpha	0.0010
最高正则化参数 α highest_alpha	541100000.0000
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: 0.800; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.933; 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 (4)

Entity 1 polymer

描述 description	TRPM2 chanzyme
分子量 formula_weight	168194.5 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	A,B,C,D
原子数 atom_count	40636

MQRARPGELVEVIMFRPTGKARVSNLDESMAMEFTDLRTRAMSSAAMIRQSVAAKTLLIENEDGKGSTRMEVQDFMKRFHMHASEDDKTGSPSTAWGTLRFPTKEATAPYLRLSVNDDPEDALLFVKAMLAQKYGETYDRPSLILSVTGGARNFTLPPRLETAIAKGLRLAAQRTNAWVVTGGTNTGVMKLTGQIMEALSKTQSHFIPPTIGIATYGVIIGGDDMTRGEPPKIGLEYEMHKKDPPKTTPLDDNHNLFLLVDDGSTNKFGKEIKFRAAFENAAGQAFAAPVVTIVVQGGPGTLGTALQAVRQGTPIVVVDGSGLAADVLAYAYNFMHNPLTRFKSYTIDDLRQKVAQTFNPKSSQQLTNLLDSALECVQDPNLVVVYSLQESGIDEFDDCILKAIFSSQGKLGNKLKQAMYFDQLDVAKRALSEASKNGQHNEIAACINDNLMAAMMHNKPHFVELYLGFDAKIYELKPSEEVAKTNITALDELPSFALAIEELYKREAKKPHSHVQRLVSLSNTDVLGRHYRVSTQRGDGTTRRIGRDLANTRAYNVLRMDQIFARLVSKDFSVNRDFTIYDSKYDKVPGIQFRRTAQASHMLFLWAICLDRFRMARHFWLIGDQSIINALVASRILERLSTHRALQGPHLAEERAKMQHNAKKFEELAVGVLGECHGSDSHMASEMLHSKNDMFNKKNAINIAYDAKSLAFLSHPATQSVINADWYGHLKSVTSFWAVLFAFFFPFFVLPFINFSEDHAEQQVEAPRDFFTDAPRSSHSANSTTSGAHRLRRKFAKFYSAPYTRFISDLLSHFVLCVVTSYFVLDKLEDTISAIEWILLVWFVALLLEELRQMIFCDGIAEYISDTWNRLDLIMITLFFVGFFTHASDPSNQDSKVVSKGIHAFLVVVLWLRFMRYYALSKNLGPKLIMMMEMMKDVSTFVFLLLIFLIGYGVAAQSLLSPDEDFSSRTFIGVLFRPYFQIYGELFLDDLNSEANCLGDTPFTECSRETVRMVPFFLAVYILGSNVLLVNLLIAMFNDTYMKVQEAAEDLWRKQNYELCAEYKDRPFLPAPFILLAHVHMLFMRLLRLCGVHTQEHEKIQDDETKRKITTFEALNTDKFLRRWERERQEMLEARVKMTNDNVVQAMGMMDQLLEHMISFRFSLDQQATKIKQEIRDDGLPSTEPTGLVSRTPSQPINRLNSAVAVHGHTAEAAEWYVPPEEYPKSGGVKRYLIDASMVPLSIMCPSYDPVEYTHPSVAAQPVWADPADPRKIKFNVKDEVNGKVVDRTSCHPSGISIDSNTGRPINPWGRTGMTGRGLLGKWGVNQAADTVVTRWKRSPDGSILERDGKKVLEFVAIQRQDNKMWAIPGGFVDNGEDVALTSGREFMEEALGMGTSADLMSAESKDSLAALFSSGTIVARIYCEDPRNTDNAWVETTCVNFHDESGRHAARLKLQGGDDAEHARWMMVHGGLNLFASHRTLLQHVTSALNAYF

来源 Source

来源生物 organism	Salpingoeca rosetta
NCBI 分类编号 ncbi_taxonomy_id	946362
宿主生物 host_organism	Homo sapiens

Entity 2 non-polymer

描述 description	ADENOSINE-5-DIPHOSPHORIBOSE
分子量 formula_weight	559.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	8

Entity 3 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	16

Entity 4 non-polymer

描述 description	CHOLESTEROL
分子量 formula_weight	386.7 kDa
来源方法 src_method	syn
拷贝数 entity_count	12

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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	2.73 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	379553

fit	/app/data/saxs_computation/sr/8sri/8sri.fit
pddf	/app/data/pr_computation/sr/8sri/8sri.pr.out
profile	/app/data/saxs_computation/sr/8sri/8sri.dat