9bs1

Cryo-EM structure of the S. cerevisiae lipid flippase Neo1 bound with PI4P in the E2P state

Method: ELECTRON MICROSCOPY D_max: 125.5 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	9bs1
沉积日期 deposition_date	2024-05-12
结构标题 title	Cryo-EM structure of the S. cerevisiae lipid flippase Neo1 bound with PI4P in the E2P state
关键词 keywords	lipid flippase, P4-ATPase, PI4P, phosphoinositide, neomycin resistance, LIPID TRANSPORT; LIPID TRANSPORT
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	36.41 Å
回转半径 Rg (电子) rg_electron	36.91 Å
零角强度 I(0) i0	349522000.00
分子量 molecular_weight	102390.0 kDa
排除体积 excluded_volume	99765 Å³
包络体积 envelope_volume	182310 Å³
水化壳体积 shell_volume	43565 Å³
包络直径 envelope_diameter	134.6 Å
壳层 Rg shell_rg	40.50 Å
包络 Rg envelope_rg	36.92 Å
形状 Rg shape_rg	36.95 Å
总 Rg total_rg	37.02 Å
总原子数 total_atoms	7760
残基数 n_residues	965
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	125.5 Å
Rg (实空间) rg_real	36.74 Å
Rg 误差 (实空间) rg_real_error	0.94 Å
I(0) (实空间) i0_real	3.4950e+08
I(0) 误差 (实空间) i0_real_error	5.5810e+06
Rg (倒空间) rg_reciprocal	36.54 Å
I(0) (倒空间) i0_reciprocal	349500000.0000
解质量估计 total_estimate	0.8263
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	37.9 Å
偏度 Skewness skewness	0.576
峰度 Kurtosis kurtosis	-0.176
角度范围 angular_range	— – 0.2150 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	46570000.0000
实空间数据点数 n_real_points	44
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.762; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.774; Smooth: 0.678

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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 (3)

Entity 1 polymer

描述 description	Phospholipid-transporting ATPase NEO1
分子量 formula_weight	131360.5 kDa
EC 编号 ec_number	7.6.2.1
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	7760

MDYKDDDDKPNPPSFKSHKQNLFNSNNNQHANSVDSFDLHLDDSFDAALDSLQINNNPEPLSKHNTVGDRESFEMRTVDDLDNFSNHSSDSHRKSSNTDTHPLMYDNRLSQDDNFKFTNIASSPPSSSNNIFSKALSYLKVSNTKNWSKFGSPIELSDQHIEREIHPDTTPVYDRNRYVSNELSNAKYNAVTFVPTLLYEQFKFFYNLYFLVVALSQAVPALRIGYLSSYIVPLAFVLTVTMAKEAIDDIQRRRRDRESNNELYHVITRNRSIPSKDLKVGDLIKVHKGDRIPADLVLLQSSEPSGESFIKTDQLDGETDWKLRVACPLTQNLSENDLINRISITASAPEKSIHKFLGKVTYKDSTSNPLSVDNTLWANTVLASSGFCIACVVYTGRDTRQAMNTTTAKVKTGLLELEINSISKILCACVFALSILLVAFAGFHNDDWYIDILRYLILFSTIIPVSLRVNLDLAKSVYAHQIEHDKTIPETIVRTSTIPEDLGRIEYLLSDKTGTLTQNDMQLKKIHLGTVSYTSETLDIVSDYVQSLVSSKNDSLNNSKVALSTTRKDMSFRVRDMILTLAICHNVTPTFEDDELTYQAASPDEIAIVKFTESVGLSLFKRDRHSISLLHEHSGKTLNYEILQVFPFNSDSKRMGIIVRDEQLDEYWFMQKGADTVMSKIVESNDWLEEETGNMAREGLRTLVIGRKKLNKKIYEQFQKEYNDASLSMLNRDQQMSQVITKYLEHDLELLGLTGVEDKLQKDVKSSIELLRNAGIKIWMLTGDKVETARCVSISAKLISRGQYVHTITKVTRPEGAFNQLEYLKINRNACLLIDGESLGMFLKHYEQEFFDVVVHLPTVIACRCTPQQKADVALVIRKMTGKRVCCIGDGGNDVSMIQCADVGVGIVGKEGKQASLAADFSITQFCHLTELLLWHGRNSYKRSAKLAQFVMHRGLIIAICQAVYSICSLFEPIALYQGWLMVGYATCYTMAPVFSLTLDHDIEESLTKIYPELYKELTEGKSLSYKTFFVWVLLSLFQGSVIQLFSQAFTSLLDTDFTRMVAISFTALVVNELIMVALEIYTWNKTMLVTEIATLLFYIVSVPFLGDYFDLGYMTTVNYYAGLLVILLISIFPVWTAKAIYRRLHPPSYAKVQEFATP

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;brewer's yeast ;
NCBI 分类编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Saccharomyces cerevisiae

Entity 2 non-polymer

描述 description	BERYLLIUM TRIFLUORIDE ION
分子量 formula_weight	66.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 3 non-polymer

描述 description	;(2R)-3-{[(S)-hydroxy{[(1R,2R,3R,4R,5S,6R)-2,3,5,6-tetrahydroxy-4-(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl di[(9Z)-octadec-9-enoate] ;
分子量 formula_weight	943.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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7. 引用文献 (2)

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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	3.71 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	1082029

fit	/app/data/saxs_computation/bs/9bs1/9bs1.fit
pddf	/app/data/pr_computation/bs/9bs1/9bs1.pr.out
profile	/app/data/saxs_computation/bs/9bs1/9bs1.dat