9omv

Cryo-EM structure of the C. neoformans lipid flippase Apt1-Cdc50 bound with butyrolactol A in the E2P state

Method: ELECTRON MICROSCOPY D_max: 168.2 Å Quality: REASONABLE

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	9omv
沉积日期 deposition_date	2025-05-14
结构标题 title	Cryo-EM structure of the C. neoformans lipid flippase Apt1-Cdc50 bound with butyrolactol A in the E2P state
关键词 keywords	Cryptococcus neoformans, lipid flippase, P4-ATPase, Cdc50 protein, butyrolactol A, TRANSLOCASE-INHIBITOR complex; TRANSLOCASE/INHIBITOR
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	46.54 Å
回转半径 Rg (电子) rg_electron	46.89 Å
零角强度 I(0) i0	752823000.00
分子量 molecular_weight	152740.0 kDa
排除体积 excluded_volume	148900 Å³
包络体积 envelope_volume	273310 Å³
水化壳体积 shell_volume	52305 Å³
包络直径 envelope_diameter	172.2 Å
壳层 Rg shell_rg	45.83 Å
包络 Rg envelope_rg	47.06 Å
形状 Rg shape_rg	46.82 Å
总 Rg total_rg	46.99 Å
总原子数 total_atoms	11594
残基数 n_residues	1437
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	168.2 Å
Rg (实空间) rg_real	47.25 Å
Rg 误差 (实空间) rg_real_error	2.10 Å
I(0) (实空间) i0_real	7.5280e+08
I(0) 误差 (实空间) i0_real_error	1.5160e+07
Rg (倒空间) rg_reciprocal	46.55 Å
I(0) (倒空间) i0_reciprocal	752200000.0000
解质量估计 total_estimate	0.5633
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	39.6 Å
偏度 Skewness skewness	0.581
峰度 Kurtosis kurtosis	-0.418
角度范围 angular_range	— – 0.1700 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	40110000.0000
实空间数据点数 n_real_points	35
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.532; Stabil: 1.000; Sysdev: 0.115; Positv: 1.000; Valcen: 0.665; Smooth: 0.713

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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	Transcription regulator
分子量 formula_weight	45938.0 kDa
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	B
原子数 atom_count	11594

MAIFNRKPKARLDGEPAPTEKEKVKWSKRPANTAFKQQRLKAWQPILTPKSVLPTLLIIGIIFAPIGALIVWGSGKVTTITLDYTECDVDAPTDGSYQAMPNSAYQYDLATSSSVSESSIASPTWTFSNDSSREVGETARCEIEFEVPYDLGPGLFLYYKLTNYYQNHRRYSSSFDATQLIGDSRSLSQINGGNCKPITSRDGKPYYPCGLIANSLFNDTFPSVVLLNPTNGAQNQTYNFSESGIAWGGIKKNYASTLTYISPSDVLPPPNWALKYPNGYVDGFPNLREDEHFQVWMRVAALPTFRKLWARNDGEIMSQGRYRIVANMNYPVKQFSGTKSIVISTVSWIGGKQPFLGWAYIAAAILCVVLAVAGLIRHLVKPRKLGDMSLLSWNQPNANGLHHHHHHHHHH

来源 Source

来源生物 organism	Cryptococcus neoformans var. grubii H99
NCBI 分类编号 ncbi_taxonomy_id	235443
宿主生物 host_organism	Saccharomyces cerevisiae

Entity 2 polymer

描述 description	Phospholipid-transporting ATPase
分子量 formula_weight	176534.6 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

MGASKPPLVPRSKKHNPSWLDRNIVKPLESLAPSKLFARRRSPPVPRSVFINEPLPSEYYDKKGKILRAHHFATNQNVTSKYTVITFIPKNLFEQFRRVANCFFLAISILQFFPKFSTISPGLVILPLIIVLAITALKDGYEDIKRHQADHRTNHAIVHVLGGQDYTNQNPMASKDKTFIPAIPLPKRRSKKAKKAEEEAALNMQGRSSSTENFAAEPVPGAEPRGQDELQRMRSQVSNWDEDPEAGDSPGELGWHRTIWEDVKVGDFVKIYENEQFPADIVICATSEEEDVAYIETKNLDGETNLKSRNGVPGLSHLNTAEACAKAHLCIDLDAPESNMFRLNGAVINLEEYDEDEQHPIHPITLETTMLRGCVLKNTAWVIGIIVYTGEDTKIIRNAGATPSKRSKVEKQMNPQVIINLVILAAIAVVCAIVDHVNEVEWDRQQAYWMLFADTSGDNPNINGLVTFANAFITFQNIVPISLYISIEAVRTIQAAFIYWDRDIKYKKDGVTTRTTARSWNLSDDLGQIEYIFSDKTGTLTQNAMIFRQCSVGGKIYTGDGLPPSHPTITHQHQPPPVHQHDDQDDPIAKSASESDDSDPKKISTEDPDEIKVTLPKEVLATFHDAELDKDLEAHDSEQSRILHGFFAVLGLCHTVLAAETEPGVIEYKAQSPDEAALVQSAADVGFVFRGRDHNILRMSTPFSDVSDEYELLHVLEFNSARKRMSVILRKLDEDGRIFLLCKGADNVIFERLTKDSNQREMREKTDQDLQYFASEGLRTLCLAYRILDPQVYEQWAKEYHNATVALQDREERIESVSSSIERDLILLGATAIEDKLQDGVPDTISDLKRAGIKVWVATGDKLETAVAIGYTTNLLTKDTNLIVVREGRHSIGDQLREALEEFFGEDAGLRTTLSRIDSRRNSMDPPRLTRVNTGVRSLVGRDNGTRPGGFSLVIEGHALAHCFDDEETEALLLALSTRCNTVICCRVSPLQKAQIVHLIKDNLGVMCLAIGDGANDVSMIQAADVGVGISGEEGLQAVNSSDYAIAQFRYLKRLLLVHGHWSYFRNSSMILNFFYKNIIGIGVLFWFMIYCGWSTTYVFAYVYLLFWNVFWTLVPVIAIGLFDRNIDDETLMALPELYRASREGKYFGLMRFAYYIFEGVYQSAVIYFFLNYTYVTTTARGDGYDVYMYEMSTTQAIGAVMVANLFSGLNIDAWTGWVWFAIWFGPFLIWVFTAVYSVIPPSSFYTGVYGNDVFLFRSAAYWFGWPFVTIIALLPRYLIKTFRQNIFPNDVDTMRLVRKYHPEVDLYNHPMLGGKLAPKKDEDESDYGEEPFDGPEGRRSSIKMANLRHSHGAFGRGDQAGDMELGMGRKSLGNRPGLRSSMDSSRFGIHSGARGSTVDMSTGLEQPPSRGFGFTMEEGGVAIQRMQSRLSQTSSHASRSRWPRFNNNSSSSHPFETKPPSSMSKLRSRAGSILTRKRADTTDTRNSDDKSLSSPVKTGFFGRHMPGQNHGQHEGRSMGTPLKSETGRGDNWEEEELEDESLGRGFGVGQNMAPPEIPRMDYKDDDDKI

来源 Source

来源生物 organism	Cryptococcus neoformans var. grubii H99
NCBI 分类编号 ncbi_taxonomy_id	235443
宿主生物 host_organism	Saccharomyces cerevisiae

Entity 3 branched

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	424.4 kDa
来源方法 src_method	man
拷贝数 entity_count	2

Entity 4 branched

描述 description	;alpha-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	1073.0 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 5 non-polymer

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	221.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 6 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 7 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	1

Entity 8 non-polymer

描述 description	;(3R,4R,5S)-3,4-dihydroxy-5-[(1R,2R,3S,4S,5R,6R,8E,10E,14E,16Z)-1,2,3,4,5-pentahydroxy-6,20,20-trimethylhenicosa-8,10,14,16-tetraen-1-yl]oxolan-2-one ;
分子量 formula_weight	526.7 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	2.95 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	187186

fit	/app/data/saxs_computation/om/9omv/9omv.fit
pddf	/app/data/pr_computation/om/9omv/9omv.pr.out
profile	/app/data/saxs_computation/om/9omv/9omv.dat

Cryo-EM structure of the C. neoformans lipid flippase Apt1-Cdc50 bound with butyrolactol A in the E2P state

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

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 branched

Entity 4 branched

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 non-polymer

7. 引用文献 (2)

8. 文件与曲线 (10)

Files (7)

Curves (3)