9bym

Cryo-EM structure of ATP synthase non-stator state

Method: ELECTRON MICROSCOPY D_max: 190.2 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	9bym
沉积日期 deposition_date	2024-05-23
结构标题 title	Cryo-EM structure of ATP synthase non-stator state
关键词 keywords	heart, ATP synthase, 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	54.48 Å
回转半径 Rg (电子) rg_electron	55.93 Å
零角强度 I(0) i0	2463200000.00
分子量 molecular_weight	424800.0 kDa
排除体积 excluded_volume	536110 Å³
包络体积 envelope_volume	681950 Å³
水化壳体积 shell_volume	106650 Å³
包络直径 envelope_diameter	206.4 Å
壳层 Rg shell_rg	56.36 Å
包络 Rg envelope_rg	55.10 Å
形状 Rg shape_rg	55.94 Å
总 Rg total_rg	55.90 Å
总原子数 total_atoms	29873
残基数 n_residues	3947
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	190.2 Å
Rg (实空间) rg_real	54.97 Å
Rg 误差 (实空间) rg_real_error	1.80 Å
I(0) (实空间) i0_real	2.4630e+09
I(0) 误差 (实空间) i0_real_error	4.8690e+07
Rg (倒空间) rg_reciprocal	54.07 Å
I(0) (倒空间) i0_reciprocal	2460000000.0000
解质量估计 total_estimate	0.7819
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	59.0 Å
偏度 Skewness skewness	0.731
峰度 Kurtosis kurtosis	0.200
角度范围 angular_range	— – 0.1450 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	342100000.0000
实空间数据点数 n_real_points	30
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.595; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.384

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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 (10)

Entity 1 polymer

描述 description	ATP synthase subunit alpha
分子量 formula_weight	59502.3 kDa
来源方法 src_method	nat
拷贝数 entity_count	3

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,C,B
原子数 atom_count	29873

MISGPLKIMTADLLKGMVSKNALGSSFVAARNLHASNTRLQKTGTAEVSSILEERILGADTSVDLEETGRVLSIGDGIARVHGLRNVQAEEMVEFSSGLKGMSLNLEPDNVGVVVFGNDKLIKEGDIVKRTGAIVDVPVGEELLGRVVDALGNAIDGKGPIGSKTRRRVGLKAPGIIPRISVREPMQTGIKAVDSLVPIGRGQRELIIGDRQTGKTSIAIDTIINQKRFNDGTDEKKKLYCIYVAIGQKRSTVAQLVKRLTDADAMKYTIVVSATASDAAPLQYLAPYSGCSMGEYFRDNGKHALIIYDDLSKQAVAYRQMSLLLRRPPGREAYPGDVFYLHSRLLERAAKMNDAFGGGSLTALPVIETQAGDVSAYIPTNVISITDGQIFLETELFYKGIRPAINVGLSVSRVGSAAQTRAMKQVAGTMKLELAQYREVAAFAQFGSDLDAATQQLLSRGVRLTELLKQGQYAPMAIEEQVAVIYAGVRGYLDKLEPSKITKFENAFLSHVISQHQALLGKIRADGKISEETDAKLKEIVTNFLAGFEA

Entity 2 polymer

描述 description	ATP synthase subunit beta
分子量 formula_weight	60893.6 kDa
EC 编号 ec_number	7.1.2.2
来源方法 src_method	nat
拷贝数 entity_count	3

聚合体 Polymer

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

MLRVISSKMIQRTCLLQSRPRPQLRGVGGQTAAALSLYPGSAMLGFVGRVASASASGALRGLSPSAPLPQAQLLLRAAPAALQPARDYATQPSPSPKAGAATGRIVAVIGAVVDVQFDEGLPPILNALEVQGRETRLVLEVAQHLGESTVRTIAMDGTEGLVRGQKVLDSGAPIKIPVGPETLGRIMNVIGEPIDERGPIKTKQFAAIHAEAPEFMEMSVEQEILVTGIKVVDLLAPYAKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYSVFAGVGERTREGNDLYHEMIESGVINLKDATSKVALVYGQMNEPPGARARVALTGLTVAEYFRDQEGQDVLLFIDNIFRFTQAGSEVSALLGRIPSAVGYQPTLATDMGTMQERITTTKKGSITSVQAIYVPADDLTDPAPATTFAHLDATTVLSRAIAELGIYPAVDPLDSTSRIMDPNIVGSEHYDVARGVQKILQDYKSLQDIIAILGMDELSEEDKLTVSRARKIQRFLSQPFQVAEVFTGHLGKLVPLKETIKGFQQILAGEYDHLPEQAFYMVGPIEEAVAKADKLAEEHS

Entity 3 polymer

描述 description	ATPase inhibitor, mitochondrial
分子量 formula_weight	12209.7 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	J

MAATALAVRSRIGAWSVWAMQSRGFSSDTPEGVRSGAGAVRDAGGAFGKKEQADEERYFRARAREQLAALKKHHENEISHHVKEIERLQKEIERHKQSIKKLKNDDDD

Entity 4 polymer

描述 description	ATP synthase subunit gamma
分子量 formula_weight	30252.8 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	G

MATLKDITRRLKSIKNIQKITKSMKMVAAAKYARAERDLKPARVYGIGSLALYEKADIKVPEDKKKHLIIGVSSDRGLCGAIHSSVAKQIKSEVANLTAAGKEVKIVGVGDKIRGILHRTHSDQFLVTFKEVGRKPPTFGDASVIALELLNSGYEFDEGSIIFNRFRSVISYKTEEKPIFSLDTVASAESMSIYDDIDADVLRNYQEYSLANIIYYSLKESTTSEQSARMTAMDNASKNASEMIDKLTLTFNRTRQAVITKELIEIISGAAAL

Entity 5 polymer

描述 description	ATP synthase F1 subunit delta
分子量 formula_weight	17489.7 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	H

MLPATLLRRSGLGRVVRQARAYAEAAAAPASAAGPGQMSFTFASPTQVFFNGANVRQVDVPTQTGAFGILASHVPTLQVLRPGLVVVHAEDGTTSKYFVSSGSVTVNADSSVQLLAEEAVTLDMLDPGVAKANLEKAQSELLGAADEASRAEIQIRIEANEALVKALE

Entity 6 polymer

描述 description	ATP synthase F1 subunit epsilon
分子量 formula_weight	14774.8 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	I

FPFNNCREQTNSLNCLGLQAAPRWTGAEGLRPLLPGLSLGTHPGLSRTSAACHGVGSPRPSWAARSEPTLTGPRDSTRRAHSSDIMVAYWRQAGLSYIRYSQICAKAVRDALKAEFKANAEKTSGSNVKIVKVKKE

Entity 7 polymer

描述 description	ATP synthase lipid-binding protein
分子量 formula_weight	14596.9 kDa
来源方法 src_method	nat
拷贝数 entity_count	8

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	K,L,N,O,P,Q,R,M

MFACTKLACTPALIRAGSRVAYRPISASVLSRPEARPGEGSTVFNGAQNGVSQPIQREFQTSAVSRDIDTAAKFIGAGAATVGVAGSGAGIGTVFGSLIIGYARNPSLKQQLFSYAILGFALSEAMGLFCLMVAFLILFAM

Entity 8 non-polymer

描述 description	ADENOSINE-5'-TRIPHOSPHATE
分子量 formula_weight	507.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 9 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	4

Entity 10 non-polymer

描述 description	ADENOSINE-5'-DIPHOSPHATE
分子量 formula_weight	427.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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7. 引用文献 (1)

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分辨率 resolution	3.11 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	19085

fit	/app/data/saxs_computation/by/9bym/9bym.fit
pddf	/app/data/pr_computation/by/9bym/9bym.pr.out
profile	/app/data/saxs_computation/by/9bym/9bym.dat

Cryo-EM structure of ATP synthase non-stator 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

冷冻电镜 EM 3D

5. 实体与聚合体信息 (10)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

Entity 3 polymer

聚合体 Polymer

Entity 4 polymer

聚合体 Polymer

Entity 5 polymer

聚合体 Polymer

Entity 6 polymer

聚合体 Polymer

Entity 7 polymer

聚合体 Polymer

Entity 8 non-polymer

Entity 9 non-polymer

Entity 10 non-polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)