8x2j

Cryo-EM structure of the photosynthetic alternative complex III with a quinone inhibitor HQNO from Chloroflexus aurantiacus

Method: ELECTRON MICROSCOPY D_max: 150.2 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	8x2j
沉积日期 deposition_date	2023-11-09
结构标题 title	Cryo-EM structure of the photosynthetic alternative complex III with a quinone inhibitor HQNO from Chloroflexus aurantiacus
关键词 keywords	Photosynthetic alternative complex III, 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	44.90 Å
回转半径 Rg (电子) rg_electron	44.60 Å
零角强度 I(0) i0	1056760000.00
分子量 molecular_weight	282990.0 kDa
排除体积 excluded_volume	358760 Å³
包络体积 envelope_volume	437050 Å³
水化壳体积 shell_volume	79791 Å³
包络直径 envelope_diameter	152.8 Å
壳层 Rg shell_rg	50.49 Å
包络 Rg envelope_rg	44.84 Å
形状 Rg shape_rg	44.63 Å
总 Rg total_rg	44.72 Å
总原子数 total_atoms	19918
残基数 n_residues	2471
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	150.2 Å
Rg (实空间) rg_real	44.93 Å
Rg 误差 (实空间) rg_real_error	1.23 Å
I(0) (实空间) i0_real	1.0570e+09
I(0) 误差 (实空间) i0_real_error	2.0720e+07
Rg (倒空间) rg_reciprocal	44.90 Å
I(0) (倒空间) i0_reciprocal	1057000000.0000
解质量估计 total_estimate	0.8811
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	47.2 Å
偏度 Skewness skewness	0.344
峰度 Kurtosis kurtosis	-0.471
角度范围 angular_range	— – 0.1750 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	240900000.0000
实空间数据点数 n_real_points	36
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.872; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.852

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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 (15)

Entity 1 polymer

描述 description	Cytochrome c7-like domain-containing protein
分子量 formula_weight	25247.0 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	A
原子数 atom_count	19918

MAQIFPRNANLLSRLSIFALVLLVVEGILILGVYFRSNYFRQVNVAIEQPVAFSHQLHVNVVGIDCRYCHTSVDQSYFANIPATETCMTCHSQIKTYSPLLEKVRESYATGKPIEWVKVYDLPNFVYFNHSIHVNKGIGCSTCHGQVNNMPVVWQQQALYMGWCLNCHRNPELYVRPREEVYNMDYVPPSNQLEIGRQLVAEYGIMPPDQLTNCYVCHR

Entity 2 polymer

描述 description	Fe-S-cluster-containing hydrogenase components 1-like protein
分子量 formula_weight	113115.4 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	B

MTQQQPDLEAIRAQLRDARGPQFWRSLDQLADAPAFRELIEREFPRGASELEDGISRRTFLKLMGASLALAGVTACTYQPRQYIAPFDRQPEGRVPGIPQYFASTLTLGGYGTGVLVRSNEGRPTKVEGNPRHPASLGGTDLFAQAEILTMYDPDRSTTVLRQGVPSTWAEFTTTLGNALTAARATQGAGVRLLTTTITSPSLAAQIEQFLQAYPQARWYQYEPINRDNVVAGARLAFGRDVTTRYDLSAAQVVVSLDADFLAPGPGFVAYARAFAERRKVRKDSTTMNRLYVVEASPSTTGTAADHRLPLRADAIAAFTGALANELGVGGAPATLSPKAEEFLRAIARDLEEHRGQSVVIAGDQQPPIVHALAHLINAELGNVGQTVFYHEPVEARPTNQTEELVALVSEMAAGRVETLIMIGGNPVYNAPGDLRFADRMASVPLTIHLSQFVDETSARATWHIPQAHPLESWGDARAFDGTASIVQPLIEPLYGGKTANELLAAMLGQPEAESYDLVRSFWLEQIGETGWQVALANGVIAETVAPVIEPTLNEGAIRATPIPQPGDGVEIVFRPDPSLFDGFYANNGWLQELPRPLTKLVWDNAALMSPRTAIKLLGLPFNADRLIGTEADDRERQQYLEQLSKVNGTIARIEYRGGIIEIPIWLLPGHAEDSITLNLGYGRTHAGRVGNNVGIDVYPIRTSDSPWFGAGARVTNTGRTYLLVSTQDHWTLEGRDIYRVGEFKKFKEDPKYIAKEVYQEEYGRETPNYQSLQPGDDYTGRNAWGMTINLNACIGCNACVVACQAENNIAVVGKDQVSRGREMHWIRIDRYFAGEDLDNPSIYMMPVNCMQCEKAPCEVVCPVAATVHDYEGLNNMVYNRCVGTKYCSNNCPYKVRRFNFLQYSDTTTETFKLAFNPDVTVRIRGVMEKCTYCVQRISGARIAAKRAAVQAGQSSYVISDGAIQTACEQACPTGAIVFGDINDSNSRVAKWKAEGHNYGLLGFLNTVPRTTYLARVRNPSEELEKVEG

Entity 3 polymer

描述 description	Polysulphide reductase NrfD
分子量 formula_weight	55223.5 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	C

MAQAQPLRTRPQDDGEAYLLPGETYTSISAKIGDVPLTPPLKTPKGWLAGFSVAFFMLMIFFVSVTWLFIRGVGIWGINIPVGWGMDIINFVWWIGIGHAGTLISAILLLLNQGWRNSINRFAEAMTLFAVACAGLYPILHLGRPWLFYWLIPYPNTHGMWPQFRSALAWDVFAISTYATVSLVFWLVGLIPDFATLRDRAKNIWVKRLYGIAALGWRGSARHWHRYEMASILLAGLSTPLVVSVHSIISLDFAISQVPGWQVTVFPPYFVAGAVFAGFAMVLLLMIPVRTFYGFENYITLHHLDVMAKVMLTTGMIVVYGYFMEVFASLYSGNEFEEYLLYNRLFGPSSWAYWGLLFCNAVAIQPLWFKKVRQNIPALLIISLIVSVGMWLERYVIIVISLERDFLPSSWDIYIPTIWDWSLYIGTFGLFFTLLFLFIRVLPMINIFEMRLFLYQETEKAKQRAGHGAHGHGHEQSPAHGAATAD

Entity 4 polymer

描述 description	Quinol:cytochrome c oxidoreductase membrane protein
分子量 formula_weight	19648.6 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	D

MRNDVYGVMAEFPTPEALIEATRKAKAAGYTKMDAFSPFPIEEVIEEIAHGDTGVPRLVLLFGLIGAASGFILQYIGNLVDYPLNVGGRPLDITNWPAMIPITFESGILLASFAAAIGMIVLNGLPSPYHPVFNVPRFQYASQDAFFLCIEATDPLFDRSRTSQFLRSLNPMQVSEVAY

Entity 5 polymer

描述 description	Cytochrome c domain-containing protein
分子量 formula_weight	23017.0 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	E

MQKPRLTSRMIRFGWVGLLVLLLTACHQDMYDQQKYTTYEPSSFFADGRSSRPNVPGTTPFEVVKTDEFLYTGLIDGQEVDAMPFPVTKDLLLRGQLKYNIYCAVCHGEAGYGASMVAERGGIVPANFHQQRLREAPLSHFFVVITNGVYRGDPENGGYQSMYGYASRITPEDRWAIAAYIRALQLSQNATIDDVPPDQRAQLGN

Entity 6 polymer

描述 description	Quinol:cytochrome c oxidoreductase quinone-binding subunit 2
分子量 formula_weight	45721.7 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	F

MATTSISQTRIPQLGQVQMLGLAAAVIGIGVLAAGYFLSPTSFFESYIYGYYVAMTIPLGCLGFLMVQHLTGGAWGVTVRRMLEAGAATLPIMGLLFIPIALGYFDTYKALGLEHPLYEWANPEVVTPGGAEFDPIIAHKVPWLSPLWVTARIAIFFIIWSALALTLRAWSRQQDAGGDAKKLATRMRRLSGIGVALFVITVTFFSFDVAMSLDPHWFSTIYGAHYMANAGLMTLAFLALMMSRVRDAALFREYVSVKPIHDIGKLIFAFTVLWTYMSYGQLVIIWSGDVAEFTPWYVHRTQHGWVFVALALMLFAFALPFFVLLFRGTKRNLNTLATIAGWIVVMRFVDMAWIILPEFREHLWDIAITDVAAPIGLIGLVIALFAANVQQAPLLPLRDPNMEQLQNSGHH

Entity 7 polymer

描述 description	Uncharacterized protein
分子量 formula_weight	12485.6 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

MSYRPNYSASRYTAGRPAQPVRTARTMAEPSLSRLMIAGLMVFLVLSLVVLLAGRLPFTPQPAPVTGNTYRTYVNDARTLLNSYGYTMEGKVHIPIDRAMDLIVERGLPVRE

Entity 8 polymer

描述 description	unknown
分子量 formula_weight	4322.1 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

MQPEWSGDPEVKPVFLAVTLTGMVAFLLMVWLFAFYW

Entity 9 non-polymer

描述 description	HEME C
分子量 formula_weight	618.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

Entity 10 non-polymer

描述 description	IRON/SULFUR CLUSTER
分子量 formula_weight	351.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 11 non-polymer

描述 description	FE3-S4 CLUSTER
分子量 formula_weight	295.8 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 12 non-polymer

描述 description	[(2~{R})-3-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-2-tetradecanoyloxy-propyl] hexadecanoate
分子量 formula_weight	663.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 13 non-polymer

描述 description	2-HEPTYL-4-HYDROXY QUINOLINE N-OXIDE
分子量 formula_weight	259.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 14 non-polymer

描述 description	[(2~{R})-3-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-2-pentadecanoyloxy-propyl] pentadecanoate
分子量 formula_weight	663.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 15 non-polymer

描述 description	1,3-bis(13-methyltetradecanoyloxy)propan-2-yl pentadecanoate
分子量 formula_weight	765.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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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	2.70 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	160264

fit	/app/data/saxs_computation/x2/8x2j/8x2j.fit
pddf	/app/data/pr_computation/x2/8x2j/8x2j.pr.out
profile	/app/data/saxs_computation/x2/8x2j/8x2j.dat

Cryo-EM structure of the photosynthetic alternative complex III with a quinone inhibitor HQNO from Chloroflexus aurantiacus

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 (15)

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 polymer

聚合体 Polymer

Entity 9 non-polymer

Entity 10 non-polymer

Entity 11 non-polymer

Entity 12 non-polymer

Entity 13 non-polymer

Entity 14 non-polymer

Entity 15 non-polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)