8z5s

Cryo-EM structure of the proximal rod-export apparatus of the polar flagellar motor

Method: ELECTRON MICROSCOPY D_max: 205.8 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	8z5s
沉积日期 deposition_date	2024-04-18
结构标题 title	Cryo-EM structure of the proximal rod-export apparatus of the polar flagellar motor
关键词 keywords	Polar flagellum, Polar flagellar motor, Proximal rod, MOTOR PROTEIN; MOTOR 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	63.80 Å
回转半径 Rg (电子) rg_electron	65.43 Å
零角强度 I(0) i0	4181090000.00
分子量 molecular_weight	553010.0 kDa
排除体积 excluded_volume	696060 Å³
包络体积 envelope_volume	973800 Å³
水化壳体积 shell_volume	128780 Å³
包络直径 envelope_diameter	250.4 Å
壳层 Rg shell_rg	61.16 Å
包络 Rg envelope_rg	65.21 Å
形状 Rg shape_rg	65.46 Å
总 Rg total_rg	65.22 Å
总原子数 total_atoms	38700
残基数 n_residues	5016
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	205.8 Å
Rg (实空间) rg_real	64.15 Å
Rg 误差 (实空间) rg_real_error	1.26 Å
I(0) (实空间) i0_real	4.1730e+09
I(0) 误差 (实空间) i0_real_error	7.8010e+07
Rg (倒空间) rg_reciprocal	63.20 Å
I(0) (倒空间) i0_reciprocal	4172000000.0000
解质量估计 total_estimate	0.8179
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	65.9 Å
偏度 Skewness skewness	0.590
峰度 Kurtosis kurtosis	-0.175
角度范围 angular_range	— – 0.1250 Å⁻¹
当前正则化参数 α current_alpha	0.0107
最高正则化参数 α highest_alpha	483800000.0000
实空间数据点数 n_real_points	26
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.801; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.226

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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 (11)

Entity 1 polymer

描述 description	Flagellar biosynthetic protein FliP
分子量 formula_weight	31314.9 kDa
来源方法 src_method	nat
拷贝数 entity_count	5

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	1,2,3,y,z
原子数 atom_count	38700

MTKGNPIRLLLSTLLLFVGVLFSSFSFAEAEESALPDNLADGSSVTVQAMQSDTGASRAMSVSSGGGIPAFTMTTNPDGSEDYSVTLQILALMTMLGFLPAMVILMTSFTRIVVVMSILRQAMGLQQTPSNQVIIGIALFLTFFVMSPVLNEINDKAVQPYLNEQVTAREAFDAAQAPMKAFMLKQTRIKDLETFVTMSGEQVDNPEDVSMAVLIPAFITSELKTAFQIGFMLFLPFLIIDLVVASVLMAMGMMMLSPMIVSLPFKLMLFVLVDGWNLILSTLAGSFAL

Entity 2 polymer

描述 description	Flagellar biosynthetic protein FliQ
分子量 formula_weight	10329.6 kDa
来源方法 src_method	nat
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	4,5,6,7

MTPEMFVELFREALWMVLIMVCAIIIPSLLIGLIVAIFQAATSINEQTLSFLPRLIVTLLALMLFGHWMTQMLMEYFYGLIERLPQVLY

Entity 3 polymer

描述 description	Flagellar basal-body rod protein FlgF
分子量 formula_weight	26987.4 kDa
来源方法 src_method	nat
拷贝数 entity_count	5

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	m,n,o,p,q

MDRALFLAMSGAKQNMQALQLRANNLANVSTTGFRADLAQARSMQAYGEGHPSRVFSMTERPGHNFAQGSVITTGRDLDVTIEGSGWISVLDHTGKEGLTRNGNLKVDQNGMLTNASGHLVLGENDAPITLPIPLSKIEIGRDGTISVLPQGAPAEEFQAVDRIKLVKPNDQSLFKDTNGLFRHKTPNQPYEADATVSLQTGAIEGSNVNAVGEMTALIDLQRQFEMQVKMMSTAEEMDKSSDSLLRMS

Entity 4 polymer

描述 description	Flagellar hook-basal body complex protein FliE
分子量 formula_weight	11135.7 kDa
来源方法 src_method	nat
拷贝数 entity_count	6

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	r,s,t,u,v,w

MKVDGIQAEMRAMMVEATNTAPTASGAKVGADFNDLLTKAINNVNTLQKASGDLQTRFDRGDADVSLSDVMIARNKSSVAFDATVQIRNKLVEAYKDLMNMPV

Entity 5 polymer

描述 description	Flagellar biosynthetic protein FlhB
分子量 formula_weight	42197.3 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	x

MAESDGQERTEEATPRRLQQAREKGQVARSKELASASVLIVGAISLMWFGEALARSLFSIMSRLFDLQREEIFDTAKLFDIALGAMTDLLFPLFLVLATLFTAAMIGAAGVGGISFSAQAAMPKLSKMNPLSGLKRMVGMQSWVELIKSILKVVLVTGVAIYLIQASQADLIQLSMDVYPQNIFHALDILLNFILLISCSLLIVVAIDIPFQIWQHADQLKMTKQEVKDEYKETEGKPEVKGRIRMLQREAAQRRMMADVPQADVIVTNPEHFSVALRYKQKTDRAPVVIAKGTDHMAMKIREVAREHDITIVPAPPLARALYHTTELEQEIPDGLFTAVAQVLAFVFQLKQYRKRGGQRPKIQDYDLPIPPEHRH

Entity 6 polymer

描述 description	Flagellar biosynthetic protein FliR
分子量 formula_weight	28905.5 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	8

MEYPTSVVLDWIANYFWPYVRISSMLMVMTVTGARFVSPRIRLYLGLAITFAVMPAIPAVPQDIELLSFRGFMTIAEQMIIGIAMGMVTQFMIQTFVLLGQILGMQSSLGFASMVDPANGQNTPLLGQLFMFLTTMFFLATDGHLKMLQLVVFSFKTLPIGSGSLNAVDFREMAGWLGIMFQTALSMSLSGIIALLTINLSFGVMTRAAPQLNIFSLGFAFALMVGLLLCWYILAGLYSHYEMFWTVGEAQICRLIRLEC

Entity 7 polymer

描述 description	Flagellar M-ring protein
分子量 formula_weight	63915.6 kDa
来源方法 src_method	nat
拷贝数 entity_count	15

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	AA,AB,AC,AD,AE,AF,AG,AH,AI,AJ,AK,AL,AM,AN,AO

MADKSTDLTVTEGGSDGALVASSDVDVESQNPDLEERSASKFDMAVGDLDLLRQVVLVLSISICVALIVMLFFWVKEPEMRPLGAYETEELIPVLDYLDQQKINYKLDGNTISVESSEYNSIKLGMVRSGVNQATEAGDDILLQDMGFGVSQRLEQERLKLSRERQLAQAIEEMKQVRKARVLLALPKHSVFVRHNQEASASVFLTLSTGTNLKQQEVDSIVDMVASAVPGMKTSRITVTDQHGRLLSSGSQDPASAARRKEQELERSQEQALREKIDSVLLPILGYGNYTAQVDIQMDFSAVEQTRKRFDPNTPATRSEYALEDYNNGNMVAGIPGALSNQPPADASIPQDVAQMKDGSVMGQGSVRKESTRNFELDTTISHERKQTGTVARQTVSVAIKDRRQVNPDTGEVTYTPMSESEINAIRQVLIGTVGFDQGRGDLLNVLSVKFAEPEAEQLEEPPIWEHPNFSDWVRWFASALVIIVVVLVLVRPAMKKLLNPTSDDEDEMYGPDGLPIGADGETSLIGSDIESSELFEFGSSIDLPNLHKDEDVLKAVRALVANEPELAAQVVKNWMNDNG

Entity 8 polymer

描述 description	Flagellar basal body rod protein FlgB
分子量 formula_weight	14240.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	5

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	b,c,d,e,f

MAISFDNALGIHQHTVGVRERNAEVISTNIAQANTPGYKARGLDFAKELQAATSGASIGLSRTDGRHIPATTTLVGDKLYRLPTQPDTGDGNTVDLDLERNLFMQNQIRHQASLDFLGSKFKNLTKAIKGE

Entity 9 polymer

描述 description	Flagellar basal-body rod protein FlgC
分子量 formula_weight	14812.6 kDa
来源方法 src_method	nat
拷贝数 entity_count	6

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	g,h,i,j,k,l

MSLFNVFNVTGSAMSAESVRLNTTSSNLANADSVSSSAKDTYKARHAVFGAELSNAMRGGDTVPVKVMGIVESDKPLSAEYNPDHPLANEEGYIYKPNVNVMEEMANMISASRAYQTNVQVADSSKQMLLRTLQMGQ

Entity 10 non-polymer

描述 description	(1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
分子量 formula_weight	751.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 11 non-polymer

描述 description	(11R,14S)-17-amino-14-hydroxy-8,14-dioxo-9,13,15-trioxa-14lambda~5~-phosphaheptadecan-11-yl decanoate
分子量 formula_weight	495.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	5

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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	3.03 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	58418

fit	/app/data/saxs_computation/z5/8z5s/8z5s.fit
pddf	/app/data/pr_computation/z5/8z5s/8z5s.pr.out
profile	/app/data/saxs_computation/z5/8z5s/8z5s.dat

Cryo-EM structure of the proximal rod-export apparatus of the polar flagellar motor

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 (11)

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 polymer

聚合体 Polymer

Entity 10 non-polymer

Entity 11 non-polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)