8oor

CryoEM Structure INO80core Hexasome complex Rvb core refinement state2

Method: ELECTRON MICROSCOPY D_max: 171.8 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	8oor
沉积日期 deposition_date	2023-04-05
结构标题 title	CryoEM Structure INO80core Hexasome complex Rvb core refinement state2
关键词 keywords	ATP-dependent chromatin remodeler, DNA BINDING PROTEIN; DNA BINDING 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	51.04 Å
回转半径 Rg (电子) rg_electron	50.73 Å
零角强度 I(0) i0	2389880000.00
分子量 molecular_weight	404230.0 kDa
排除体积 excluded_volume	505070 Å³
包络体积 envelope_volume	681110 Å³
水化壳体积 shell_volume	110190 Å³
包络直径 envelope_diameter	184.5 Å
壳层 Rg shell_rg	56.01 Å
包络 Rg envelope_rg	50.65 Å
形状 Rg shape_rg	50.78 Å
总 Rg total_rg	50.73 Å
总原子数 total_atoms	28371
残基数 n_residues	3626
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	171.8 Å
Rg (实空间) rg_real	51.09 Å
Rg 误差 (实空间) rg_real_error	1.55 Å
I(0) (实空间) i0_real	2.3900e+09
I(0) 误差 (实空间) i0_real_error	4.7600e+07
Rg (倒空间) rg_reciprocal	51.00 Å
I(0) (倒空间) i0_reciprocal	2390000000.0000
解质量估计 total_estimate	0.8467
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	61.0 Å
偏度 Skewness skewness	0.478
峰度 Kurtosis kurtosis	0.036
角度范围 angular_range	— – 0.1550 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	359200000.0000
实空间数据点数 n_real_points	32
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.780; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.664

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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 (9)

Entity 1 polymer

描述 description	RuvB-like protein 1
分子量 formula_weight	50451.8 kDa
EC 编号 ec_number	3.6.4.12
来源方法 src_method	man
拷贝数 entity_count	3

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C
原子数 atom_count	28371

MVQISEVRGNTRDHRTAAHTHIKGLGLNSSGIAEKQAAGFVGQCAAREACGVVVDLIKAHKMAGRGVLLAGGPGTGKTALALAISQELGTKIPFCPITGSEIYSTEVKKTEVLMENFRRAIGLRVRETKDVYEGEVTEMTPEEAENPLGGYGKTISTLLIGLKSARGQKKLRLDPSIYEAIQKERVQVGDVIYIETNTGACKRVGRSDAYATEFDLEAEEYVPIPKGEVHKKKEIVQDVTLHDLDVANARPQGGQDIISMMGQLMKPKMTEITDKLRMEINKVVQKYINQGVAELIPGVLFIDEAHMLDIECFTYLNKALESPIAPIVVLASNRGIATIRGADDLKAAHGIPPDFLQRLLIIPTHPYEPDEIRRIVRIRAQTEGVQLTDAAVDRVAEHGVRISLRYCLQLLAPASILARVNGRTQVDVQDIAEAEELFLDARRSANILTSTGESGGLHGFIS

来源 Source

来源生物 organism	Thermochaetoides thermophila
NCBI 分类编号 ncbi_taxonomy_id	209285
宿主生物 host_organism	Trichoplusia ni

Entity 2 polymer

描述 description	RuvB-like protein 2
分子量 formula_weight	53212.7 kDa
EC 编号 ec_number	3.6.4.12
来源方法 src_method	man
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

MAAPLVTSVTETKELRGLNLIAAHSHIRGLGVDADTLEPRPSSQGLVGQEKARKAAAVVLEMIKQGKIAGRAVLIAGPPSTGKTAIAMGMAQSLGQDVPFTTLAASEIFSLEMSKTEALTQAFRKSIGVRIKEESEIMEGEVVEIQIDRSVTGGAKQGKLTIKTTDMEAIYDMGSKMIDAMTKERVMAGDIISIDKSSGKITKLGRSYARSRDYDAMGVDTKFLQCPEGELQKRKEVVHTVSLHEIDVINSRTQGFLALFSGDTGEIRSEIRDQINTKVAEWKEEGKAEIVPGVLFIDEVHMLDIECFSYINRALESDLAPIVIMASNRGVSRIRGTDYKSPHGLPLDFLDRVVIINTHPYTPDELRQILSIRAQEEEVDLTPDALALLTKIGQEAGLRYASNLITTSQLIAAKRRAKQVGVEDVQRSFKLFYDPARSVRFVQESEKRLIGNDGVVDFSYQGAAEAAAPTLPAAAPVDPVGGEKMDMS

来源 Source

来源生物 organism	Thermochaetoides thermophila
NCBI 分类编号 ncbi_taxonomy_id	209285
宿主生物 host_organism	Trichoplusia ni

Entity 3 polymer

描述 description	Chromatin-remodeling ATPase Ino80
分子量 formula_weight	130887.7 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	G

LELKFQSKGYNQIYDQIWRDLARKDVSKVFRLATDSYATKASNLKKTAILASKEAKRWQLRTNKGTKDLQARAKRVMRDMMGFWKRNEREERDLRKAAERLELENARKEEADREAARQRRKLNFLISQTELYSHFISKKIKTHEVERSTDHPDVATDEKDKIPEPTLNINVPEPTGPIAPKVTDFNSLDFDNEDESALQAAAMANAQNAIAEAQKKAREFNKDETKLDEDGEMNFQHPELTEFEVAQPKLLNCQLKEYQLKGLNWLVNLYEQGINGILADEMGLGKTVQSISVMAYLAERYDIWGPFLVVAPASTLHNWQQEVSKFVPDFKVLPYWGTAADRKVLRKFWDRKHTTYKKDSPFHVMITSYQLVVSDVAYFQKMKWQYMILDEAQAIKSSQSSRWKCLLGFHCRNRLLLTGTPIQNNMQELWALLHFIMPSLFDSHDEFSEWFSKDIESHAQSNTKLNEDQLKRLHMILKPFMLRRVKKHVQKELGDKIEIDVFCELSYRQRAMYQSLRNQISIMDLIEKATVGDNEDSATLMNLVMQFRKVCNHPDLFERADTSSPFFCGHFAETGSFLREGTNVALGYSTRSLVEYRLPRLIWCDGGRLDKPGPGNLVAGFRSKYLNHMMNIWTPENIRSSLEGIENFTWLRFVDTSLQEAYRASHTDVFARAVDLASKQNRLGHMQIVYDEPEDKKWTPVHALFQICERENPKAVAEITTEGVLRDLMNIARVKYRELGLCRLEKAARPRASAPPIEVVCDSRSAVIERENIMFHPAMRKALFGPTPSEIKEASFGPRPVTLYPPRALLPAPDHDKQRFTNITVPSMARFVTDSGKLAKLDELLRELKEGGHRVLLYFQMTRMIDLMEEYLTYRNYKYCRLDGSTKLEDRRDTVADFQTRPEIFIFLLSTRAGGLGINLTTADTVIFYDSDWNPTIDSQAMDRAHRLGQTKQVTVYRLITRGTIEERIRKRALQKEEVQRVVITGTGSVDFSGRRPPENRNRDIAMWLADDEQAEMIERREKELIESGEYDKIMQQRRKGGKRKRGAANGDTVPSLEDMYHEGEGHFDDNKGSGAATPVDADSLGRGGKRKKAGGSKKAKTTKQRLAIADGEIDIDYKDDDDKGTDYKDDDDK

来源 Source

来源生物 organism	Thermochaetoides thermophila
NCBI 分类编号 ncbi_taxonomy_id	209285
宿主生物 host_organism	Trichoplusia ni

Entity 4 polymer

描述 description	Ino eighty subunit 2
分子量 formula_weight	53346.0 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	H

MSTRPRRHAAQRASQAITDLADRDRESDHSHGPISSRMSSFNSSSRSRLPGKGIASVSRSEAGGASDPEHIHLTVKLPSSKLRQATSSSGIKKAGSVGSSSSSSGGGKAAVKRARGGKRSRVLESSEEEEEENEVEVLGDEDEEEEEEEDEIEVREGEGYDEDEEDVEDEDEEMQDLGEEDADGEDDEMDVDAEGEEDADGDVNMDAGVVGARATTVRAVPPAIKVTKPPKESPSNGKAATASKANDNAVPVKRPAPDSDDESLSSLESEPEEEVNVAGGEDAEGEDDDAEGEVDAEGEEEEEEEEIEVADEDAEGEDVEQDEDEDEEEEDDDDEMISRAQTPDMSRLTARQRARLGEASGEYLKLSDEVQSKKHFTAEELSMRRAEMARRRRNLSEKRNEEIKMETVNKLLKKQAPRTTRRAAQAAAAAEEAEEAAKQPKRPDPMMIRWVNNKMGSVVAVPEELLGTHAGVVFGAGPGKGLPAGKMVEEVS

来源 Source

来源生物 organism	Thermochaetoides thermophila
NCBI 分类编号 ncbi_taxonomy_id	209285
宿主生物 host_organism	Trichoplusia ni

Entity 5 polymer

描述 description	Chromatin-remodeling complex subunit IES6
分子量 formula_weight	23127.5 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	I

MSNPDAQSAQAAHQALVEQLDLHSIHKTFRNPNWRPNQRRNKTIKAILGESQRKEASSTSAVATPRADDNGGGSGADTPANNDNNDGLSTSGTSTPANGNGSGAGTPASNGQPNLAQASRSLQKLVLEKSLASAQAPDKKAANGFASSAPTATYTNIESAPSLAPMKHYCDVTGLPAPYLDPKTRLRYHNKEIFAMIRNLPQGMGEQFLEARGAHTVLK

来源 Source

来源生物 organism	Thermochaetoides thermophila
NCBI 分类编号 ncbi_taxonomy_id	209285
宿主生物 host_organism	Trichoplusia ni

Entity 6 polymer

描述 description	Actin-related protein 5
分子量 formula_weight	87773.1 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	J

MAPSAVAEPPPIPQRDEPWKRLPPPTVYPVKEARFEKYIPPQLDGRERALAQPPGQVAIVIDNGSHSVRAGWNFEDKPRLAIPPIMSKYRDRKMGKTFSFAGSDCYADTTARSHIRNAFEAGTGIVSNWDVMEHVLDYVFVKLGMNECDGAIDMPIVMTEAVANLPYSRKSMSEIIFECYGAPSLVYGIDSLFSFRHNQGQTGLVVSSSYSATHVIPVYNRKALLSQAIRLNWGGWHMAEYMLKLLKLKYYTGFPGKLNSSQTEHMVRDFCYVSLDYDRELAGYLDWTGLEDRERIVQYPYTEEVVVQKTEEELARIAERKKESGRRLQEQAAKMRLERLMKKEQELEYYKDIQRRMQGESKKEIKRLLDEAELKDEAALERVIRDLERSIKRARQKDLGEPEEEEVPDFSLLDVPDDQLDEAGLRQKRQQRLLKSNWEARQRAKAEKEAEKARLAEEARLDEERRKNDLEGWLEEKRQLRLAKLNQLKERERLKADLGNRKSLASQIRMKNIANLASDNPTGSGSRKRRRGGAGADQDDDFGADDADWGVYRSVAIGANKGDDSDDEEGEEDLEAAIRSLENDLLRYDKTFSYDMTLDAQRDWSKSLLHAFRYGPRPFDPSSQAETHRVHLNVERIRVPEVLFQPAAIAGVDQAGLVEIAGDILCQRLPSLPGIQDAPDAFLRDVFLTGGNTLFQNFDERLRQGLMALLPVGAPLRVRRAQDAILDAWRGAAGWACTEEAKAAWITREEYLEKGGEYIKEHDLGNAFA

来源 Source

来源生物 organism	Thermochaetoides thermophila
NCBI 分类编号 ncbi_taxonomy_id	209285
宿主生物 host_organism	Trichoplusia ni

Entity 7 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	6

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	1

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	1

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7. 引用文献 (5)

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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	triclinic

分辨率 resolution	2.87 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	98967

fit	/app/data/saxs_computation/oo/8oor/8oor.fit
pddf	/app/data/pr_computation/oo/8oor/8oor.pr.out
profile	/app/data/saxs_computation/oo/8oor/8oor.dat

CryoEM Structure INO80core Hexasome complex Rvb core refinement state2

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 (9)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 polymer

聚合体 Polymer

来源 Source

Entity 4 polymer

聚合体 Polymer

来源 Source

Entity 5 polymer

聚合体 Polymer

来源 Source

Entity 6 polymer

聚合体 Polymer

来源 Source

Entity 7 non-polymer

Entity 8 non-polymer

Entity 9 non-polymer

7. 引用文献 (5)

8. 文件与曲线 (10)

Files (7)

Curves (3)