8e9b

Cryo-EM structure of S. pombe Arp2/3 complex in the branch junction

Method: ELECTRON MICROSCOPY D_max: 246.8 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

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8e9b
沉积日期 deposition_date	2022-08-26
最后修订 last_revision	2023-02-01
结构标题 title	Cryo-EM structure of S. pombe Arp2/3 complex in the branch junction
关键词 keywords	Arp2-3 complex, branch juction, polymerization, STRUCTURAL PROTEIN; STRUCTURAL PROTEIN
实验方法 method	ELECTRON MICROSCOPY

▼

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	63.06 Å
回转半径 Rg (电子) rg_electron	63.13 Å
零角强度 I(0) i0	4421470000.00
分子量 molecular_weight	557550.0 kDa
排除体积 excluded_volume	696250 Å³
包络体积 envelope_volume	984600 Å³
水化壳体积 shell_volume	132340 Å³
包络直径 envelope_diameter	219.0 Å
壳层 Rg shell_rg	62.48 Å
包络 Rg envelope_rg	62.35 Å
形状 Rg shape_rg	63.10 Å
总 Rg total_rg	63.21 Å
总原子数 total_atoms	39160
残基数 n_residues	4925
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

▼

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	246.8 Å
Rg (实空间) rg_real	67.62 Å
Rg 误差 (实空间) rg_real_error	1.86 Å
I(0) (实空间) i0_real	4.4780e+09
I(0) 误差 (实空间) i0_real_error	9.7080e+07
Rg (倒空间) rg_reciprocal	62.96 Å
I(0) (倒空间) i0_reciprocal	4420000000.0000
解质量估计 total_estimate	0.8671
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	69.1 Å
偏度 Skewness skewness	0.663
峰度 Kurtosis kurtosis	0.301
角度范围 angular_range	— – 0.1250 Å⁻¹
当前正则化参数 α current_alpha	0.8615
最高正则化参数 α highest_alpha	380700000.0000
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: 0.676; Stabil: 0.823; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.834

▶

4. 晶体学与实验 4. Crystallography & Experiment

▶

5. 实体与聚合体信息 (11)

Entity 1 polymer

描述 description	Actin-related protein 3
分子量 formula_weight	47427.1 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	A
原子数 atom_count	39160

MASFNVPIIMDNGTGYSKLGYAGNDAPSYVFPTVIATRSAGASSGPAVSSKPSYMASKGSGHLSSKRATEDLDFFIGNDALKKASAGYSLDYPIRHGQIENWDHMERFWQQSLFKYLRCEPEDHYFLLTEPPLNPPENRENTAEIMFESFNCAGLYIAVQAVLALAASWTSSKVTDRSLTGTVVDSGDGVTHIIPVAEGYVIGSSIKTMPLAGRDVTYFVQSLLRDRNEPDSSLKTAERIKEECCYVCPDIVKEFSRFDREPDRYLKYASESITGHSTTIDVGFERFLAPEIFFNPEIASSDFLTPLPELVDNVVQSSPIDVRKGLYKNIVLSGGSTLFKNFGNRLQRDLKRIVDERIHRSEMLSGAKSGGVDVNVISHKRQRNAVWFGGSLLAQTPEFGSYCHTKADYEEYGASIARRYQIFGNSL

Entity 2 polymer

描述 description	Actin-related protein 2
分子量 formula_weight	44286.8 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	B

MESAPIVLDNGTGFVKVGYAKDNFPRFQFPSIVGRPILRAEEKTGNVQIKDVMVGDEAEAVRSLLQVKYPMENGIIRDFEEMNQLWDYTFFEKLKIDPRGRKILLTEPPMNPVANREKMCETMFERYGFGGVYVAIQAVLSLYAQGLSSGVVVDSGDGVTHIVPVYESVVLNHLVGRLDVAGRDATRYLISLLLRKGYAFNRTADFETVREMKEKLCYVSYDLELDHKLSEETTVLMRNYTLPDGRVIKVGSERYECPECLFQPHLVGSEQPGLSEFIFDTIQAADVDIRKYLYRAIVLSGGSSMYAGLPSRLEKEIKQLWFERVLHGDPARLPNFKVKIEDAPRRRHAVFIGGAVLADIMAQNDHMWVSKAEWEEYGVRALDKLGPRTT

Entity 3 polymer

描述 description	Actin-related protein 2/3 complex subunit 1
分子量 formula_weight	41643.5 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

MATSQVLHILPKPSYEHAFNSQRTEFVTTTATNQVELYEQDGNGWKHARTFSDHDKIVTCVDWAPKSNRIVTCSQDRNAYVYEKRPDGTWKQTLVLLRLNRAATFVRWSPNEDKFAVGSGARVISVCYFEQENDWWVSKHLKRPLRSTILSLDWHPNNVLLAAGCADRKAYVLSAYVRDVDAKPEASVWGSRLPFNTVCAEYPSGGWVHAVGFSPSGNALAYAGHDSSVTIAYPSAPEQPPRALITVKLSQLPLRSLLWANESAIVAAGYNYSPILLQGNESGWAHTRDLDAGTSKTSFTHTGNTGEGREEEGPVSFTALRSTFRNMDLKGSSQSISSLPTVHQNMIATLRPYAGTPGNITAFTSSGTDGRVVLWTL

Entity 4 polymer

描述 description	Actin-related protein 2/3 complex subunit 2
分子量 formula_weight	37025.2 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

MLSLDYNNIFIYELLTERFSSENPSSIDQVVTDFDGVTFHISTPEEKTKILISLSMKCYPELVNYGTLDLLKQIYGAYVHEPEMGYNFSILIDLQQLPATDEEKEQLAMSISMLKRNVLAAPFHRAFTKQAELADLARKDPENAPMLDKQATSQELMAIHYRDEETIVLWPEHDRVTVVFSTKFREETDRIFGKVFLQEFVDARRRPAIQTAPQVLFSYRDPPLEIRDIQGIQKGDDFGFVTFVLFERHFTPQNREDCISHIQVFRNTLHFHIKASKAYMHQRMRKRVADFQKVLNRAKPDVELERKTATGRSFVRA

Entity 5 polymer

描述 description	Actin-related protein 2/3 complex subunit 3
分子量 formula_weight	19865.7 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	E

MPAYHSSFLSLTDVPTTGNIAMLPLKTKFRGPAYPADESQMDIIDECIGLFRANCFFRNFEIKGPADRTLIYGTLFISECLGRVNGLNYRDAERQLNSLALENFSIPGSAGFPLNALYAPPLSPQDAEIMRTYLTQFRQELAYRLLSHVYATEKDHPSKWWTCFSKRRFMNKAL

Entity 6 polymer

描述 description	Actin-related protein 2/3 complex subunit 4
分子量 formula_weight	19637.7 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

MSNTLRPYLNAVRSTLTASLALEEFSSEIVERQSQPEVEVGRSPEILLKPLVVSRNEQEQCLIESSVNSVRFSIRIKQVDEIERILVRKFMQFLMGRAESFFILRRKPVQGYDISFLITNYHTEEMLKHKLVDFIIEFMEEVDAEISEMKLFLNGRARLVAETYLSCF

Entity 7 polymer

描述 description	Actin-related protein 2/3 complex subunit 5
分子量 formula_weight	16922.1 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	G

MTFRTLDVDSITEPVLTEQDIFPIRNETAEQVQAAVSQLIPQARSAIQTGNALQGLKTLLSYVPYGNDVQEVRTQYLNAFVDVLSNIRAADIPAFVKECSTEEIDNIVNFIYRGLANPQAYNSSVLLNWHEKVVEISGIGCIVRVLNSRPDL

Entity 8 polymer

描述 description	Actin, alpha skeletal muscle
分子量 formula_weight	41875.6 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	M,N,O,P,Q,R,H,I

DEDETTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREKMTQIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDLAGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEKSYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNVMSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWITKQEYDEAGPSIVHRKCF

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	10

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	9

Entity 11 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

▼

6. 折叠分类 (SCOP + CATH) 5 domains

CATH v4.4 (5 domains)

结构域编号 domain_id	8e9bA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	640 — Actin; Chain A, domain 4
同源超家族 H-superfamily homologous superfamily	10 — ATPase, substrate binding domain, subdomain 4

结构域编号 domain_id	8e9bB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	640 — Actin; Chain A, domain 4
同源超家族 H-superfamily homologous superfamily	10 — ATPase, substrate binding domain, subdomain 4

结构域编号 domain_id	8e9bC01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	130 — 7 Propeller
拓扑 Topology topology	10 — Methylamine Dehydrogenase; Chain H
同源超家族 H-superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

结构域编号 domain_id	8e9bD01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1460 — Yope Regulator; Chain: A,
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	8e9bG01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	25 — Alpha Horseshoe
拓扑 Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
同源超家族 H-superfamily homologous superfamily	190 — Actin-related protein 2/3 complex subunit 5

▶

7. 引用文献 (1)

▶

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	3.50 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	79467

fit	/app/data/saxs_computation/e9/8e9b/8e9b.fit
pddf	/app/data/pr_computation/e9/8e9b/8e9b.pr.out
profile	/app/data/saxs_computation/e9/8e9b/8e9b.dat

Cryo-EM structure of S. pombe Arp2/3 complex in the branch junction

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 non-polymer

Entity 10 non-polymer

Entity 11 non-polymer

6. 折叠分类 (SCOP + CATH) 5 domains

CATH v4.4 (5 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)