9n4t

Composite map for GluK2-2xNeto2 in the open state, in complex with the positive allosteric modulator BPAM344 and agonist kainate

Method: ELECTRON MICROSCOPY D_max: 194.2 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	9n4t
沉积日期 deposition_date	2025-02-03
结构标题 title	Composite map for GluK2-2xNeto2 in the open state, in complex with the positive allosteric modulator BPAM344 and agonist kainate
关键词 keywords	Kainate receptor, GluK2, Ion Channel, Neto2, 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	63.60 Å
回转半径 Rg (电子) rg_electron	64.28 Å
零角强度 I(0) i0	2981100000.00
分子量 molecular_weight	477910.0 kDa
排除体积 excluded_volume	605680 Å³
包络体积 envelope_volume	941390 Å³
水化壳体积 shell_volume	127820 Å³
包络直径 envelope_diameter	216.3 Å
壳层 Rg shell_rg	62.26 Å
包络 Rg envelope_rg	61.94 Å
形状 Rg shape_rg	64.25 Å
总 Rg total_rg	64.34 Å
总原子数 total_atoms	33560
残基数 n_residues	4006
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	194.2 Å
Rg (实空间) rg_real	63.75 Å
Rg 误差 (实空间) rg_real_error	1.13 Å
I(0) (实空间) i0_real	2.9800e+09
I(0) 误差 (实空间) i0_real_error	5.9030e+07
Rg (倒空间) rg_reciprocal	63.40 Å
I(0) (倒空间) i0_reciprocal	2979000000.0000
解质量估计 total_estimate	0.8440
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	77.7 Å
偏度 Skewness skewness	0.438
峰度 Kurtosis kurtosis	-0.139
角度范围 angular_range	— – 0.1250 Å⁻¹
当前正则化参数 α current_alpha	0.0004
最高正则化参数 α highest_alpha	191000000.0000
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: 0.922; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.214

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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	Glutamate receptor ionotropic, kainate 2
分子量 formula_weight	102510.0 kDa
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	33572

MKIISPVLSNLVFSRSIKVLLCLLWIGYSQGTTHVLRFGGIFEYVESGPMGAEELAFRFAVNTINRNRTLLPNTTLTYDTQKINLYDSFEASKKACDQLSLGVAAIFGPSHSSSANAVQSICNALGVPHIQTRWKHQVSDNKDSFYVSLYPDFSSLSRAILDLVQFFKWKTVTVVYDDSTGLIRLQELIKAPSRYNLRLKIRQLPADTKDAKPLLKEMKRGKEFHVIFDCSHEMAAGILKQALAMGMMTEYYHYIFTTLDLFALDVEPYRYSGVNMTGFRILNTENTQVSSIIEKWSMERLQAPPKPDSGLLDGFMTTDAALMYDAVHVVSVAVQQFPQMTVSSLQCNRHKPWRFGTRFMSLIKEAHWEGLTGRITFNKTNGLRTDFDLDVISLKEEGLEKIGTWDPASGLNMTESQKGKPANITDSLSNRSLIVTTILEEPYVLFKKSDKPLYGNDRFEGYCIDLLRELSTILGFTYEIRLVEDGKYGAQDDVNGQWNGMVRELIDHKADLAVAPLAITYVREKVIDFSKPFMTLGISILYRKPNGTNPGVFSFLNPLSPDIWMYVLLACLGVSCVLFVIARFSPYEWYNPHPCNPDSDVVENNFTLLNSFWFGVGALMQQGSELMPKALSTRIVGGIWWFFTLIIISSYTANLAAFLTVERMESPIDSADDLAKQTKIEYGAVEDGATMTFFKKSKISTYDKMWAFMSSRRQSVLVKSNEEGIQRVLTSDYAFLMESTTIEFVTQRNCNLTQIGGLIDSKGYGVGTPMGSPYRDKITIAILQLQEEGKLHMMKEKWWRGNGCPEEESKEASALGVQNIGGIFIVLAAGLVLSVFVAVGEFLYKSKKNAQLEKRSFCSAMVEELRMSLKCQRRLKHKPQAPVIVKTEEVINMHTFNDRRLPGKETMA

来源 Source

来源生物 organism	Rattus norvegicus
通用名 common_name	Norway rat
NCBI 分类编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Homo sapiens

Entity 2 polymer

描述 description	Neuropilin and tolloid-like protein 2
分子量 formula_weight	59413.7 kDa
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

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

MALEQLCAVLKVLLITVLVVEGIAVAQKTQDGQNIGIKHVPATQCGIWVRTSNGGHFASPNYPDSYPPNKECIYILEAAPRQRIELTFDERYYIEPSFECRFDHLEVRDGPFGFSPLIDRYCGMKSPALIRSTGRFMWIKFSSDEELEGLGFRAKYSFIPDPDFTYLGGILNPIPDCQFELSGADGIVRSSQVEQEEKTKPGQAVDCIWTIKATPKAKIYLRFLDYQMEHSNECKRNFVAVYDGSSAIENLKAKFCSTVANDVMLKTGVGVIRMWADEGSRLSRFRMLFTSFVEPPCTSSTFFCHSNMCINNSLVCNGVQNCAYPWDENHCKEKKKAGLFEQITKTHGTIIGVTSGIVLVLLIISILVQVKQPRKKVMACKTAFNKTGFQEVFDPPHYELFSLREKEISADLADLSEELDNYQKLRRSSTASRCIHDHHCGSQASSVKQSRTNLSSMELPFRNDFAQPQPMKTFNSTFKKSSYTFKQTHDCPEQALEDRVMEEIPCEIYVRGRDDSAQASISIDF

来源 Source

来源生物 organism	Rattus norvegicus
通用名 common_name	Norway rat
NCBI 分类编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Homo sapiens

Entity 3 branched

描述 description	;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	910.8 kDa
来源方法 src_method	man
拷贝数 entity_count	4

Entity 4 branched

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	424.4 kDa
来源方法 src_method	man
拷贝数 entity_count	4

Entity 5 branched

描述 description	;beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	748.7 kDa
来源方法 src_method	man
拷贝数 entity_count	2

Entity 6 non-polymer

描述 description	4-cyclopropyl-7-fluoro-3,4-dihydro-2H-1,2,4-benzothiadiazine 1,1-dioxide
分子量 formula_weight	242.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 7 non-polymer

描述 description	3-(CARBOXYMETHYL)-4-ISOPROPENYLPROLINE
分子量 formula_weight	213.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 8 non-polymer

描述 description	(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
分子量 formula_weight	760.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	18

Entity 9 non-polymer

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	221.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	20

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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	3.22 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	226630

fit	/app/data/saxs_computation/n4/9n4t/9n4t.fit
pddf	/app/data/pr_computation/n4/9n4t/9n4t.pr.out
profile	/app/data/saxs_computation/n4/9n4t/9n4t.dat

Composite map for GluK2-2xNeto2 in the open state, in complex with the positive allosteric modulator BPAM344 and agonist kainate

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 branched

Entity 4 branched

Entity 5 branched

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 non-polymer

Entity 9 non-polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)