9nnz

Structure of rod opsin in complex with a megabody

Method: ELECTRON MICROSCOPY D_max: 93.9 Å Quality: REASONABLE

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	9nnz
沉积日期 deposition_date	2025-03-06
结构标题 title	Structure of rod opsin in complex with a megabody
关键词 keywords	opsin, membrane protein, megabody, nanobody; 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	24.97 Å
回转半径 Rg (电子) rg_electron	24.17 Å
零角强度 I(0) i0	21598100.00
分子量 molecular_weight	34768.0 kDa
排除体积 excluded_volume	42993 Å³
包络体积 envelope_volume	59915 Å³
水化壳体积 shell_volume	22132 Å³
包络直径 envelope_diameter	90.7 Å
壳层 Rg shell_rg	29.79 Å
包络 Rg envelope_rg	24.93 Å
形状 Rg shape_rg	24.19 Å
总 Rg total_rg	24.87 Å
总原子数 total_atoms	2484
残基数 n_residues	374
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	93.9 Å
Rg (实空间) rg_real	25.28 Å
Rg 误差 (实空间) rg_real_error	1.14 Å
I(0) (实空间) i0_real	2.1600e+07
I(0) 误差 (实空间) i0_real_error	3.5380e+05
Rg (倒空间) rg_reciprocal	25.21 Å
I(0) (倒空间) i0_reciprocal	21600000.0000
解质量估计 total_estimate	0.6809
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	3
主峰位置 r_peak_primary	23.8 Å
偏度 Skewness skewness	0.645
峰度 Kurtosis kurtosis	0.007
角度范围 angular_range	— – 0.3200 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	7528000.0000
实空间数据点数 n_real_points	64
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.476; Stabil: 0.977; Sysdev: 1.000; Positv: 1.000; Valcen: 0.488; Smooth: 0.000

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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 (4)

Entity 1 polymer

描述 description	Megabody 7
分子量 formula_weight	55284.6 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	A
原子数 atom_count	2484

QVQLVESGGGLVQTKTTTSVIDTTNDAQNLLTQAQTIVNTLKDYCPILIAKSSSSNGGTNNANTPSWQTAGGGKNSCATFGAEFSAASDMINNAQKIVQETQQLSANQPKNITQPHNLNLNSPSSLTALAQKMLKNAQSQAEILKLANQVESDFNKLSSGHLKDYIGKCDASAISSANMTMQNQKNNWGNGCAGVEETQSLLKTSAADFNNQTPQINQAQNLANTLIQELGNNTYEQLSRLLTNDNGTNSKTSAQAINQAVNNLNERAKTLAGGTTNSPAYQATLLALRSVLGLWNSMGYAVICGGYTKSPGENNQKDFHYTDENGNGTTINCGGSTNSNGTHSYNGTNTLKADKNVSLSIEQYEKIHEAYQILSKALKQAGLAPLNSKGEKLEAHVTTSKYGSLRLSCAASGFTFSRYVMNWVRQAPGKGLEWVSGISRDGSYTDYADSVKGRFTISRDNAKDTLYLQMNSLKPEDTAVYYCSKYNSVVTTPPGQGTQVTVSSHHHHHHEPEA

来源 Source

来源生物 organism	synthetic construct
NCBI 分类编号 ncbi_taxonomy_id	32630
宿主生物 host_organism	Escherichia coli

Entity 2 polymer

描述 description	Rhodopsin
分子量 formula_weight	39031.5 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	B

MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA

Entity 3 branched

描述 description	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	586.5 kDa
来源方法 src_method	man
拷贝数 entity_count	1

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	1

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7. 引用文献 (1)

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分辨率 resolution	3.940 Å
最低分辨率 resolution_low	— Å
R 因子 r_factor	—
R_work r_work	—
R_free r_free	—

分辨率 resolution	3.94 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	337101

fit	/app/data/saxs_computation/nn/9nnz/9nnz.fit
pddf	/app/data/pr_computation/nn/9nnz/9nnz.pr.out
profile	/app/data/saxs_computation/nn/9nnz/9nnz.dat

Structure of rod opsin in complex with a megabody

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

精修参数 Refinement

冷冻电镜 EM 3D

5. 实体与聚合体信息 (4)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

Entity 3 branched

Entity 4 branched

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)