8gap

Structure of LARP7 protein p65-telomerase RNA complex in telomerase

Method: ELECTRON MICROSCOPY D_max: 177.5 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	8gap
沉积日期 deposition_date	2023-02-23
结构标题 title	Structure of LARP7 protein p65-telomerase RNA complex in telomerase
关键词 keywords	La protein, La-related protein, telomerase, ribonucleoprotein, RNA BINDING PROTEIN; RNA 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	49.88 Å
回转半径 Rg (电子) rg_electron	50.35 Å
零角强度 I(0) i0	1561520000.00
分子量 molecular_weight	296350.0 kDa
排除体积 excluded_volume	357230 Å³
包络体积 envelope_volume	534670 Å³
水化壳体积 shell_volume	90038 Å³
包络直径 envelope_diameter	185.3 Å
壳层 Rg shell_rg	52.95 Å
包络 Rg envelope_rg	49.52 Å
形状 Rg shape_rg	50.36 Å
总 Rg total_rg	50.38 Å
总原子数 total_atoms	20630
残基数 n_residues	2205
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	177.5 Å
Rg (实空间) rg_real	49.93 Å
Rg 误差 (实空间) rg_real_error	1.71 Å
I(0) (实空间) i0_real	1.5620e+09
I(0) 误差 (实空间) i0_real_error	3.3930e+07
Rg (倒空间) rg_reciprocal	49.88 Å
I(0) (倒空间) i0_reciprocal	1561000000.0000
解质量估计 total_estimate	0.8584
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	61.0 Å
偏度 Skewness skewness	0.402
峰度 Kurtosis kurtosis	-0.140
角度范围 angular_range	— – 0.1600 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	120900000.0000
实空间数据点数 n_real_points	33
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.754; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.895

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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	Telomerase reverse transcriptase
分子量 formula_weight	133486.9 kDa
EC 编号 ec_number	2.7.7.49
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	20630

MQKINNINNNKQMLTRKEDLLTVLKQISALKYVSNLYEFLLATEKIVQTSELDTQFQEFLTTTIIASEQNLVENYKQKYNQPNFSQLTIKQVIDDSIILLGNKQNYVQQIGTTTIGFYVEYENINLSRQTLYSSNFRNLLNIFGEEDFKYFLIDFLVFTKVEQNGYLQVAGVCLNQYFSVQVKQKKWYKNNFNMNGKATSNNNQNNANLSNEKKQENQYIYPEIQRSQIFYCNHMGREPGVFKSSFFNYSEIKKGFQFKVIQEKLQGRQFINSDKIKPDHPQTIIKKTLLKEYQSKNFSCQEERDLFLEFTEKIVQNFHNINFNYLLKKFCKLPENYQSLKSQVKQIVQSENKANQQSCENLFNSLYDTEISYKQITNFLRQIIQNCVPNQLLGKKNFKVFLEKLYEFVQMKRFENQKVLDYICFMDVFDVEWFVDLKNQKFTQKRKYISDKRKILGDLIVFIINKIVIPVLRYNFYITEKHKEGSQIFYYRKPIWKLVSKLTIVKLEEENLEKVEEKLIPEDSFQKYPQGKLRIIPKKGSFRPIMTFLRKDKQKNIKLNLNQILMDSQLVFRNLKDMLGQKIGYSVFDNKQISEKFAQFIEKWKNKGRPQLYYVTLDIKKCYDSIDQMKLLNFFNQSDLIQDTYFINKYLLFQRNKRPLLQIQQTNNLNSAMEIEEEKINKKPFKMDNINFPYYFNLKERQIAYSLYDDDDQILQKGFKEIQSDDRPFIVINQDKPRCITKDIIHNHLKHISQYNVISFNKVKFRQKRGIPQGLNISGVLCSFYFGKLEEEYTQFLKNAEQVNGSINLLMRLTDDYLFISDSQQNALNLIVQLQNCANNNGFMFNDQKITTNFQFPQEDYNLEHFKISVQNECQWIGKSIDMNTLEIKSIQKQTQQEINQTINVAISIKNLKSQLKNKLRSLFLNQLIDYFNPNINSFEGLCRQLYHHSKATVMKFYPFMTKLFQIDLKKSKQYSVQYGKENTNENFLKDILYYTVEDVCKILCYLQFEDEINSNIKEIFKNLYSWIMWDIIVSYLKKKKQFKGYLNKLLQKIRKSRFFYLKEGCKSLQLILSQQKYQLNKKELEAIEFIDLNNLIQDIKTLIPKISAKSNQQNTN

Entity 2 polymer

描述 description	Telomerase holoenzyme Teb1 subunit
分子量 formula_weight	82040.3 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	D

MKLTKGGSYILKKVDRKQFYQDEEIVMQIKKILGQKTTDCKQYIKCECIDGLGDEALIYFEMLANQNQHLQKNDVIMIQDYLNDKTQNDKIVVLVTRFQFCKASHVQPKTAQKESIQLLNTEKTIIQKSKITKNPAEEVLKFIEVNEKDNSSNSEDMIIEQQKQEIKNNQKEKQSINGFNLEDSYSNISDITNFGGKSNFNIGSLSDQLSKQTLLISQLQVGKNRFSFKFEGRVVYKSSTFQNQQDSKYFFITAQDANNQEINLSFWQKVDQSYQTLKVGQYYYFIGGEVKQFKNNLELKFKFGDYQIIPKETLSANYVQPLALQPSKQFGNDSIGDSDYSIHNLIEKEESIAQKGYNGQKNNKYRQNNNNSKHTLLISEVLKTSKQYLSVLAQVVDIQSSDKNIRLKICDNSCNQELKVVIFPDLCYEWRDKFSINKWYYFNEFVRQIYNDEVQLKNNIHSSIKESDDQRKVITYNQEQGVFKKSISINSNDSFEIKPKISYKNNSNQEQRIYSSIEEIIQQAQASEIGQKKEFYVYGNLVSIQMKNKLYYYRCTCQGKSVLKYHGDSFFCESCQQFINPQVHLMLRAFVQDSTGTIPVMIFDQQSSQLINQIDPSIHVQEAGQYVKNCIENGQEEIIRQLFSKLDFARFIFEIQFENKEFNNEQEIAYKVLKIEKENIKEESKYLLKKLEHLINNNQNN

Entity 3 polymer

描述 description	Telomerase holoenzyme Teb2 subunit
分子量 formula_weight	30993.0 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

MSNRVQGGFDNNSGNNQSAQKQQAEKIPQITVPLNCFMINQIVKAAKENPQAHSGNHYEWYGAFENAIITAKFEFLQSINDSPKIMGKLSDSTGCIEVVIQKSKMSDELPEFVQAYEIELQNNGNRHKYVRAMLKMRKNAQIQLLYFSIVNDANEISRHGLDLCLRYLQRKHGIEDFMHMTNDKAHNNHNASAQKVHYQIDRNQQPKEQVLELMRQILKHNPNDQIPKSKIIEFFQSQLNQVQINQILQQLVSANEIFSVGSDNYLLNV

Entity 4 polymer

描述 description	Telomerase holoenzyme Teb3 subunit
分子量 formula_weight	14007.6 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

MDAEQEQVMYPRILFEQMAQFRGKKVTVVGNVCNEDQNDSLVIEFGPTGLNQHVVIDNYRRVDLNNTTKFVEIRGVVLNQNIVSCEELTEFEQKDPFDFDTYSKLIHLSQSDKLSSLFTDQ

Entity 5 polymer

描述 description	Telomerase associated protein p50
分子量 formula_weight	50049.7 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	G

MKLLLQNQNIFQKLKNTLNGCIKKFYDTYQDLEQMQKFEMIVEDKLLFRYSCSQSEMFSAQIQAHYLEKRVLQLTDGNVKYIVNFRDKGVLDKANFFDTPNNSLVIIRQWSYEIYYTKNTFQINLVIDEMRCIDIITTIFYCKLELDFTQGIKGISKSSSFSNQIYEYSAQYYKAIQLLKKLLINDSYISELYNSTKSKQQPRLFIFQSFKPKMNLAEQNLSRQFEQCQQDDFGDGCLLQIVNYTHQSLKQIENKNNSNQIVNGQNEISKKKRVLKSNEDLYKISLQKQLKIFQEEEIELHSQSTIRNQTNQQLETFESDTSKRNSEKILHSINELNTSKQKVNQMNSSQHQIQKLENNNLNKNILNQINENDIKNELEERQQQHLTQSFNSKAQLKKIITLKKNQDILLFKPQEQEGSKKY

Entity 6 polymer

描述 description	telomere DNA
分子量 formula_weight	9581.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polydeoxyribonucleotide
链编号 strand_id	C

GTTGGGGTTGGGGTTGGGGTTGGGGTTGGG

Entity 7 polymer

描述 description	Telomerase RNA
分子量 formula_weight	50747.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polyribonucleotide
链编号 strand_id	B

AUACCCGCUUAAUUCAUUCAGAUCUGUAAUAGAACUGUCAUUCAACCCCAAAAAUCUAGUGCUGAUAUAACCUUCACCAAUUAGGUUCAAAUAAGUGGUAAUGCGGGACAAAAGACUAUCGACAUUUGAUACACUAUUUAUCAAUGGAUGUCUUAUUUU

Entity 8 polymer

描述 description	Telomerase La-related protein p65
分子量 formula_weight	64207.4 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	H

MDEYLENTNLEELEQECFMEDYQHEDVVEQENHQVDANDIYENQQMNDESQLNQDVKISQQKEQAVEMIEEQQQNNQDKFKQFQDCMAHITELNFKRNYQNLTEQSSSNNVVAEELDIKESLKLQMEYYFCDTNLTHDSYLRGIISKSPKNCVDIKVFLKFNKIQQILKQIQDKQIVSTYGIENQSQKKNHKNYKNQNATFSKKDLIHLIRDSLKESKILKVKMDSLKVKRRFPFNLEQALKNSKQRTLYIDFLPPKCSKQTLVSIFGNFRIININLPLQKNSQLCQGFAFIEFFSEEEANQALITKNSSIPKELILLTEKKIGQGSIRIITYKKWQEEKQSFKELSKNQNEQKNKNMNQSRKASDEFVSIDVEIKQNCLIKIINIPQGTLKAEVVLAVRHLGYEFYCDYIDENSNQINSNKISLSTQQQNTAQCSNIQIENNLIQQDQHPQLNDLLKEGQAMIRFQNSDEQRLAIQKLLNHNNNKLQIEIRGQICDVISTIPEDEEKNYWNYIKFKKNEFRKFFFMKKQQKKQNITQNYNK

Entity 9 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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6. 折叠分类 (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

结构域编号 domain_id	8gapF01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
同源超家族 H-superfamily homologous superfamily	140 — Nucleic acid-binding proteins

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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	3.80 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	162358

fit	/app/data/saxs_computation/ga/8gap/8gap.fit
pddf	/app/data/pr_computation/ga/8gap/8gap.pr.out
profile	/app/data/saxs_computation/ga/8gap/8gap.dat

Structure of LARP7 protein p65-telomerase RNA complex in telomerase

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

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

6. 折叠分类 (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)