SAXSdb — 8h69

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8h69
沉积日期 deposition_date	2022-10-16
结构标题 title	Cryo-EM structure of influenza RNA polymerase
关键词 keywords	RNA polymerase, VIRAL PROTEIN; VIRAL 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	41.77 Å
回转半径 Rg (电子) rg_electron	41.14 Å
零角强度 I(0) i0	1067280000.00
分子量 molecular_weight	257920.0 kDa
排除体积 excluded_volume	318470 Å³
包络体积 envelope_volume	438410 Å³
水化壳体积 shell_volume	84656 Å³
包络直径 envelope_diameter	143.8 Å
壳层 Rg shell_rg	49.25 Å
包络 Rg envelope_rg	40.94 Å
形状 Rg shape_rg	41.14 Å
总 Rg total_rg	41.53 Å
总原子数 total_atoms	18028
残基数 n_residues	2190
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	135.4 Å
Rg (实空间) rg_real	41.61 Å
Rg 误差 (实空间) rg_real_error	0.84 Å
I(0) (实空间) i0_real	1.0670e+09
I(0) 误差 (实空间) i0_real_error	1.6680e+07
Rg (倒空间) rg_reciprocal	41.77 Å
I(0) (倒空间) i0_reciprocal	1067000000.0000
解质量估计 total_estimate	0.8858
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	53.4 Å
偏度 Skewness skewness	0.211
峰度 Kurtosis kurtosis	-0.399
角度范围 angular_range	— – 0.1900 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	209000000.0000
实空间数据点数 n_real_points	39
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.872; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.918

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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 (5)

Entity 1 polymer

描述 description	;RNA (5'-R(UPAPAPAPCPUPCPCPUPGPCPUPUPUPUPGPCPU)-3') ;
分子量 formula_weight	5608.3 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polyribonucleotide
链编号 strand_id	3
原子数 atom_count	18028

UAAACUCCUGCUUUUGCU

来源 Source

来源生物 organism	Influenza A virus (A/goose/Guangdong/1/1996(H5N1))
NCBI 分类编号 ncbi_taxonomy_id	93838
宿主生物 host_organism	Insect cell expression vector pTIE1

Entity 2 polymer

描述 description	;RNA (5'-R(PAPGPUPAPGPAPAPAPCPAPAPGPGPAPGPUPUPUP*U)-3') ;
分子量 formula_weight	6150.7 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polyribonucleotide
链编号 strand_id	5

AGUAGAAACAAGGAGUUUU

来源 Source

来源生物 organism	Influenza A virus (A/goose/Guangdong/1/1996(H5N1))
NCBI 分类编号 ncbi_taxonomy_id	93838
宿主生物 host_organism	Insect cell expression vector pTIE1

Entity 3 polymer

描述 description	Polymerase acidic protein
分子量 formula_weight	82669.5 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	A

MEDFVRQCFNPMIVELAEKAMKEYGEDPKIETNKFAAICTHLEVCFMYSDFHFIDERGESTIIESGDPNALLKHRFEIIEGRDRTMAWTVVNSICNTTGVEKPKFLPDLYDYKENRFIEIGVTRREVHTYYLEKANKIKSEKTHIHIFSFTGEEMATKADYTLDEESRARIKTRLFTIRQEMASRGLWDSFRQSERGEETIEERFEITGTMCRLADQSLPPNFSSLEKFRAYVDGFEPNGCIEGKLSQMSKEVNARIEPFLKTTPRPLRLPDGPPCSQRSKFLLMDALKLSIEDPSHEGEGIPLYDAIKCMKTFFGWKEPNIVKPHEKGINPNYLLAWKQVLAELQDIENEEKIPKTKNMRKTSQLKWALGENMAPEKVDFEDCKDVSDLRQYDSDEPKPRSLASWIQSEFNKACELTDSSWIELDEIGEDVAPIEHIASMRRNYFTAEVSHCRATEYIMKGVYINTALLNASCAAMDDFQLIPMISKCRTKEGRRKTNLYGFIIKGRSHLRNDTDVVNFVSMEFSLTDPRLEPHKWEKYCVLEIGDMLLRTAIGQVSRPMFLYVRTNGTSKIKMKWGMEMRRCLLQSLQQIESMIEAESSVKEKDMTKEFFENKSETWPIGESPKGMEEGSIGKVCRTLLAKSVFNSLYASPQLEGFSAESRKLLLIVQALRDNLEPGTFDLGGLYEAIEECLINDPWVLLNASWFNSFLTHALK

来源 Source

来源生物 organism	Influenza A virus (A/goose/Guangdong/1/1996(H5N1))
NCBI 分类编号 ncbi_taxonomy_id	93838
宿主生物 host_organism	Insect cell expression vector pTIE1

Entity 4 polymer

描述 description	RNA-directed RNA polymerase catalytic subunit
分子量 formula_weight	86492.2 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	B

MDVNPTLLFLKVPAQNAISTTFPYTGDPPYSHGTGTGYTMDTVNRTHQYSEKGKWTTNTETGAPQLNPIDGPLPEDNEPSGYAQTDCVLEAMAFLEKSHPGIFENSCLETMEIVQQTRVDKLTQGRQTYDWTLNRNQPAATALANTIEVFRSNGLTANESGRLIDFLKDVMESMDKGEMEIITHFQRKRRVRDNMTKKMVTQRTIGKKKQRLNKRSYLIRALTLNTMTKDAERGKLKRRAIATPGMQIRGFVYFVETLARSICEKLEQSGLPVGGNEKKAKLANVVRKMMTNSQDTELSFTITGDNTKWNENQNPRMFLAMITYITRNQPEWFRNVLSIAPIMFSNKMARLGKGYMFESKSMKLRTQIPAEMLASIDLKYFNESTRKKIEKIRPLLIDGTASLSPGMMMGMFNMLSTVLGVSILNLGQKRYTKTTYWWDGLQSSDDFALIVNAPNHEGIQAGVDRFYRTCKLVGINMSKKKSYINRTGTFEFTSFFYRYGFVANFSMELPSFGVSGINESADMSIGVTVIKNNMINNDLGPATAQMALQLFIKDYRYTYRCHRGDTQIQTRRSFELKKLWEQTRSKAGLLVSDGGPNLYNIRNLHIPEVCLKWELMDEDYQGRLCNPLNPFVSHKEIESVNNAVVMPAHGPAKSMEYDAVATTHSWIPKRNRSILNTSQRGILEDEQMYQKCCNLFEKFFPSSSYRRPVGISSMVEAMVSRARIDARIDFESGRIKKEEFAEIMKICSTIEELRRQK

来源 Source

来源生物 organism	Influenza A virus (A/goose/Guangdong/1/1996(H5N1))
NCBI 分类编号 ncbi_taxonomy_id	93838
宿主生物 host_organism	Insect cell expression vector pTIE1

Entity 5 polymer

描述 description	Polymerase basic protein 2
分子量 formula_weight	85954.0 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	C

MERIKELRDLMSQSRTREILTKTTVDHMAIIKKYTSGRQEKNPALRMKWMMAMKYPITADKRIMEMIPERNEQGQTLWSKTNDAGSDRVMVSPLAVTWWNRNGPTTSTVHYPKVYKTYFEKVERLKHGTFGPVHFRNQVKIRRRVDINPGHADLSAKEAQDVIMEVVFPNEVGARILTSESQLTITKEKKEELQDCKIAPLMVAYMLERELVRKTRFLPVAGGTSSVYIEVLHLTQGTCWEQMYTPGGEVRNDDVDQSLIIAARNIVRRATVSADPLASLLEMCHSTQIGGIRMVDILRQNPTEEQAVDICKAAMGLRISSSFSFGGFTFKRTSGSSVKKEEEVLTGNLQTLKIRVHEGYEEFTMVGRRATAILRKATRRLIQLIVSGRDEQSIAEAIIVAMVFSQEDCMIKAVRGDLNFVNRANQRLNPMHQLLRHFQKDAKVLFQNWGIEPIDNVMGMIGILPDMTPSAEMSLRGVRVSKMGVDEYSSTERVVVSIDRFLRVRDQQGNVLLSPEEVSETQGTEKLTITYSSSMMWEINGPESVLVNTYQWIIRNWETVKIQWSQDPTMLYNKMEFESFQSLVPKAARGQYSGFVRTLFQQMRDVLGTFDTVQIIKLLPFAAAPPEQSRMQFSSLTVNVRGSGMRILVRGNSPVFNYNKATKRLTVLGKDAGALTEDPDEGTAGVESAVLRGFLILGREDKRYGPALSINELSNLAKGEKANVLIGQGDVVLVMKRKRDSSILTDSQTATKRIRMAIN

来源 Source

来源生物 organism	Influenza A virus (A/goose/Guangdong/1/1996(H5N1))
NCBI 分类编号 ncbi_taxonomy_id	93838
宿主生物 host_organism	Insect cell expression vector pTIE1

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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	8h69A01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	91 — Restriction Endonuclease
同源超家族 H-superfamily homologous superfamily	90 — Influenza RNA-dependent RNA polymerase subunit PA, endonuclease domain

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7. 引用文献 (1)

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分辨率 resolution	3.70 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	790730

fit	/app/data/saxs_computation/h6/8h69/8h69.fit
pddf	/app/data/pr_computation/h6/8h69/8h69.pr.out
profile	/app/data/saxs_computation/h6/8h69/8h69.dat

Cryo-EM structure of influenza RNA polymerase

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

冷冻电镜 EM 3D

5. 实体与聚合体信息 (5)

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

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)