SAXSdb — 9ip2

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	9ip2
沉积日期 deposition_date	2024-07-10
结构标题 title	Cryo-EM structure of the RNA-dependent RNA polymerase complex from Marburg virus
关键词 keywords	RNA-dependent RNA polymerase complex, 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	38.31 Å
回转半径 Rg (电子) rg_electron	37.52 Å
零角强度 I(0) i0	535399000.00
分子量 molecular_weight	193100.0 kDa
排除体积 excluded_volume	243750 Å³
包络体积 envelope_volume	329390 Å³
水化壳体积 shell_volume	70463 Å³
包络直径 envelope_diameter	124.4 Å
壳层 Rg shell_rg	45.58 Å
包络 Rg envelope_rg	37.05 Å
形状 Rg shape_rg	37.48 Å
总 Rg total_rg	38.18 Å
总原子数 total_atoms	13606
残基数 n_residues	1701
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	118.1 Å
Rg (实空间) rg_real	38.03 Å
Rg 误差 (实空间) rg_real_error	0.64 Å
I(0) (实空间) i0_real	5.3540e+08
I(0) 误差 (实空间) i0_real_error	8.1550e+06
Rg (倒空间) rg_reciprocal	38.21 Å
I(0) (倒空间) i0_reciprocal	535500000.0000
解质量估计 total_estimate	0.8881
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	51.8 Å
偏度 Skewness skewness	0.122
峰度 Kurtosis kurtosis	-0.418
角度范围 angular_range	— – 0.2050 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	113000000.0000
实空间数据点数 n_real_points	42
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.904; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.968; Smooth: 0.861

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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 (3)

Entity 1 polymer

描述 description	RNA-directed RNA polymerase L,Maltose/maltodextrin-binding periplasmic protein
分子量 formula_weight	313963.7 kDa
EC 编号 ec_number	2.7.7.48,3.6.1.-,2.7.7.88,2.1.1.375
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	13606

MQHPTQYPDARLSSPIILDQCDLLARSLGLYSHYSHNPKLRNCRIPHHIYRLRNSTALKTFLQNCSILTVPFHSIWDHILTSIQYDAINHVDDFKYLLPSELVKYANWDNEFLKAYLNKILGLDHVFSASARSQCEDFSPKENPYYWGMLLLVHLSQLARRIKGQRGSLRSNWKFIGTDLELFGIADFVIFKVPVKTIIRNAVSLQASKPGLRIWYRDQNLTPYLCDDEFIVSVASYECFIMIKDVFIERYNTWEICARAWLEDSDGADYPPLDVLGELYNQGDQIIAMYLEDGFKLIKHLEPLCVSCIQTHGIFTPRKYWFQSQMIKSYYDELHDLNLKLQISDNKAECAQNFIKTIVQAKLTPQQYCELFSLQKHWGHPVLYNDVALDKVKKHAQSTKILKPKVMFETFCVFKFIVAKNHYHSQGSWYKTTHDLHLTPYLRQHIVSNSFPSQAEIYQHLWEWYFVEHEPLFSTKIISDLSIFIKDRATAVNQECWDSVFDRSVLGYNPPVRFQSKRVPEQFLGQADFSLNQILEFAEKLEYLAPSYRNFSFSLKEKELNIGRTFGKLPYRVRNVQTLAEALLADGLAKAFPSNMMVVTEREQKEALLHQASWHHNSASIGENAIVRGASFVTDLEKYNLAFRYEFTRHFIDYCNRCYGVKNLFDWMHFLIPLCYMHVSDFYSPPHCVTEDNRNNPPDCANAYHYHLGGIEGLQQKLWTCISCAQITLVELKTKLKLKSSVMGDNQCITTLSLFPIDAPNDYQENEAELNAARVAVELAITTGYSGIFLKPEETFVHSGFIYFGKKQYLNGVQLPQSLKTMARCGPLSDSIFDDLQGSLASIGTSFERGTSETRHIFPSRWIASFHSMLAINLLNQNHLGFPLGFNIDISCFKKPLTFSEKLIALITPQVLGGLSFLNPEKLFYRNISDPLTSGLFQLKNALEFLEKEELFYILISKKPGLADASDFVMNPLGLNVPGSKEIITFLRQTVRENITITSQNRIINSLFHIGSDLEDQRVCEWLLSSNPVMSRFAADIFSRTPSGKRLQVLGYLEGTRTLLASRTISLTTEGTMLMKLRELTRNRWKSWFSYIDALDDDLSESLEKFTCTVDVANFLRAYSWSDVLKGKRLIGATLPCLLEQFEVKWINLSEDLREQFNLSSDSKSTINLLPYDCKELRLEGSNDTELNYVSCALDRKVVQKHPSVNRLAWTIGNRAPYIGSRTEDKIGYPPLRVNCPSAALKEAIEMVSRLLWVTQGTADREKLLIPLLNSRVNLDYQTVLNFLPTHYSGNIVHRYNDQYGQHSFMANRMSNTSTRAIISTNTLGKYAGGGQAAIDSNIIFQNTINLGVAVLDIALSLAKLSSASNVTFRLMLNKCCTRHVPSEYLYFDKPLDVDLNKYMDNELVYDNDPLCSGIKGRLGRVSRSTLTLSLNVSDIGSYDFPTIAAWTLGETIVGSIFSDESSQSTDPISSGCTKTFVTHFLVYPVESIFYAFGANLIVESLSLSRIKSIKNLSDLTFLISSTIRNLSHRSLRILQSTFRHELVLTRLAHHIPLISLMLGGSAGEKSSSDAVRLFLTASYQNFINNFSCLMKKGQSSLPVWLYFPSEGQQLKPILKILQRLSDLLSPDKIQKRKILADTCCPIGSFWVYPSKSTRTNHYYASLNYWRDKANKVKNTPFSHLINCSFPEFSSHTSSVSSNQQVTNSKYIVYPENITEINARTRLINYGSTALQGMDTKMPLSEQNLVENCRPSEGIRFKDNQKITKHDQRCEREESSPQQMFPEDNMQTPAHIHSSSPFQILIKSLDAHEDFDASKIILNSEINNLNLTEYTLNTKLLTTPTRTEILDTSPLQSSRYSSTSRERSLLSREQASYLYVDCSNIPSISLDPGFRSMSDQNQVQMLINTYKRDLHACFDSNQFCRFTGVVSSMHYKLYDLLPPGKLKKAICLAEGEGSGARLLLKWKETDYLFFNTLATDSQQEAEILSGRVIPRMLYNIDRLSALLESRRLILNNLTIQITDITNPLWLDSVIQYLPEDSDILTMDAETTKDETREQLYKTIVNIWTRTSPNIPKISIIKVFLLDYEGTLFLMKNAIQYYGQVQLKKPYSSNAKNSEWYLCCGKRRIQRLQIDFSDQVGIFLICKAMSRQRQAIPYWLKHIEKNYPASLHEFFLTLGFPSLESSFCHRYTIPFSEGKALFHKVQSYVRQGKQHLHSLMLDYENNSPLLDLRNHFICSLRGKITKYYNDILKLNLVIKAVEKGKNWSQLVEILPNMHSVCIVHVDHECSGCEKRLLLKLDFIRNTKIAEQKLLNRVIGYILFFPFGLFKSGSLRASRENLYFQGSGWSHPQFEKGGGSGGGSGGSAWSHPQFEKGSASHHHHHHGTKTEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDEALKDAQTGDYKDDDDK

来源 Source

来源生物 organism	Escherichia coli K-12
NCBI 分类编号 ncbi_taxonomy_id	83333
宿主生物 host_organism	Spodoptera frugiperda

Entity 2 polymer

描述 description	Maltose/maltodextrin-binding periplasmic protein,Polymerase cofactor VP35
分子量 formula_weight	79881.0 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	B,C,D,E

MGSSHHHHHHGTKTEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDEALKDAQTGTDYDIPTTLEVLFQGPLGSMWDSSYMQQVSEGLMTGKVPIDQVFGANPLEKLYKRRKPKGTVGLQCSPCLMSKATSTDDIIWDQLIVKRTLADLLIPINRQISDIQSTLSEVTTRVHEIERQLHEITPVLKMGRTLEAISKGMSEMLAKYDHLVISTGRTTAPAAAFDAYLNEHGVPPPQPAIFKDLGVAQQACSKGTMVKNATTDAADKMSKVLELSEETFSKPNLSAKDLALLLFTHLPGNNTPFHILAQVLSKIAYKSGKSGAFLDAFHQILSEGENAQAALTRLSRTFDAFLGVVPPVIRVKNFQTVPRPCQKSLRAVPPNPTIDKGWVCVYSSEQGETRALKI

来源 Source

来源生物 organism	Marburg virus - Musoke, Kenya, 1980
NCBI 分类编号 ncbi_taxonomy_id	33727
宿主生物 host_organism	Spodoptera frugiperda

Entity 3 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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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	2.700 Å
最低分辨率 resolution_low	306.360 Å
R 因子 r_factor	0.2944
R_work r_work	0.2944
R_free r_free	0.3006

分辨率 resolution	2.70 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	319722

fit	/app/data/saxs_computation/ip/9ip2/9ip2.fit
pddf	/app/data/pr_computation/ip/9ip2/9ip2.pr.out
profile	/app/data/saxs_computation/ip/9ip2/9ip2.dat

Cryo-EM structure of the RNA-dependent RNA polymerase complex from Marburg virus

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

精修参数 Refinement

冷冻电镜 EM 3D

5. 实体与聚合体信息 (3)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 non-polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)