9gdp

Cryo-EM structure of Vibrio cholerae RNA polymerase holoenzyme bound to an ompU promoter DNA fragment and 5-mer RNA

Method: ELECTRON MICROSCOPY D_max: 176.0 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	9gdp
沉积日期 deposition_date	2024-08-06
结构标题 title	Cryo-EM structure of Vibrio cholerae RNA polymerase holoenzyme bound to an ompU promoter DNA fragment and 5-mer RNA
关键词 keywords	RNA polymerase, Open promoter complex, ompU, Vibrio cholerae, TRANSCRIPTION; TRANSCRIPTION
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	51.93 Å
回转半径 Rg (电子) rg_electron	51.53 Å
零角强度 I(0) i0	2984650000.00
分子量 molecular_weight	431560.0 kDa
排除体积 excluded_volume	530290 Å³
包络体积 envelope_volume	791670 Å³
水化壳体积 shell_volume	122340 Å³
包络直径 envelope_diameter	190.6 Å
壳层 Rg shell_rg	58.47 Å
包络 Rg envelope_rg	51.83 Å
形状 Rg shape_rg	51.54 Å
总 Rg total_rg	51.70 Å
总原子数 total_atoms	30165
残基数 n_residues	3658
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	176.0 Å
Rg (实空间) rg_real	51.83 Å
Rg 误差 (实空间) rg_real_error	1.48 Å
I(0) (实空间) i0_real	2.9850e+09
I(0) 误差 (实空间) i0_real_error	5.8620e+07
Rg (倒空间) rg_reciprocal	52.01 Å
I(0) (倒空间) i0_reciprocal	2985000000.0000
解质量估计 total_estimate	0.8622
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	64.5 Å
偏度 Skewness skewness	0.329
峰度 Kurtosis kurtosis	-0.162
角度范围 angular_range	— – 0.1500 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	500400000.0000
实空间数据点数 n_real_points	31
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.788; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.965; Smooth: 0.876

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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 (10)

Entity 1 polymer

描述 description	DNA-directed RNA polymerase subunit beta
分子量 formula_weight	149696.5 kDa
EC 编号 ec_number	2.7.7.6
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
原子数 atom_count	30186

MVYSYTEKKRIRKDFGTRPQVLDIPYLLSIQLDSFEKFIEQDPEGQYGLEAAFRSVFPIQSYNGNSELQYVSYRLGEPVFDVKECQIRGVTYSKPLRVKLRLVIFDKDAPAGTVKDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNARIIPYRGSWLDFEFDPKDNLYVRIDRRRKLPASIILRVLGKTSAEILDIFFEKVNFEVKDQTLMMELVPERLRGETATFDIEADGKVYVEKGRRVTARHIRQLEKDGVNFIEVPVEYIVGKVSAKDYVNEATGELIITANQEISLEALANLSQAGYKKLEVLFTNDLDHGPFMSETLRVDSTTDRISALVEIYRMMRPGEPPTKEAAESLFESLFFSAERYDLSTVGRMKFNSSIGREDAEEQGTLDEVDIIEVMKKLISIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDNVMPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHVTHYGRLCPIETPEGPNIGLINSLSAFARCNEYGFLETPYRRVVNGVVTDEVDYLSAIEEGQFVIAQANAKLTEEGGFADELVTARQKGESGLHPREHVDYMDVATNQVVSIAASLIPFLEHDDANRALMGANMQRQAVPTLRSEKPLVGTGIERNVAVDSGVTAVAKRGGVIQSVDASRIVVKVNEEELIPGEAGIDIYNLTKYTRSNQNTCINQRPCVMPGEPVARGDVLADGPSTDLGELALGQNMRIAFMPWNGYNFEDSILVSERVVQDDRFTTIHIQELSCVARDTKLGAEEITADIPNVGEAALSKLDESGIVYIGAEVKGGDILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVPNSVAGTVIDVQVFTRDGVEKDKRALEIEQMQLKEAKKDLTEEFQILEGGLLARVRSVLLAGGYTEAKLSSIERKKWLEQTLENEELQNQLEQLAEQYDELKADFDKKFEAKRRKITQGDDLAPGVLKIVKVYLAVKRRIQPGDKMAGRHGNKGVISKINPVEDMPYDENGQPVDIVLNPLGVPSRMNIGQILEVHLGLAAKGIGDKINQMIKEQQELAKLREFLQKVYDLGDTRQRVDISELSDEDVRTLAHNLRAGLPVATPVFDGAPESSIKAMLELADLPASGQLTLFDGRTGDAFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYKNIVDGNHAMEPGMPESFNVLLKEIRSLGINIELEDE

来源 Source

来源生物 organism	Vibrio cholerae O395
NCBI 分类编号 ncbi_taxonomy_id	345073
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

描述 description	;DNA-directed RNA polymerase subunit beta' ;
分子量 formula_weight	155234.3 kDa
EC 编号 ec_number	2.7.7.6
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	D

MKDLLNFLKAQHKTEEFDAIKIGLASPDMIRSWSFGEVKKPETINYRTFKPERDGLFCARIFGPVKDYECLCGKYKRLKHRGVICEKCGVEVTQTKVRRDRMGHIELASPVAHIWFLKSLPSRIGLLMDMPLRDIERVLYFEMYVVTEPGMTDLERGQMLTEEEYLDRLEEWGDEFTAKMGAEAIKDLLASMDLPAEAEQMREELDTTNSETKRKKLTKRLKLVEAFVASGNKPEWMILTVLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLELAAPDIIVRNEKRMLQESVDALLDNGRRGRAITGSNKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPYLRLHQCGLPKKMALELFKPFIYSKLETRGLATTIKAAKKMVEREEAVVWDILDEVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEARTLMMSTNNILSPASGDPIIVPSQDVVLGLYYMTREKINAKGEGMYLTGPAEAEKAYRTKTAELHARVKVRITETIKHENGKLTTETKMIDTTVGRAMLWQIVPKGLPYSLVNQKLGKKQISNLLNEAYRKLGLKDTVIFADQIMYTGFAYAALSGVSVGIDDMVVPAAKYTEIAEAEEEVREIQEQFQSGLVTAGERYNKVIDIWASTNDRVAKAMMENLSSEQVINRQGEQEKQESFNSIYMMADSGARGSAAQIRQLAGMRGLMARPDGSIIETPITANFKEGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDVVVTEHDCGTLEGVVMTPHIEGGDVKVALTELALGRVVSEDILKPGTDEVLIPRNTLLDEKWCKVINDNSVDQIKVRSVVTCDSDFGCCAQCYGRDLARGHLVNQGEAVGVIAAQSIGEPGTQLTMRTFHIGGAASTAAAENSIQAKNNGSVKLHNAKFVTNKDGKLVITSRASELTIIDEFGRTKEKHKLPYGSMLSKADGDAVAAGETVANWEAHTMPIITEVAGRVQFVDMIDGVTVSRQTDDLTGLSSSEVTEAAARPAAGKDMRPAIKLVDANGKDVLIPGTDMPAQYFLPGKAIVNLDDGAEVNVGDTLARIPQKSGGNKDITGGLPRVADLFEARKPKEPAILAEHSGTVSFGKETKGKRRLIITRDSGDTYEEMIPKHRQLNVFEGERIERGDVIADGPESPHDILRLRGIHAVTTYIANEVQEVYRLQGVKINDKHIETIVRQMLRKCTITFAGDSEFLPGETVEYSQVKIANRKLVEEGKEPARFERELLGITKASLATESFISAASFQETTRVLTEAAVSGKRDDLRGLKENVIVGRLIPAGTGFAYHQDRQAKRAQEQQGPSAEQATDNLAALLNAGFSSDDE

来源 Source

来源生物 organism	Vibrio cholerae O395
NCBI 分类编号 ncbi_taxonomy_id	345073
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 3 polymer

描述 description	DNA-directed RNA polymerase subunit omega
分子量 formula_weight	10068.4 kDa
EC 编号 ec_number	2.7.7.6
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	E

MARVTVQDAVEKIGNRFDLVLVAARRARQMQSGGKDALVPEENDKPTVIALREIEEGLITKDVLDARERQEQQEQEAAELAAVSSIMHNR

来源 Source

来源生物 organism	Vibrio cholerae O395
NCBI 分类编号 ncbi_taxonomy_id	345073
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 4 polymer

描述 description	DNA-directed RNA polymerase subunit alpha
分子量 formula_weight	36461.5 kDa
EC 编号 ec_number	2.7.7.6
来源方法 src_method	man
拷贝数 entity_count	3

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,G

MQGSVTEFLKPRLVDIEQISTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIVNPEHVICHLTSDNAAIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATFSPVDKIAYSVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEEKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLGMRLENWPPASIAED

来源 Source

来源生物 organism	Vibrio cholerae O395
NCBI 分类编号 ncbi_taxonomy_id	345073
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 5 polymer

描述 description	RNA polymerase sigma factor RpoD
分子量 formula_weight	70749.6 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	F

MDQNPQSQLKQLVLRGKEQGYLTYAEVNDHLPAEIVDSEQVEDIIQMINDMGIKVVETAPDADDLALSDDTTITDEDAAEAAAAALSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGINQVQSAIAEYPGTIPYILEQFDRVQAEELRLTDLISGFVDPNDMETEAPTATHIGSELSEADLADEDDAVVEDEDEDGDGESSDSEEEVGIDPELAREKFNELRGKFQNLQLAVNEFGRDSHQASEASDLVLDIFREFRLTPKQFDHLVETLRTSMDRVRTQERLVMKAVVEVAKMPKKSFIALFTGNESNEEWLDKVLASDKPYVAKVREQEEEIRRSIQKLQMIEQETSLSVERIKDISHRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATATSLKAATRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLDE

来源 Source

来源生物 organism	Vibrio cholerae O395
NCBI 分类编号 ncbi_taxonomy_id	345073
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 6 polymer

描述 description	;RNA 5-mer (5'-AAUAG-3') ;
分子量 formula_weight	1594.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polyribonucleotide
链编号 strand_id	H

AAUAG

Entity 7 polymer

描述 description	ompU promoter non-template DNA strand
分子量 formula_weight	21329.7 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	T

GTTGGATTTATATCATTTTACTAACTGATAGCGGAACTTTGGGACACCCACAGGTTACGCGAAAATGGC

Entity 8 polymer

描述 description	ompU promoter template DNA strand
分子量 formula_weight	21109.6 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	L

GCCATTTTCGCGGCTATTTTTTTACTCCCAAAGTTCCGCTATCAGTTAGTAAAATGATATAAATCCAAC

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	2

Entity 10 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 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	triclinic

分辨率 resolution	2.60 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	123792

fit	/app/data/saxs_computation/gd/9gdp/9gdp.fit
pddf	/app/data/pr_computation/gd/9gdp/9gdp.pr.out
profile	/app/data/saxs_computation/gd/9gdp/9gdp.dat

Cryo-EM structure of Vibrio cholerae RNA polymerase holoenzyme bound to an ompU promoter DNA fragment and 5-mer RNA

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 (10)

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

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

Entity 10 non-polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)