9pgh

The cryo-EM structure of C. crescentus RNAP-Sigma73-CCNA_03891/CCNA_01149 promoter complex

Method: ELECTRON MICROSCOPY D_max: 176.8 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	9pgh
沉积日期 deposition_date	2025-07-07
结构标题 title	The cryo-EM structure of C. crescentus RNAP-Sigma73-CCNA_03891/CCNA_01149 promoter complex
关键词 keywords	CCNA_03891-CCNA_01149 promoter complex, DriD, Caulobacter, RNA Polymerase, Transcription, TRANSCRIPTION-DNA complex; TRANSCRIPTION/DNA
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	53.23 Å
回转半径 Rg (电子) rg_electron	52.39 Å
零角强度 I(0) i0	2916380000.00
分子量 molecular_weight	428840.0 kDa
排除体积 excluded_volume	527850 Å³
包络体积 envelope_volume	831800 Å³
水化壳体积 shell_volume	126980 Å³
包络直径 envelope_diameter	190.4 Å
壳层 Rg shell_rg	59.39 Å
包络 Rg envelope_rg	52.23 Å
形状 Rg shape_rg	52.40 Å
总 Rg total_rg	52.53 Å
总原子数 total_atoms	30040
残基数 n_residues	3815
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	176.8 Å
Rg (实空间) rg_real	53.08 Å
Rg 误差 (实空间) rg_real_error	1.15 Å
I(0) (实空间) i0_real	2.9160e+09
I(0) 误差 (实空间) i0_real_error	4.9260e+07
Rg (倒空间) rg_reciprocal	53.35 Å
I(0) (倒空间) i0_reciprocal	2917000000.0000
解质量估计 total_estimate	0.8666
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	64.8 Å
偏度 Skewness skewness	0.284
峰度 Kurtosis kurtosis	-0.232
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	506800000.0000
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: 0.819; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.957; Smooth: 0.848

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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	DNA-directed RNA polymerase subunit alpha
分子量 formula_weight	37315.5 kDa
EC 编号 ec_number	2.7.7.6
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	30040

MIERNWNELIRPEKPQIETGADATRKARIVAEPLERGFGVTLGNALRRVLLSSLQGAAVTAIQIDGVVHEFSSLEGVREDVVDIVLNIKQLAVRMHAEGPKRMTLRATGPGPVTAGQIETPADIEILNPDHVLCTLDDGASVRMEFTVNNGKGYVPADRNRPEDAPIGLIAVDALYSPVKRVAYRVEPTRQGQSLDYDKLILEVETNGAVTPVDAVAYAARILQDQLQIFITFEEPKAKSADESKPELPFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGRKSLNEIKEVLAGMGLHLGMDVPNWPPENIEDLAKKFEDQI

Entity 2 polymer

描述 description	DNA-directed RNA polymerase subunit beta
分子量 formula_weight	151085.6 kDa
EC 编号 ec_number	2.7.7.6
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	C

MAQSFTGKKRIRKSFGRIPEAVQMPNLIEVQRSSYEQFLQRETRPGLRRDEGVEAVFKSVFPIKDFNERAVLEYVSYEFEEPKYDVEECIQRDMTFAAPLKVKLRLIVFETEEETGARSVKDIKEQDVYMGDIPLMTDKGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHASGKLLFAARVIPYRGSWLDFEFDAKDIVYVRIDRRRKLPATTFLYALGMDGEEILTTFYDVVPFEKRSGGWATPYKPERWRGVKPEFPLVDADTGEEVAPAGTKITARQAKKFADGGLKTLLLAPEALTGRYLARDAVNMATGEIYAEAGDELDVTSIQALADQGFSTIDVLDIDHVTVGAYMRNTLRVDKNAIREDALFDIYRVMRPGEPPTVEAAEAMFKSLFFDAERYDLSSVGRVKMNMRLEQDVSDEVRILRKEDVLAVLKVLVGLRDGRGEIDDIDNLGNRRVRSVGELLENQYRVGLLRMERAIKERMSSVDIDTVMPHDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATHARVNKYGFIESPYRRVKDGKPQDEVVYMSAMEESKHVIAQSNIKVAEGEIVEDLVPGRINGEPTLLQKETVDLMDVSPRQVVSVAAALIPFLENDDANRALMGSNMQRQAVPLVQSDAPLVGTGMEAVVARDSGAVVIAKRTGVVEQIDGTRIVIRATEETDPARSGVDIYRMSKFQRSNQSTCINQRPLVKVGDRIVAGDIIADGPSTELGELALGRNALVAFMPWNGYNFEDSILISERIVRDDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVGEEALRNLDEAGIVAIGAEVQPGDILVGKVTPKGESPMTPEEKLLRAIFGEKASDVRDTSLRLPPGVAGTIVDVRVFNRHGVDKDERALAIERAEIDRLGKDRDDEFAILNRNISGRLKELLIGKVALSGPKGLSRGEITAEGLAQVASGLWWQIALEDEKAMGELESLRRLFDENRKRLDRRFEDKVDKLQRGDELPPGVMKMVKVFVAVKRKLQPGDKMAGRHGNKGVISRILPIEDMPFLADGTHVDVVLNPLGVPSRMNVGQIFETHLGWACANLGKQITNLLEDWQQGGQKQALVERLTEIYGPDEELPDTEEGLVELARNLGKGVPIATPVFDGARMDDIEGHLEMAGVNKSGQSILFDGLTGEQFKRPVTVGYIYMLKLHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVAGRTKVYESIVRGDDTFEAGIPESFNVLVKEMRSLGLNVELENS

Entity 3 polymer

描述 description	;DNA-directed RNA polymerase subunit beta' ;
分子量 formula_weight	154467.0 kDa
EC 编号 ec_number	2.7.7.6
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

MNQEVLNIFNPVQAAPTFDQIRISLASPEKIRSWSFGEIKKPETINYRTFKPERDGLFCARIFGPTKDYECLCGKYKRMKYKGIICEKCGVEVTLARVRRERMGHIELASPVAHIWFLKSLPSRIAMMLDMPLKDIERVLYFEYYIVTEPGLTPLKQHQLLSEDDYMRAQEEYGDDSFTAEIGAEAIQNLLKAIDLEKEAERLREELSGTVSDMKQKKFSKRLKILEAFQESGNRPEWMVLTVVPVIPPELRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLIELRAPDIIIRNEKRMLQESVDALFDNGRRGRVITGANKRPLKSLADMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHECGLPKKMALELFKPFIYARLDAKGLSGTVKQSKRMVEREQPQVWDILEEVIREHPVLLNRAPTLHRLGIQAFEPKLIEGKAIQLHPLVCAAFNADFDGDQMAVHVPLSLEAQLEARVLMMSTNNILSPANGRPIIVPSQDIVLGLYYLSVARDGEPGEGKIFADLGEIEAAMDAGVVSLHAKIKARHTEMTPEGVLLRKVIDTTPGRMKIAALLPHHPQIGHRLIEKALTKKEIGNLIDIVYRHCGQKATVIFADKVMGLGFKEAAKAGISFGKDDIIIPVRKTAIVEETRKLAEEYEQQYADGLITKGEKYNKVVDAWAKATDRVADEMMAELQMKHKDENGREKEINAIYMMAHSGARGSQAQMKQLGGMRGLMAKPSGEIIETPIVSNFKEGLTVQEYFNSTHGARKGLADTALKTANSGYLTRRLVDVAQDCIIVEEDCGTTKGITLRAVVEGGDVLVSLGSRVLGRFTAEDVKDPGTGELVVPADTYIDENIADAIEAAVVQSVKVRSVLTCEAKIGVCGACYGRDLARGTPVNIGEAVGVIAAQSIGEPGTQLTMRTFHIGGTAQVAEQSFFEASNEGTVRVIGPTVVGSDGALVIMSRNTSVSVLVDGKERETYKPPYGARLRVKDGDLVKRGQRLGDWDPYTTPIITEVAGKIRAEDLVDGLSIREEVDEATGIAQRVVADWRTSARGSDLRPAMGVLSEDGSYKRLSNGGEARYLLSAGAILSVADGDEVKPGEVIARIPTEGAKTRDITGGLPRVAELFEARRPKDCAVIAEMDGRVEFGKDYKNKRRIKITPDVDADGNQPEAVEFLIPKGKHIAVHDGDYITKGEYIIDGNPDPHDILRILGVEALANFLVDEIQEVYRLQGVPINDKHIETIVRQMLQKVEILEPGDTGLIKGDHLDKPEFDKEQEKAIARGGRPAVTQPVLLGITKASLQTKSFISAASFQETTRVLTEASVHGKTDTLEGLKENVIVGRLIPAGTGSYLRSLQRVAAKRDEQLAQQREDAMEPLPAEIALSDAE

Entity 4 polymer

描述 description	DNA-directed RNA polymerase subunit omega
分子量 formula_weight	13289.8 kDa
EC 编号 ec_number	2.7.7.6
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

MARVTVEDCVEKVPNRFALVLLSAHRARGISAGAALMVDRDNDKNPVVALREIADDVIDHEGLKEHLISTLQRVDEHTEAEEEAETLALLADPSHMQMSELELVRALQSDRDGGQEERY

Entity 5 polymer

描述 description	RNA polymerase sigma factor RpoD
分子量 formula_weight	72770.2 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	F

MSNNSSAETEAPETTGGDGPLLDLTDAGVKKFIKQAKARGYVTMDELNKVLPSEEVSPDAIEDTLAMLSEMGVNVVEAEEDAENAEGGEVATRDENTTVIASDKPAAYDRTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGRDTMIRGLCESALTFEAIMVWREELGTGRILLREVIDLEGTYAAINGVAAQPAAEDDEGPAEPVDDEAGEAKAEGAEGEDEDDFDDGAGPTVSAMEGELREGVMAILDAIASEFEAFRKLQDKLVGSRLKGEDLSDADRKAYEGLSATIIQHLKTLKLNNNRIEALVEQLYAINKRLIGLEGRLLRLADSYGISRGEFLKAYFGSELNPTWSEQVKAMGVRWTKFVENDSQSVTDIRSEIAALATETGVPIDDYRRIVQTVQKGEREARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFIEDKNAILPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLDS

来源 Source

来源生物 organism	Caulobacter vibrioides NA1000
NCBI 分类编号 ncbi_taxonomy_id	565050
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 6 polymer

描述 description	DNA (55-MER)-non template
分子量 formula_weight	30196.2 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	H

CATGCCGCCCGTCATACGACCGTTTCTGTCGCAATGCGCGGACAATCTTCCATCATCGCCCCTGGAGAACCCAAGGACCTTCGATGACCCGCTTCGCCT

Entity 7 polymer

描述 description	DNA (43-MER)-template
分子量 formula_weight	30894.7 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	I

AGGCGAAGCGGGTCATCGAAGGTCCTTGGGTTCTCCAGGGGCGATGATGGAAGATTGTCCGCGCATTGCGACAGAAACGGTCGTATGACGGGCGGCATG

Entity 8 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

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

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7. 引用文献 (4)

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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	3.540 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	3.54 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	150644

fit	/app/data/saxs_computation/pg/9pgh/9pgh.fit
pddf	/app/data/pr_computation/pg/9pgh/9pgh.pr.out
profile	/app/data/saxs_computation/pg/9pgh/9pgh.dat

The cryo-EM structure of C. crescentus RNAP-Sigma73-CCNA_03891/CCNA_01149 promoter complex

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 (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

来源 Source

Entity 6 polymer

聚合体 Polymer

Entity 7 polymer

聚合体 Polymer

Entity 8 non-polymer

Entity 9 non-polymer

7. 引用文献 (4)

8. 文件与曲线 (10)

Files (7)

Curves (3)