8k60

Cryo-EM structure of Streptomyces coelicolor transcription initiation complex with the global transcription factor AfsR

Method: ELECTRON MICROSCOPY D_max: 182.4 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	8k60
沉积日期 deposition_date	2023-07-24
结构标题 title	Cryo-EM structure of Streptomyces coelicolor transcription initiation complex with the global transcription factor AfsR
关键词 keywords	transcription factor, TRANSCRIPTION-DNA complex, GENE REGULATION; GENE REGULATION
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	54.43 Å
回转半径 Rg (电子) rg_electron	53.65 Å
零角强度 I(0) i0	3285010000.00
分子量 molecular_weight	452310.0 kDa
排除体积 excluded_volume	555280 Å³
包络体积 envelope_volume	829990 Å³
水化壳体积 shell_volume	125020 Å³
包络直径 envelope_diameter	193.9 Å
壳层 Rg shell_rg	59.38 Å
包络 Rg envelope_rg	53.55 Å
形状 Rg shape_rg	53.64 Å
总 Rg total_rg	53.83 Å
总原子数 total_atoms	31659
残基数 n_residues	3895
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	182.4 Å
Rg (实空间) rg_real	54.33 Å
Rg 误差 (实空间) rg_real_error	1.21 Å
I(0) (实空间) i0_real	3.2850e+09
I(0) 误差 (实空间) i0_real_error	5.7310e+07
Rg (倒空间) rg_reciprocal	54.49 Å
I(0) (倒空间) i0_reciprocal	3286000000.0000
解质量估计 total_estimate	0.8736
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	62.9 Å
偏度 Skewness skewness	0.307
峰度 Kurtosis kurtosis	-0.342
角度范围 angular_range	— – 0.1450 Å⁻¹
当前正则化参数 α current_alpha	0.0002
最高正则化参数 α highest_alpha	589400000.0000
实空间数据点数 n_real_points	30
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.841; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; 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 (10)

Entity 1 polymer

描述 description	DNA-directed RNA polymerase subunit alpha
分子量 formula_weight	36734.6 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,K
原子数 atom_count	31659

MLIAQRPSLTEEVVDEFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVKEDVTDLILNIKQLVVSSEHDEPVVMYLRKQGPGLVTAADIAPPAGVEVHNPDLVLATLNGKGKLEMELTVERGRGYVSAVQNKQVGQEIGRIPVDSIYSPVLKVTYKVEATRVEQRTDFDKLIVDVETKQAMRPRDAMASAGKTLVELFGLARELNIDAEGIDMGPSPTDAALAADLALPIEELELTVRSYNCLKREGIHSVGELVARSEADLLDIRNFGAKSIDEVKAKLAGMGLALKDSPPGFDPTAAADAFGADDDADAGFVETEQY

来源 Source

来源生物 organism	Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)
NCBI 分类编号 ncbi_taxonomy_id	100226
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	128644.9 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

MAASRNASTANTNNAASTAPLRISFAKIKEPLEVPNLLALQTESFDWLLGNDAWKARVESALESGQDVPTKSGLEEIFEEISPIEDFSGSMSLTFRDHRFEPPKNSIDECKDRDFTYAAPLFVTAEFTNNETGEIKSQTVFMGDFPLMTNKGTFVINGTERVVVSQLVRSPGVYFDSSIDKTSDKDIFSAKIIPSRGAWLEMEIDKRDMVGVRIDRKRKQSVTVLLKALGWTTEQILEEFGEYESMRATLEKDHTQGQDDALLDIYRKLRPGEPPTREAAQTLLENLYFNPKRYDLAKVGRYKVNKKLGADEPLDAGVLTTDDVIATIKYLVKLHAGETETVGESGREIVVETDDIDHFGNRRIRNVGELIQNQVRTGLARMERVVRERMTTQDVEAITPQTLINIRPVVASIKEFFGTSQLSQFMDQNNPLSGLTHKRRLNALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGLIGSLASYGRINPFGFIETPYRKVVEGQVTDDVDYLTADEEDRFVIAQANAALGDDMRFAEARVLVRRRGGEVDYVPGDDVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMMRQAVPLIKSESPLVGTGMEYRSAADAGDVVKAEKAGVVQEVSADYITTTNDDGTYITYRLAKFSRSNQGTSVNQKVIVAEGDRIIEGQVLADGPATENGEMALGKNLLVAFMPWEGHNYEDAIILSQRLVQDDVLSSIHIEEHEVDARDTKLGPEEITRDIPNVSEEVLADLDERGIIRIGAEVVAGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGEIGKVIGVRVFDREEGDELPPGVNQLVRVYVAQKRKITDGDKLAGRHGNKGVISKINPIEDMPFLEDGTPVDIILNPLAVPSRMNPGQVLEIHLGWLASRGWDVSGLAEEWAQRLQVIGADKVEPGTNVATPVFDGAREDELAGLLQHTIPNRDGERMVLPSGKARLFDGRSGEPFPEPISVGYMYILKLHHLVDDKLHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYALQELLTIKSDDVTGRVKVYEAIVKGENIPEPGIPESFKVLIKEMQSLCLNVEVLSSDGMSIEMRDTDEDVFRAAEELGIDLSRREPSSVEEV

来源 Source

来源生物 organism	Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)
NCBI 分类编号 ncbi_taxonomy_id	100226
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 3 polymer

描述 description	;DNA-directed RNA polymerase subunit beta' ;
分子量 formula_weight	144807.1 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

MLDVNFFDELRIGLATADDIRQWSHGEVKKPETINYRTLKPEKDGLFCEKIFGPTRDWECYCGKYKRVRFKGIICERCGVEVTRAKVRRERMGHIELAAPVTHIWYFKGVPSRLGYLLDLAPKDLEKVIYFAAYMITFVDEERRTRDLPSLEAHVSVERQQIEQRRDSDLEARAKKLETDLAELEAEGAKADVRRKVREGAEREMKQLRDRAQREIDRLDEVWNRFKNLKVQDLEGDELLYRELRDRFGTYFDGSMGAAALQKRLESFDLDEEAERLREIIRTGKGQKKTRALKRLKVVSAFLQTSNSPKGMVLDCVPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDLGAPEIIVNNEKRMLQEAVDALFDNGRRGRPVTGPGNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSARSVIVVGPQLKLHQCGLPKAMALELFKPFVMKRLVDLNHAQNIKSAKRMVERGRTVVYDVLEEVIAEHPVLLNRAPTLHRLGIQAFEPQLVEGKAIQIHPLVCTAFNADFDGDQMAVHLPLSAEAQAEARILMLSSNNILKPADGRPVTMPTQDMVLGLFFLTTDSEGRSPKGEGRAFGSSAEAIMAFDAGDLTLQAKIDIRFPVGTIPPRGFEPPAREEGEPEWQQGDTFTLKTTLGRALFNELLPEDYPFVDYEVGKKQLSEIVNDLAERYPKVIVAATLDNLKAAGFFWATRSGVTVAISDIVVPDAKKEIVKGYEGQDEKVQKQYERGLITKEERTQELIAIWTKATNEVAEAMNDNFPKTNPVSMMVNSGARGNMMQMRQIAGMRGLVSNAKNETIPRPIKASFREGLSVLEYFISTHGARKGLADTALRTADSGYLTRRLVDVSQDVIIREEDCGTERGLKLPIATRDADGTLRKAEDVETSVYARMLAEDVVIDGKVIAPANVDLGDVLIDALVAHGVEEVKTRSILTCESQVGTCAMCYGRSLATGKLVDIGEAVGIIAAQSIGEPGTQLTMRTFHTGGVAGDDITQGLPRVVELFEARTPKGVAPISEASGRVRIEETEKTKKIVVTPDDGSDETAFPISKRARLLVGEGDHVEVGQKLTVGATNPHDVLRILGQRAVQVHLVGEVQKVYNSQGVSIHDKHIEIIIRQMLRRVTIIESGDAELLPGELVERTKFETENRRVVQEGGHPASGRPQLMGITKASLATESWLSAASFQETTRVLTDAAINAKSDSLIGLKENVIIGKLIPAGTGLSRYRNIRVEPTEEAKAAMYSAVGYDDIDYSPFGTGSGQAVPLEDYDYGPYNQ

来源 Source

来源生物 organism	Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)
NCBI 分类编号 ncbi_taxonomy_id	100226
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 4 polymer

描述 description	DNA-directed RNA polymerase subunit omega
分子量 formula_weight	9716.9 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

MSSSISAPEGIINPPIDELLEATDSKYSLVIYAAKRARQINAYYSQLGEGLLEYVGPLVDTHVHEKPLSIALREINAGLLTSEAIEGPAQ

来源 Source

来源生物 organism	Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)
NCBI 分类编号 ncbi_taxonomy_id	100226
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 5 polymer

描述 description	RNA polymerase principal sigma factor HrdB
分子量 formula_weight	56017.6 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

MSASTSRTLPPEIAESVSVMALIERGKAEGQIAGDDVRRAFEADQIPATQWKNVLRSLNQILEEEGVTLMVSAAEPKRTRKSVAAKSPAKRTATKAVAAKPVTSRKATAPAAPAAPATEPAAVEEEAPAKKAAAKKTTAKKATAKKTTAKKAAAKKTTAKKEDGELLEDEATEEPKAATEEPEGTENAGFVLSDEDEDDAPAQQVAAAGATADPVKDYLKQIGKVPLLNAEQEVELAKRIEAGLFAEDKLANSDKLAPKLKRELEIIAEDGRRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVIEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADAVSFTLLQEQLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLD

来源 Source

来源生物 organism	Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)
NCBI 分类编号 ncbi_taxonomy_id	100226
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 6 polymer

描述 description	Non-template strand DNA for AfsS promoter
分子量 formula_weight	18177.6 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	G

CCGGAGCGTTCAGCGTTCGTTTATCTCCCCCTGGTATAATGGGAGCTGTCACGGATGCA

Entity 7 polymer

描述 description	Template strand DNA for AfsS promoter
分子量 formula_weight	18360.8 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

TGCATCCGTGAGTCGAGGGTAATAACCAGGGGGAGATAAACGAACGCTGAACGCTCCGG

Entity 8 polymer

描述 description	Regulatory protein AfsR
分子量 formula_weight	105842.6 kDa
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	I,J

MDGGPRVPEQRRPGFPAEEEESGALRFGVLGPVRAWRDGETLATGSPQQRALLAALLLREGRTATAGELIDALWGEEPPSQALAAVRTYASRLRKVLDPGVLVSESGGYAVRGLAEGALDLARAQDLASAAEKARSAGDLCHARDLLRRALDLWDGEVLAGVPGPYAQTQRVRLGEWRLQLLETRLDMDLDQGCHAEAVSELTALTAAHPLRERLRELLMLALYRSGRQAEALAVYADTRRLLADELGVDPRPGLQELQQRILQADPALAELSAATAETATATLRPAQLPATVSDFTGRAAFVRELSDVLSAASGESASGRVMAVSALAGIGGVGKTTLAVHVAHRARAAFPDGQLYVDLQGAGARPAEPETVLGSFLRALGTADSAIPDSLEERAALYRSVLDGRRVLVLLDNARDAAQVRPLLPGTDGCAALVTARVRMVDLAGAHLVDLDVMAPEEALALFTKIVGEERVASERQAALDVVGACGFLPLAIRIAASRLAARRTWTVSVLAAKLADERRRLDELQAGDQAVEATFELGYGQLEPAQARAFRLLGLADGPDISLAAAAAVLDLPAQDTEDLLESLVDTSLLESAAPGRYRFHDLVRLYARACAERTERDGNAPSERGAALSRLLDFYLATAAGVYAIERPGDRLVDGLEPTEYPGLTFTEGSAALDWLYTEAAPLLACVRQSAGTARLRRAVDLLWAAKDLTESGANSHQYEATARAMCDATGSAADTRAEGRARTVLSDVLLVSGRIEHAEEEARLAMRLAGSAEDSAAVSWVANNRGLVCLHQRRYAEGKGLFHQAIAGFRATDNRAGEASALSNLSRAQLGMGNVAEAVDIARQGLAVYAELGRTMRLANGHFALGVALTRAGRHEEALGEFAEALDLFGDHRQRLWEGATNFRLAEVHLAAGRPSSAAQHAEQALALGCIGGDRMRGNVLALLGRALSALGQADRARACWREALSLYEQHDAQEVGEVRALLARSVAR

来源 Source

来源生物 organism	Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)
NCBI 分类编号 ncbi_taxonomy_id	100226
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 9 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 10 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 (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	3.40 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	231221

fit	/app/data/saxs_computation/k6/8k60/8k60.fit
pddf	/app/data/pr_computation/k6/8k60/8k60.pr.out
profile	/app/data/saxs_computation/k6/8k60/8k60.dat

Cryo-EM structure of Streptomyces coelicolor transcription initiation complex with the global transcription factor AfsR

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

来源 Source

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)