8hsr

Thermus thermophilus Rho-engaged RNAP elongation complex (composite structure)

Method: ELECTRON MICROSCOPY D_max: 201.1 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	8hsr
沉积日期 deposition_date	2022-12-20
结构标题 title	Thermus thermophilus Rho-engaged RNAP elongation complex (composite structure)
关键词 keywords	Transcription elongation complex, Transcription termination, 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	60.00 Å
回转半径 Rg (电子) rg_electron	60.05 Å
零角强度 I(0) i0	5446990000.00
分子量 molecular_weight	606900.0 kDa
排除体积 excluded_volume	754360 Å³
包络体积 envelope_volume	1100900 Å³
水化壳体积 shell_volume	147790 Å³
包络直径 envelope_diameter	203.7 Å
壳层 Rg shell_rg	65.27 Å
包络 Rg envelope_rg	59.10 Å
形状 Rg shape_rg	60.11 Å
总 Rg total_rg	59.96 Å
总原子数 total_atoms	42577
残基数 n_residues	5238
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	201.1 Å
Rg (实空间) rg_real	59.82 Å
Rg 误差 (实空间) rg_real_error	2.12 Å
I(0) (实空间) i0_real	5.4470e+09
I(0) 误差 (实空间) i0_real_error	1.1270e+08
Rg (倒空间) rg_reciprocal	60.12 Å
I(0) (倒空间) i0_reciprocal	5449000000.0000
解质量估计 total_estimate	0.8729
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	69.6 Å
偏度 Skewness skewness	0.249
峰度 Kurtosis kurtosis	-0.470
角度范围 angular_range	— – 0.1300 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	773000000.0000
实空间数据点数 n_real_points	27
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.854; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.962; Smooth: 0.822

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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 (12)

Entity 1 polymer

描述 description	Transcription termination factor Rho
分子量 formula_weight	47996.3 kDa
来源方法 src_method	man
拷贝数 entity_count	6

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F
原子数 atom_count	42577

GPMRRKETLQETPLTYQELASKILPELHLLAQEAGIEGYKRMKKDQLIMALLERQTQGEGLRLVKGYLEISQDGYGFLTENLHNLESRVAIVSAGLIKQYALRAGDYVVGQARPPRENERYATLLKVEAVNNLDPEAAKNRPRFDELTPQFPDRQIRLETTPDELSTRVIDLLAPIGRGQRGLIVAPPKAGKTTLLKKIANAVLKNEPDIKVIVLLIDERPEEVTDFRESVQGAEVIASTFDEPPQNHIRVAEFVHERAKRIVEEGGHVMILLDSITRLARANNLVTPPTGRTLSGGLDSAALYFPKRFLGAARNIRGGGSLTILATALVETGSRMDDVIFEEFKGTGNMELHLSRRLEERRIFPAIDILKSGTRREELLLGEEVTHKMWLLRKVLADMDPAEAMEMLLARLARTKNNKEFLASLAAR

来源 Source

来源生物 organism	Thermus thermophilus HB8
NCBI 分类编号 ncbi_taxonomy_id	300852
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

描述 description	DNA-directed RNA polymerase subunit alpha
分子量 formula_weight	35056.2 kDa
EC 编号 ec_number	2.7.7.6
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	G,H

MLDSKLKAPVFTVRTQGREYGEFVLEPLERGFGVTLGNPLRRILLSSIPGTAVTSVYIEDVLHEFSTIPGVKEDVVEIILNLKELVVRFLNPSLQTVTLLLKAEGPKEVKARDFLPVADVEIMNPDLHIATLEEGGRLNMEVRVDRGVGYVPAEKHGIKDRINAIPVDAVFSPVRRVAFQVEDTRLGQRTDLDKLTLRIWTDGSVTPLEALNQAVEILREHLTYFSNPQAAAVAAPEEAKEPEAPPEQEEELDLPLEELGLSTRVLHSLKEEGIESVRALLALNLKDLKNIPGIGERSLEEIKEALEKKGFTLKE

来源 Source

来源生物 organism	Thermus thermophilus HB8
NCBI 分类编号 ncbi_taxonomy_id	300852
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	125436.5 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	I

MEIKRFGRIREVIPLPPLTEIQVESYRRALQADVPPEKRENVGIQAAFRETFPIEEEDKGKGGLVLDFLEYRLGEPPFPQDECREKDLTYQAPLYARLQLIHKDTGLIKEDEVFLGHIPLMTEDGSFIINGADRVIVSQIHRSPGVYFTPDPARPGRYIASIIPLPKRGPWIDLEVEPNGVVSMKVNKRKFPLVLLLRVLGYDQETLARELGAYGELVQGLMDESVFAMRPEEALIRLFTLLRPGDPPKRDKAVAYVYGLIADPRRYDLGEAGRYKAEEKLGIRLSGRTLARFEDGEFKDEVFLPTLRYLFALTAGVPGHEVDDIDHLGNRRIRTVGELMTDQFRVGLARLARGVRERMLMGSEDSLTPAKLVNSRPLEAAIREFFSRSQLSQFKDETNPLSSLRHKRRISALGPGGLTRERAGFDVRDVHRTHYGRICPVETPEGANIGLITSLAAYARVDELGFIRTPYRRVVGGVVTDEVVYMTATEEDRYTIAQANTPLEGNRIAAERVVARRKGEPVIVSPEEVEFMDVSPKQVFSVNTNLIPFLEHDDANRALMGSNMQTQAVPLIRAQAPVVMTGLEERVVRDSLAALYAEEDGEVAKVDGNRIVVRYEDGRLVEYPLRRFYRSNQGTALDQRPRVVVGQRVRKGDLLADGPASENGFLALGQNVLVAIMPFDGYNFEDAIVISEELLKRDFYTSIHIERYEIEARDTKLGPERITRDIPHLSEAALRDLDEEGVVRIGAEVKPGDILVGRTSFKGESEPTPEERLLRSIFGEKARDVKDTSLRVPPGEGGIVVRTVRLRRGDPGVELKPGVREVVRVYVAQKRKLQVGDKLANRHGNKGVVAKILPVEDMPHLPDGTPVDVILNPLGVPSRMNLGQILETHLGLAGYFLGQRYISPIFDGAKEPEIKELLAQAFEVYFGKRKGEGFGVDKREVEVLRRAEKLGLVTPGKTPEEQLKELFLQGKVVLYDGRTGEPIEGPIVVGQMFIMKLYHMVEDKMHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEMLTLKSDDIEGRNAAYEAIIKGEDVPEPSVPESFRVLVKELQALALDVQTLDEKDNPVDIFEGLASKR

来源 Source

来源生物 organism	Thermus thermophilus HB8
NCBI 分类编号 ncbi_taxonomy_id	300852
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 4 polymer

描述 description	;DNA-directed RNA polymerase subunit beta' ;
分子量 formula_weight	171994.4 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	J

MKKEVRKVRIALASPEKIRSWSYGEVEKPETINYRTLKPERDGLFDERIFGPIKDYECACGKYKRQRFEGKVCERCGVEVTKSIVRRYRMGHIELATPAAHIWFVKDVPSKIGTLLDLSATELEQVLYFSKYIVLDPKGAILNGVPVEKRQLLTDEEYRELRYGKQETYPLPPGVDALVKDGEEVVKGQELAPGVVSRLDGVALYRFPRRVRVEYVKKERAGLRLPLAAWVEKEAYKPGEILAELPEPYLFRAEEEGVVELKELEEGAFLVLRREDEPVATYFLPVGMTPLVVHGEIVEKGQPLAEAKGLLRMPRQVRAAQVEAEEEGETVYLTLFLEWTEPKDYRVQPHMNVVVPEGARVEAGDKIVAAIDPEEEVIAEAEGVVHLHEPASILVVKARVYPFEDDVEVSTGDRVAPGDVLADGGKVKSDVYGRVEVDLVRNVVRVVESYDIDARMGAEAIQQLLKELDLEALEKELLEEMKHPSRARRAKARKRLEVVRAFLDSGNRPEWMILEAVPVLPPDLRPMVQVDGGRFATSDLNDLYRRLINRNNRLKKLLAQGAPEIIIRNEKRMLQEAVDALLDNGRRGAPVTNPGSDRPLRSLTDILSGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMALELFKPFLLKKMEEKGIAPNVKAARRMLERQRDIKDEVWDALEEVIHGKVVLLNRAPTLHRLGIQAFQPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITQVRKEKKGAGLEFATPEEALAAHERGEVALNAPIKVAGRETSVGRLKYVFANPDEALLAVAHGIVDLQDVVTVRYMGKRLETSPGRILFARIVAEAVEDEKVAWELIQLDVPQEKNSLKDLVYQAFLRLGMEKTARLLDALKYYGFTFSTTSGITIGIDDAVIPEEKKQYLEEADRKLLQIEQAYEMGFLTDRERYDQILQLWTETTEKVTQAVFKNFEENYPFNPLYVMAQSGARGNPQQIRQLCGLRGLMQKPSGETFEVPVRSSFREGLTVLEYFISSHGARKGGADTALRTADSGYLTRKLVDVTHEIVVREADCGTTNYISVPLFQPDEVTRSLRLRKRADIEAGLYGRVLAREVEVLGVRLEEGRYLSMDDVHLLIKAAEAGEIQEVPVRSPLTCQTRYGVCQKCYGYDLSMARPVSIGEAVGIVAAQSIGEPGTQLTMRTFHTGGVAGAADITQGLPRVIELFEARRPKAKAVISEIDGVVRIEETEEKLSVFVESEGFSKEYKLPKEARLLVKDGDYVEAGQPLTRGAIDPHQLLEAKGPEAVERYLVEEIQKVYRAQGVKLHDKHIEIVVRQMMKYVEVTDPGDSRLLEGQVLEKWDVEALNERLIAEGKTPVAWKPLLMGVTKSALSTKSWLSAASFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTGSDFVRFTQVVDQKTLKAIEEARKEAVEAKERPAARRGVKREQPGKQADYKDDDDK

来源 Source

来源生物 organism	Thermus thermophilus HB8
NCBI 分类编号 ncbi_taxonomy_id	300852
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 5 polymer

描述 description	DNA-directed RNA polymerase subunit omega
分子量 formula_weight	11533.3 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	K

MAEPGIDKLFGMVDSKYRLTVVVAKRAQQLLRHGFKNTVLEPEERPKMQTLEGLFDDPNAVTWAMKELLTGRLVFGENLVPEDRLQKEMERLYPVEREE

来源 Source

来源生物 organism	Thermus thermophilus HB8
NCBI 分类编号 ncbi_taxonomy_id	300852
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 6 polymer

描述 description	DNA (41-MER)
分子量 formula_weight	57785.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polydeoxyribonucleotide
链编号 strand_id	T

GAACGCATTACCAGAGAATTCACGGGAAAGTCGACAGGGATCGGTGCACTACCACAAGCACCCAGGTGGATGTGGAGATATGGTTATGGGTAAGATAGATGGTGAGGTGATGAGTTTAAAGGAGTGAAGTATGGAGTGAAGAGAGATGGGTAGATAGTAGTTGAGTAGGGAGTGAAGTCCTGCA

Entity 7 polymer

描述 description	RNA (29-MER)
分子量 formula_weight	39054.0 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	R

AAUUUGCAGGACUUCACUCCCUACUCAACUACUAUCUACCCAUCUCUCUUCACUCCAUACUUCACUCCUUUAAACUCAUCACCUCACCAUCUAUCUUACCCAUAACCAUAUCUCCACAUCCACCU

Entity 8 polymer

描述 description	DNA (31-MER)
分子量 formula_weight	54576.8 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	N

GGACTTCACTCCCTACTCAACTACTATCTACCCATCTCTCTTCACTCCATACTTCACTCCTTTAAACTCATCACCTCACCATCTATCTTACCCATAACCATATCTCCACATCCACCTGGGTGCTTGTGGTAGTGCACCGATCCCTGTCGACTTTCCCGTGAATTCTCTGGTAATGCGTTC

Entity 9 non-polymer

描述 description	ADENOSINE-5'-DIPHOSPHATE
分子量 formula_weight	427.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

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	7

Entity 11 non-polymer

描述 description	BERYLLIUM TRIFLUORIDE ION
分子量 formula_weight	66.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

Entity 12 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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6. 折叠分类 (SCOP + CATH) 5 domains

CATH v4.4 (5 domains)

结构域编号 domain_id	8hsrG01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	170 — Beta Complex
拓扑 Topology topology	120 — RNA Polymerase Alpha Subunit; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	12 — DNA-directed RNA polymerase, insert domain

结构域编号 domain_id	8hsrH01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	170 — Beta Complex
拓扑 Topology topology	120 — RNA Polymerase Alpha Subunit; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	12 — DNA-directed RNA polymerase, insert domain

结构域编号 domain_id	8hsrI01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	1110 — Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3
同源超家族 H-superfamily homologous superfamily	10 — RNA polymerase Rpb2, domain 2

结构域编号 domain_id	8hsrI02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
同源超家族 H-superfamily homologous superfamily	150 — RNA polymerase II, Rpb2 subunit, wall domain

结构域编号 domain_id	8hsrJ01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	274 — Enzyme I; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	100 — RNA polymerase Rpb1, domain 3

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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	4.00 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	43245

fit	/app/data/saxs_computation/hs/8hsr/8hsr.fit
pddf	/app/data/pr_computation/hs/8hsr/8hsr.pr.out
profile	/app/data/saxs_computation/hs/8hsr/8hsr.dat

Thermus thermophilus Rho-engaged RNAP elongation complex (composite structure)

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 (12)

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

Entity 11 non-polymer

Entity 12 non-polymer

6. 折叠分类 (SCOP + CATH) 5 domains

CATH v4.4 (5 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)