8him

A cryo-EM structure of B. oleracea RNA polymerase V elongation complex at 2.73 Angstrom

Method: ELECTRON MICROSCOPY D_max: 151.6 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	8him
沉积日期 deposition_date	2022-11-21
结构标题 title	A cryo-EM structure of B. oleracea RNA polymerase V elongation complex at 2.73 Angstrom
关键词 keywords	DNA-dependent RNA polymerase V, 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	47.71 Å
回转半径 Rg (电子) rg_electron	47.40 Å
零角强度 I(0) i0	1842270000.00
分子量 molecular_weight	342580.0 kDa
排除体积 excluded_volume	422730 Å³
包络体积 envelope_volume	609150 Å³
水化壳体积 shell_volume	102270 Å³
包络直径 envelope_diameter	156.1 Å
壳层 Rg shell_rg	55.09 Å
包络 Rg envelope_rg	46.82 Å
形状 Rg shape_rg	47.40 Å
总 Rg total_rg	47.67 Å
总原子数 total_atoms	23948
残基数 n_residues	2912
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	151.6 Å
Rg (实空间) rg_real	47.47 Å
Rg 误差 (实空间) rg_real_error	0.98 Å
I(0) (实空间) i0_real	1.8420e+09
I(0) 误差 (实空间) i0_real_error	3.3600e+07
Rg (倒空间) rg_reciprocal	47.71 Å
I(0) (倒空间) i0_reciprocal	1843000000.0000
解质量估计 total_estimate	0.8217
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	59.7 Å
偏度 Skewness skewness	0.204
峰度 Kurtosis kurtosis	-0.468
角度范围 angular_range	— – 0.1650 Å⁻¹
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	279000000.0000
实空间数据点数 n_real_points	34
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.903; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.970; Smooth: 0.000

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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 (15)

Entity 1 polymer

描述 description	DNA (34-MER)
分子量 formula_weight	10482.8 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	T
原子数 atom_count	23948

AAGCTCAAGTATCGTAGCCTGGTCATTACGAGTA

Entity 2 polymer

描述 description	DNA (34-MER)
分子量 formula_weight	10463.7 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	N

TACTCGTAAGCTAGTATTGACGATACTTGAGCTT

Entity 3 polymer

描述 description	;RNA (5'-R(UPAPUPAPUPGPCPAPUPAPAPAPGPAPCPCPAPGPGPC)-3') ;
分子量 formula_weight	6414.9 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	P

UAUAUGCAUAAAGACCAGGC

Entity 4 polymer

描述 description	DNA-directed RNA polymerase V largest subunit
分子量 formula_weight	222876.9 kDa
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	A

MEEASSSDILEAEIVGISFALATHRQIRLASISDAGINHASQLSNAFLGLPLEFGKCEACGATEPDKCEGHFGYIHLPVPIYHPAHVSELKQMLSLLCLKCLKIKKIKSTSSGLAERLLGVCCEEASNITIKDKSSDGASYLQLKLPSRTRLQEGFWNFLERYGYRYGSDHTRPLLAREVKEILRRIPEETRKKLTAKGHIPQEGYILEYLPVPPNCLSVPEVSDGSNSMSVDPSRIELKDVLRKVVAINNSRSGETNFESHRAEANEMFRVVDTYLQVRGTAKPTRNIDMRFGVSKISDSSSSKAWTEKMRTLFIRKGSGFSSRSVITGDAFRNVNEVGIPMEIAHRITFEERVSVHNIGYLQELVDNKMCLSYTQGSTTYSLRDGSKGHTVLKPGQIVHRRVMDGDVVFINRPPTTHKHSLQALRVYVHEDNTVKINPLMCGPLSADFDGDCVHLFYPQSLTAKAEVLELFSVDKQLRSSHTGQLILQLGLDSLLSLRVMMEQVFLDKASAQQLAMYGSRSLPSPAVVKSSKSGPAWTFFQILQLAFPERLSCRGDGFIVGGSDLLSFDFGVDALASIINGIVTGIMVEKGPKEALAFFDSLQPLLMEHLDPQGFSLSLEDLSMSREDMGVIHNLIVREISPMVSRLRLSYEDELQLENSIQKVKEVAANFMLKSYSMRNLIDIKSNSAINKLVQQIGFLGLQLSDKKKLYTKTLVEDMAQFYKKKYVSTSSSGDFGIVKGCFFHGLDPYEEMAHSVAAREVIVRSSRGLAEPGTLFKNLMAVLRDIVITNDGTVRNTCSNSIVQFKYELSSDNENQGLFEAGDPVGVLAATAMSNPAYKAVLDSSPNSNSSWELMKEVLLCKVNFQNTTNDRRVILYLNECRCGKKYCQENSAYTVRNKLKKVSLKDTAVEFLVEYRKQQAISEIFGMDICLHGHIHLNKTLLEGWNISMQDILQRCEDAINSLVQKKKKKAEDFKKMNLSVSECCSFRGPGSSKDSDMPCLMFSSYNATDPDLERTLDVLCNTIYPVLLETVIKGDPRIASANIIWNSPETTTWIRSLHASRRGEWVLDVTVEKSDVKQSGDAWRVVIDSCLSVLHLIDTKRSIPYSIKQVQELLGLSCAFEQAVQRLSASVRKVSKGVLKEHIILVANNMTCSGDMLGFNYGGYKALTRSLNIKAPFTEATLIAPRKCFEKAAEKCHKDSLSTVVGSCSWGKRVDVGTGSQFELLWNKKETGLENDDETDVFSFLQMVRSTKTADAYVSSPGFDVTEEEMAEWAESPERDSALGEPKFDDSAEFQNLLDEGKASESKWDNGSLWENGCSSGSEWGVSKNAGGEENTQSGWGKAANVENEDASSGWNSKKDAQEATNTDSWGAWGSKTKDDAENATPNWGTKPAQNDSVVIENGEPSSDVWGPKAVSDKPWGKKNSETEPAPAAWGKTNSESESAAAAWGSDDEKNTGTESDAAGWGSTYKKNPETELNAAAWGSGAKMNKETEPAPAAWGSWGKKSSETVSGGADWGNRGKRVSETESGAGGWASRNRSLENQSGGATWGSRDKSKFETESGGAAWGSQAKNNSETEPGSGAAALGTWDKKKPETETGGGGAAWGSQAKNNSETESGSGAAAWGTWDKKKSETESGGGAWGSQAKKNSETESGAGASTWGAWDKKKPETESGGGGAAWGSQAKNNSETESGSGAAAWGSQAKKNSESQLGTANWGSKDTNNSENGSDSAAWGKKKNSEAEPTSVAWCSWGQPSPPASDKDAQEDDGNPWVSLKATSSGDKEGNETSQWGVPNKRYPSAGSQSQGGGGGADWKRNRPPRTPGSESILGPMFTATRQRVDMFTSEEQELLSDVDPVMRRLRKIMHQSGYTDGEPISDEDKTYVLEQILNYHPDKDAKLGPGLDFITVDKHTTFTESRCFFVVSTDGTKQDFSYRKCINNYLVEKHPNLAEEFIAKYFRKRDNENRDKNSQEATPPGEQESQTQPIDNGSQDSQPQPIGNEGGDTQPQSQIEDIQPIGNGGEDSQTEPQA

Entity 5 polymer

描述 description	RPOLD domain-containing protein
分子量 formula_weight	35484.1 kDa
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

MDTGATYQRFPKVKIRELKDDYAKFELRDTDVSMANALRRVMISEVPTVAIDLVEIEVNSSVLNDEFIAHRLGLIPLTSERAMSMRFSRDCDACDGDGQCEFCSVEFRLSAKCVTDQTLDVTSKDLYSADPTVTPVDFGDSSGADSSEQRGIIIVKLRRGQELKLRAIARKGIGKDHAKWSPAATVTFMYEPDIIINEDMMDTLTDDEKIDLIESSPTKVFDFDAVTRQVVVVDPEAYTYDEEVIKKAEAMGKQGLIEIRPKDDSFIFTVESTGAVKASQLVLNAIDLLKQKLDAVRLSDDTVEADDQFGELGAHMRGG

Entity 6 polymer

描述 description	DNA-directed RNA polymerases I, II, and III subunit RPABC2
分子量 formula_weight	16686.3 kDa
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	F

MAEDDYNEVDDLGYEDEPAEPEIEEGIEEDADMKDNDDINGEPLETEDKVETEPVQRPRKTSKFMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRQRKIPFTIRRYLPDGSFEEWGVDELIVEDSWKRQVGGD

Entity 7 polymer

描述 description	DNA-directed RNA polymerases I, II, and III subunit RPABC5
分子量 formula_weight	7982.3 kDa
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	J

MIIPVRCFTCGKVIGNKWDTYLDLLQADYTEGDALDAIGLVRYCCRRMLMTHVDLIEKLLNYNTLEKSD

Entity 8 polymer

描述 description	RNA_pol_L_2 domain-containing protein
分子量 formula_weight	13538.3 kDa
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	K

MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREDHTIGNIVRMQLHRDENVLFAGYQLPHPLKYKIIVRIHTTSQSSPMQAYNQAINDLDKELDFLKSQFEAEVAKFSNPY

Entity 9 polymer

描述 description	DNA-directed RNA polymerases II, IV and V subunit 12
分子量 formula_weight	5983.8 kDa
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	L

MDQQSEPVTYVCGDCGQENTLKSGDVIQCRECGYRILYKKRTRRVVQYEAR

Entity 10 polymer

描述 description	DNA-directed RNA polymerases I, II, and III subunit RPABC3
分子量 formula_weight	16607.3 kDa
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	H

MASSIIMFEDIFVVDKLDPDGKKFDKVTRIEATSHNLDMFMHLDVNTEVYPMAVGDKFTLAMAPTLNLDGTPDTGYFTPGAKKTLADKYEYVMHGKLYKITERDGQTPKAEMYVSFGGLLMLLRGDPAHISHFELDQRLFLLMRKL

Entity 11 polymer

描述 description	DNA-directed RNA polymerase subunit
分子量 formula_weight	13123.8 kDa
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	I

MSTMKFCRECNNILYPKEDREQSILLYACRNCDHQEAADDNCVYRNEVHHSVSEQTQILSDVASDPTLPRTKAVRCAKCQHGEAVFFQATARGEEGMTLFFVCCNPNCGHRWRE

Entity 12 polymer

描述 description	DNA-directed RNA polymerases I, II, and III subunit RPABC1
分子量 formula_weight	26260.1 kDa
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

MEGIGNDKSSCSSSSTVPSPCLSKYVDPSSEESHRYYLARRNALEMLRDRGYEVSLEDINLSLQDFRTVYGERPDVDRLRISAHHRSDSSNKVKVVFFGTGKVKVNTIRSVAAEILSQETITGLILVLQNQVTDKALKAIELFTFKVEIFQITDLLVNLTKHVLSLRHRVLTDGEKKALLKQFNIEEKQLPRISKKDAVVRYYGLEKGQIVKVSYRGELTESYVAYRCVW

Entity 13 polymer

描述 description	DNA-directed RNA polymerase IV and V subunit 2
分子量 formula_weight	132377.8 kDa
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	B

MTDIDIEEIEAAGEVDLRDLGEPFLQSFCKKAATSFFDEYGLVSHQLNSYNFFIEHGLQSVFESSGEMLVEPSFDPTKNKDHEWRYATVKFGEVSVDKPTLYSDDKELVFLPWHARLQNMTYSARMKVNVDVEVFVKKVVKRDKFKTGQDEYVEKQILSKKTQDIPIGRIPVMVKSVLCNTTEKGKNGESYRKGECAFDQGGYFVIKGAEKVFIAQEQICTKRLWISNSPWTVSYRSETKRNRFIVRLSENQKAEDFKRKEKVLTVYFLSTEIPVWVLFFALGVASDKEAVDLIAFDGGDASITNSVVASIQEADSVCEDFRHGRNALAYVEQQIKGTKFPPGESVDECLSLYLFPGLKSLTQKARFLGYMVKCLFSAYAGKRKCENRDNFRNKRIELAGELLERELRVHLAHARRTMTKAMQRHLTGDGDLKPIEHYLDASIITNGLSRAFSTGAWCHPFRKMERVSGVVANLGRANPLQSLIDLRRTRQQVLYTGRVGDARYPHPSHWGRLCFLSTPDGENCGLVKNLSLLGLVSTQIMEPVVEELFDSGMEELMDDTSTPLSGKHKVLLNGDWVGVCSDSDYFVADLKSRRRQSELPRQMEIKLDKDDKEVRIFTDAGRLLRPLLVVENLHKLKQSKPSKYTFEHLLDQGILELIGIEEEEDCTTAWGTKQLLKQQKSYTHCELDLSFLLGVSCAIVPFANHDHGRRVLYQSQKHCQQAIGFCSTNPNIRCDTLSQQLFYPQRPLFKTMASECLQKDVLFNGQNAIVAVNVHLGFNQEDSIVMNKASLERGMFRSEQIRSYKADVDSKDSEKRKKMDEVVQFGKTHSKIGRVDSLDDDGFPFVGANMHSGDIVIGRCTESGTDHSVKLKHTERGIVQKVVLSSNDDGKNYATVSLRQVRSPCLGDKFSSMHGQKGVLGYIEEQENFAFTNQGIVPDIVINPHAFPSRQTPGQLLEAALSKGIACPMQKKKGKSDAYSKVTRHATPFSTPSVDDITDQLHRAGFSRSGNERVYNGRTGEMMRSLIFMGPNFYQRLIHMSEDKVKFRNTGPVHPLTRQPVADRKRFGGIKFGEMERDCLIAHGASANLHERLFTLSDSSQMHICRNCKSAANVIERVASSGRRIRGPYCRLCESPDYVVMVNVPYGAKLLYQELFSMGICLNFETNLC

Entity 14 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 15 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	6

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6. 折叠分类 (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

结构域编号 domain_id	8himB01
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	8himK01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1360 — Gyrase A; domain 2
同源超家族 H-superfamily homologous superfamily	10 — RNA polymerase, RBP11-like subunit

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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	2.80 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	503124

fit	/app/data/saxs_computation/hi/8him/8him.fit
pddf	/app/data/pr_computation/hi/8him/8him.pr.out
profile	/app/data/saxs_computation/hi/8him/8him.dat

A cryo-EM structure of B. oleracea RNA polymerase V elongation complex at 2.73 Angstrom

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 (15)

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

Entity 6 polymer

聚合体 Polymer

Entity 7 polymer

聚合体 Polymer

Entity 8 polymer

聚合体 Polymer

Entity 9 polymer

聚合体 Polymer

Entity 10 polymer

聚合体 Polymer

Entity 11 polymer

聚合体 Polymer

Entity 12 polymer

聚合体 Polymer

Entity 13 polymer

聚合体 Polymer

Entity 14 non-polymer

Entity 15 non-polymer

6. 折叠分类 (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)