9g23

Yeast RNA polymerase I elongation complex stalled by an apurinic site bound to nucleotide analog AMPCPP at A-site

Method: ELECTRON MICROSCOPY D_max: 170.9 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	9g23
沉积日期 deposition_date	2024-07-10
最后修订 last_revision	2025-06-18
结构标题 title	Yeast RNA polymerase I elongation complex stalled by an apurinic site bound to nucleotide analog AMPCPP at A-site
关键词 keywords	DNA lesion, 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	50.87 Å
回转半径 Rg (电子) rg_electron	50.79 Å
零角强度 I(0) i0	3572360000.00
分子量 molecular_weight	487240.0 kDa
排除体积 excluded_volume	603990 Å³
包络体积 envelope_volume	833690 Å³
水化壳体积 shell_volume	128100 Å³
包络直径 envelope_diameter	184.9 Å
壳层 Rg shell_rg	60.34 Å
包络 Rg envelope_rg	50.66 Å
形状 Rg shape_rg	50.81 Å
总 Rg total_rg	50.95 Å
总原子数 total_atoms	34137
残基数 n_residues	4187
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	170.9 Å
Rg (实空间) rg_real	50.67 Å
Rg 误差 (实空间) rg_real_error	1.09 Å
I(0) (实空间) i0_real	3.5720e+09
I(0) 误差 (实空间) i0_real_error	6.8030e+07
Rg (倒空间) rg_reciprocal	51.03 Å
I(0) (倒空间) i0_reciprocal	3574000000.0000
解质量估计 total_estimate	0.8745
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	66.2 Å
偏度 Skewness skewness	0.181
峰度 Kurtosis kurtosis	-0.403
角度范围 angular_range	— – 0.1550 Å⁻¹
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	850600000.0000
实空间数据点数 n_real_points	32
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.800; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.978

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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 (20)

Entity 1 polymer

描述 description	DNA-directed RNA polymerase I subunit RPA190
分子量 formula_weight	186677.0 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	A
原子数 atom_count	34137

MDISKPVGSEITSVDFGILTAKEIRNLSAKQITNPTVLDNLGHPVSGGLYDLALGAFLRNLCSTCGLDEKFCPGHQGHIELPVPCYNPLFFNQLYIYLRASCLFCHHFRLKSVEVHRYACKLRLLQYGLIDESYKLDEITLGSLNSSMYTDDEAIEDNEDEMDGEGSKQSKDISSTLLNELKSKRSEYVDMAIAKALSDGRTTERGSFTATVNDERKKLVHEFHKKLLSRGKCDNCGMFSPKFRKDGFTKIFETALNEKQITNNRVKGFIRQDMIKKQKQAKKLDGSNEASANDEESFDVGRNPTTRPKTGSTYILSTEVKNILDTVFRKEQCVLQYVFHSRPNLSRKLVKADSFFMDVLVVPPTRFRLPSKLGEEVHENSQNQLLSKVLTTSLLIRDLNDDLSKLQKDKVSLEDRRVIFSRLMNAFVTIQNDVNAFIDSTKAQGRTSGKVPIPGVKQALEKKEGLFRKHMMGKRVNYAARSVISPDPNIETNEIGVPPVFAVKLTYPEPVTAYNIAELRQAVINGPDKWPGATQIQNEDGSLVSLIGMSVEQRKALANQLLTPSSNVSTHTLNKKVYRHIKNRDVVLMNRQPTLHKASMMGHKVRVLPNEKTLRLHYANTGAYNADFDGDEMNMHFPQNENARAEALNLANTDSQYLTPTSGSPVRGLIQDHISAGVWLTSKDSFFTREQYQQYIYGCIRPEDGHTTRSKIVTLPPTIFKPYPLWTGKQIITTVLLNVTPPDMPGINLISKNKIKNEYWGKGSLENEVLFKDGALLCGILDKSQYGASKYGIVHSLHEVYGPEVAAKVLSVLGRLFTNYITATAFTCGMDDLRLTAEGNKWRTDILKTSVDTGREAAAEVTNLDKDTPADDPELLKRLQEILRDNNKSGILDAVTSSKVNAITSQVVSKCVPDGTMKKFPCNSMQAMALSGAKGSNVNVSQIMCLLGQQALEGRRVPVMVSGKTLPSFKPYETDAMAGGYVKGRFYSGIKPQEYYFHCMAGREGLIDTAVKTSRSGYLQRCLTKQLEGVHVSYDNSIRDADGTLVQFMYGGDAIDITKESHMTQFEFCLDNYYALLKKYNPSALIEHLDVESALKYSKKTLKYRKKHSKEPHYKQSVKYDPVLAKYNPAKYLGSVSENFQDKLESFLDKNSKLFKSSDGVNEKKFRALMQLKYMRSLINPGEAVGIIASQSVGEPSTQMTLNTFHFAGHGAANVTLGIPRLREIVMTASAAIKTPQMTLPIWNDVSDEQADTFCKSISKVLLSEVIDKVIVTETTGTSNTAGGNAARSYVIHMRFFDNNEYSEEYDVSKEELQNVISNQFIHLLEAAIVKEIKKQKRTTGPDIGVAVPRLQTDVANSSSNSKRLEEDNDEEQSHKKTKQAVSYDEPDEDEIETMREAEKSSDEEGIDSDKESDSDSEDEDVDMNEQINKSIVEANNNMNKVQRDRQSAIISHHRFITKYNFDDESGKWCEFKLELAADTEKLLMVNIVEEICRKSIIRQIPHIDRCVHPEPENGKRVLVTEGVNFQAMWDQEAFIDVDGITSNDVAAVLKTYGVEAARNTIVNEINNVFSRYAISVSFRHLDLIADMMTRQGTYLAFNRQGMETSTSSFMKMSYETTCQFLTKAVLDNEREQLDSPSARIVVGKLNNVGTGSFDVLAKVPNAA

Entity 2 polymer

描述 description	DNA-directed RNA polymerase I subunit RPA135
分子量 formula_weight	135910.3 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	B

MSKVIKPPGQARTADFRTLERESRFINPPKDKSAFPLLQEAVQPHIGSFNALTEGPDGGLLNLGVKDIGEKVIFDGKPLNSEDEISNSGYLGNKLSVSVEQVSIAKPMSNDGVSSAVERKVYPSESRQRLTSYRGKLLLKLKWSVNNGEENLFEVRDCGGLPVMLQSNRCHLNKMSPYELVQHKEESDEIGGYFIVNGIEKLIRMLIVQRRNHPMAIIRPSFANRGASYSHYGIQIRSVRPDQTSQTNVLHYLNDGQVTFRFSWRKNEYLVPVVMILKALCHTSDREIFDGIIGNDVKDSFLTDRLELLLRGFKKRYPHLQNRTQVLQYLGDKFRVVFQASPDQSDLEVGQEVLDRIVLVHLGKDGSQDKFRMLLFMIRKLYSLVAGECSPDNPDATQHQEVLLGGFLYGMILKEKIDEYLQNIIAQVRMDINRGMAINFKDKRYMSRVLMRVNENIGSKMQYFLSTGNLVSQSGLDLQQVSGYTVVAEKINFYRFISHFRMVHRGSFFAQLKTTTVRKLLPESWGFLCPVHTPDGSPCGLLNHFAHKCRISTQQSDVSRIPSILYSLGVAPASHTFAAGPSLCCVQIDGKIIGWVSHEQGKIIADTLRYWKVEGKTPGLPIDLEIGYVPPSTRGQYPGLYLFGGHSRMLRPVRYLPLDKEDIVGPFEQVYMNIAVTPQEIQNNVHTHVEFTPTNILSILANLTPFSDFNQSPRNMYQCQMGKQTMGTPGVALCHRSDNKLYRLQTGQTPIVKANLYDDYGMDNFPNGFNAVVAVISYTGYDMDDAMIINKSADERGFGYGTMYKTEKVDLALNRNRGDPITQHFGFGNDEWPKEWLEKLDEDGLPYIGTYVEEGDPICAYFDDTLNKTKIKTYHSSEPAYIEEVNLIGDESNKFQELQTVSIKYRIRRTPQIGDKFSSRHGQKGVCSRKWPTIDMPFSETGIQPDIIINPHAFPSRMTIGMFVESLAGKAGALHGIAQDSTPWIFNEDDTPADYFGEQLAKAGYNYHGNEPMYSGATGEELRADIYVGVVYYQRLRHMVNDKFQVRSTGPVNSLTMQPVKGRKRHGGIRVGEMERDALIGHGTSFLLQDRLLNSSDYTQASVCRECGSILTTQQSVPRIGSISTVCCRRCSMRFEDAKKLLTKSEDGEKIFIDDSQIWEDGQGNKFVGGNETTTVAIPFVLKYLDSELSAMGIRLRYNVEPK

Entity 3 polymer

描述 description	DNA-directed RNA polymerases I and III subunit RPAC1
分子量 formula_weight	37732.6 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

MSNIVGIEYNRVTNTTSTDFPGFSKDAENEWNVEKFKKDFEVNISSLDAREANFDLINIDTSIANAFRRIMISEVPSVAAEYVYFFNNTSVIQDEVLAHRIGLVPLKVDPDMLTWVDSNLPDDEKFTDENTIVLSLNVKCTRNPDAPKGSTDPKELYNNAHVYARDLKFEPQGRQSTTFADCPVVPADPDILLAKLRPGQEISLKAHCILGIGGDHAKFSPVSTASYRLLPQINILQPIKGESARRFQKCFPPGVIGIDEGSDEAYVKDARKDTVSREVLRYEEFADKVKLGRVRNHFIFNVESAGAMTPEEIFFKSVRILKNKAEYLKNCPITQ

Entity 4 polymer

描述 description	DNA-directed RNA polymerase I subunit RPA14
分子量 formula_weight	14599.1 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	D

MMKGSRRTGNNTATTLNTPVVIHATQLPQHVSTDEVLQFLESFIDEKENIIDSTTMNTISGNAADADAAAVANTSLNIDTNLSSSISQLKRIQRDFKGLPPAQDFSAAPIQVSTTEKKETSIGVSATGGKKTTFADE

Entity 5 polymer

描述 description	DNA-directed RNA polymerases I, II, and III subunit RPABC1
分子量 formula_weight	25117.1 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

MDQENERNISRLWRAFRTVKEMVKDRGYFITQEEVELPLEDFKAKYCDSMGRPQRKMMSFQANPTEESISKFPDMGSLWVEFCDEPSVGVKTMKTFVIHIQEKNFQTGIFVYQNNITPSAMKLVPSIPPATIETFNEAALVVNITHHELVPKHIRLSSDEKRELLKRYRLKESQLPRIQRADPVALYLGLKRGEVVKIIRKSETSGRYASYRICM

Entity 6 polymer

描述 description	DNA-directed RNA polymerases I, II, and III subunit RPABC2
分子量 formula_weight	17931.8 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	F

MSDYEEAFNDGNENFEDFDVEHFSDEETYEEKPQFKDGETTDANGKTIVTGGNGPEDFQQHEQIRRKTLKEKAIPKDQRATTPYMTKYERARILGTRALQISMNAPVFVDLEGETDPLRIAMKELAEKKIPLVIRRYLPDGSFEDWSVEELIVDL

Entity 7 polymer

描述 description	DNA-directed RNA polymerase I subunit RPA43
分子量 formula_weight	36264.9 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	G

MSQVKRANENRETARFIKKHKKQVTNPIDEKNGTSNCIVRVPIALYVSLAPMYLENPLQGVMKQHLNPLVMKYNNKVGGVVLGYEGLKILDADPLSKEDTSEKLIKITPDTPFGFTWCHVNLYVWQPQVGDVLEGYIFIQSASHIGLLIHDAFNASIKKNNIPVDWTFVHNDVEEDADVINTDENNGNNNNEDNKDSNGGSNSLGKFSFGNRSLGHWVDSNGEPIDGKLRFTVRNVHTTGRVVSVDGTLISDADEEGNGYNSSRSQAESLPIVSNKKIVFDDEVSIENKESHKELDLPEVKEDNGSEIVYEENTSESNDGESSDSD

Entity 8 polymer

描述 description	DNA-directed RNA polymerases I, II, and III subunit RPABC3
分子量 formula_weight	16525.4 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

MSNTLFDDIFQVSEVDPGRYNKVCRIEAASTTQDQCKLTLDINVELFPVAAQDSLTVTIASSLNLEDTPANDSSATRSWRPPQAGDRSLADDYDYVMYGTAYKFEEVSKDLIAVYYSFGGLLMRLEGNYRNLNNLKQENAYLLIRR

Entity 9 polymer

描述 description	DNA-directed RNA polymerase I subunit RPA12
分子量 formula_weight	13676.6 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

MSVVGSLIFCLDCGDLLENPNAVLGSNVECSQCKAIYPKSQFSNLKVVTTTADDAFPSSLRAKKSVVKTSLKKNELKDGATIKEKCPQCGNEEMNYHTLQLRSADEGATVFYTCTSCGYKFRTNN

Entity 10 polymer

描述 description	DNA-directed RNA polymerases I, II, and III subunit RPABC5
分子量 formula_weight	8290.7 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

MIVPVRCFSCGKVVGDKWESYLNLLQEDELDEGTALSRLGLKRYCCRRMILTHVDLIEKFLRYNPLEKRD

Entity 11 polymer

描述 description	DNA-directed RNA polymerases I and III subunit RPAC2
分子量 formula_weight	16167.9 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	K

MTEDIEQKKTATEVTPQEPKHIQEEEEQDVDMTGDEEQEEEPDREKIKLLTQATSEDGTSASFQIVEEDHTLGNALRYVIMKNPDVEFCGYSIPHPSENLLNIRIQTYGETTAVDALQKGLKDLMDLCDVVESKFTEKIKSM

Entity 12 polymer

描述 description	DNA-directed RNA polymerases I, II, and III subunit RPABC4
分子量 formula_weight	7730.0 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

MSREGFQIPTNLDAAAAGTSQARTATLKYICAECSSKLSLSRTDAVRCKDCGHRILLKARTKRLVQFEAR

Entity 13 polymer

描述 description	DNA-directed RNA polymerase I subunit RPA49
分子量 formula_weight	46721.7 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	M

MSVKRSVSEIEIESVQDQPSVAVGSFFKGFRAPSDTTFDLYKKKKSEKDEFVLHGENERLEYEGYTDSSSQASNQYVVGLFNPEKKSIQLYKAPVLVSKVVSKSSKNLRGPKIKSKSDTRPSALRNALGEAFGTKKAKKAIADLERNRIDSDKLTDSAIDIVDSVRTASKDLPTRAQLDEITSNDRPTPLANIDATDVEQIYPIESIIPKKELQFIRVSSILKEADKEKKLELFPYQNNSKYVAKKLDSLTQPSQMTKLQLLYYLSLLLGVYENRRVNNKTKLLERLNSPPEILVDGILSRFTVIKPGQFGRSKDRSYFIDPQNEDKILCYILAIIMHLDNFIVEITPLAHELNLKPSKVVSLFRVLGAIVKGATVAQAEAFGIPKSTAASYKIATMKVPFKLPEMTRRGRGPRR

Entity 14 polymer

描述 description	DNA-directed RNA polymerase I subunit RPA34
分子量 formula_weight	26933.5 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	N

MSKLSKDYVSDSDSDDEVISNEFSIPDGFKKCKHLKNFPLNGDNKKKAKQQQVWLIKFPSNVDISKLKSLPVDFESSTTMTIDKHDYKIMDDTDIESSLTQDNLSNMTLLVPSESKESLKIASTAKDNAPLQFDKVFSVSETAKIPAIDYSKVRVPRKDVPKVEGLKLEHFATGYDAEDFHVAEEVKENKKEPKKRSHHDDEEESSEKKKKKKEKREKREKKDKKDKKKKHRD

Entity 15 polymer

描述 description	RNA
分子量 formula_weight	3883.4 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

AUAAAUCGAGAG

Entity 16 polymer

描述 description	Non-template DNA
分子量 formula_weight	11553.4 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	S

GATTTCATACGCCATTCCTTCTCTCTGCTTATCGGTAG

Entity 17 polymer

描述 description	Template DNA
分子量 formula_weight	11529.4 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

CTACCGATAAGCAGATNCTCTCGATTGCGTATGAAATC

Entity 18 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

Entity 19 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 20 non-polymer

描述 description	DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
分子量 formula_weight	505.2 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	3.40 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	207080

fit	/app/data/saxs_computation/g2/9g23/9g23.fit
pddf	/app/data/pr_computation/g2/9g23/9g23.pr.out
profile	/app/data/saxs_computation/g2/9g23/9g23.dat

Yeast RNA polymerase I elongation complex stalled by an apurinic site bound to nucleotide analog AMPCPP at A-site

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 (20)

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 polymer

聚合体 Polymer

Entity 15 polymer

聚合体 Polymer

Entity 16 polymer

聚合体 Polymer

Entity 17 polymer

聚合体 Polymer

Entity 18 non-polymer

Entity 19 non-polymer

Entity 20 non-polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)