8w9f

Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 3

Method: ELECTRON MICROSCOPY D_max: 175.5 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	8w9f
沉积日期 deposition_date	2023-09-05
最后修订 last_revision	2024-05-15
结构标题 title	Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 3
关键词 keywords	Rpd3S, HDAC, Sin3, Rpd3, DNA BINDING PROTEIN-DNA COMPLEX; DNA BINDING PROTEIN/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	54.00 Å
回转半径 Rg (电子) rg_electron	53.41 Å
零角强度 I(0) i0	2999480000.00
分子量 molecular_weight	401640.0 kDa
排除体积 excluded_volume	478840 Å³
包络体积 envelope_volume	759250 Å³
水化壳体积 shell_volume	116380 Å³
包络直径 envelope_diameter	176.8 Å
壳层 Rg shell_rg	59.07 Å
包络 Rg envelope_rg	51.62 Å
形状 Rg shape_rg	53.38 Å
总 Rg total_rg	53.64 Å
总原子数 total_atoms	27868
残基数 n_residues	2990
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	175.5 Å
Rg (实空间) rg_real	53.76 Å
Rg 误差 (实空间) rg_real_error	1.17 Å
I(0) (实空间) i0_real	2.9990e+09
I(0) 误差 (实空间) i0_real_error	5.0410e+07
Rg (倒空间) rg_reciprocal	54.19 Å
I(0) (倒空间) i0_reciprocal	3001000000.0000
解质量估计 total_estimate	0.8775
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	72.6 Å
偏度 Skewness skewness	0.129
峰度 Kurtosis kurtosis	-0.435
角度范围 angular_range	— – 0.1450 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	280400000.0000
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: 0.862; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.960; Smooth: 0.858

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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 (11)

Entity 1 polymer

描述 description	Transcriptional regulatory protein SIN3
分子量 formula_weight	175047.3 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	A
原子数 atom_count	27868

MSQVWHNSNSQSNDVATSNDATGSNERNEKEPSLQGNKPGFVQQQQRITLPSLSALSTKEEDRRDSNGQQALTSHAAHILGYPPPHSNAMPSIATDSALKQPHEYHPRPKSSSSSPSINASLMNAGPAPLPTVGAASFSLSRFDNPLPIKAPVHTEEPKSYNGLQEEEKATQRPQDCKEVPAGVQPADAPDPSSNHADANDDNNNNENSHDEDADYRPLNVKDALSYLEQVKFQFSSRPDIYNLFLDIMKDFKSQAIDTPGVIERVSTLFRGYPILIQGFNTFLPQGYRIECSSNPDDPIRVTTPMGTTTVNNNISPSGRGTTDAQELGSFPESDGNGVQQPSNVPMVPSSVYQSEQNQDQQQSLPLLATSSGLPSIQQPEMPAHRQIPQSQSLVPQEDAKKNVDVEFSQAISYVNKIKTRFADQPDIYKHFLEILQTYQREQKPINEVYAQVTHLFQNAPDLLEDFKKFLPDSSASANQQVQHAQQHAQQQHEAQMHAQAQAQAQAQAQVEQQKQQQQFLYPASGYYGHPSNRGIPQQNLPPIGSFSPPTNGSTVHEAYQDQQHMQPPHFMPLPSIVQHGPNMVHQGIANENPPLSDLRTSLTEQYAPSSIQHQQQHPQSISPIANTQYGDIPVRPEIDLDPSIVPVVPEPTEPIENNISLNEEVTFFEKAKRYIGNKHLYTEFLKILNLYSQDILDLDDLVEKVDFYLGSNKELFTWFKNFVGYQEKTKCIENIVHEKHRLDLDLCEAFGPSYKRLPKSDTFMPCSGRDDMCWEVLNDEWVGHPVWASEDSGFIAHRKNQYEETLFKIEEERHEYDFYIESNLRTIQCLETIVNKIENMTENEKANFKLPPGLGHTSMTIYKKVIRKVYDKERGFEIIDALHEHPAVTAPVVLKRLKQKDEEWRRAQREWNKVWRELEQKVFFKSLDHLGLTFKQADKKLLTTKQLISEISSIKVDQTNKKIHWLTPKPKSQLDFDFPDKNIFYDILCLADTFITHTTAYSNPDKERLKDLLKYFISLFFSISFEKIEESLYSHKQNVSESSGSDDGSSIASRKRPYQQEMSLLDILHRSRYQKLKRSNDEDGKVPQLSEPPEEEPNTIEEEELIDEEAKNPWLTGNLVEEANSQGIIQNRSIFNLFANTNIYIFFRHWTTIYERLLEIKQMNERVTKEINTRSTVTFAKDLDLLSSQLSEMGLDFVGEDAYKQVLRLSRRLINGDLEHQWFEESLRQAYNNKAFKLYTIDKVTQSLVKHAHTLMTDAKTAEIMALFVKDRNASTTSAKDQIIYRLQVRSHMSNTENMFRIEFDKRTLHVSIQYIALDDLTLKEPKADEDKWKYYVTSYALPHPTEGIPHEKLKIPFLERLIEFGQDIDGTEVDEEFSPEGISVSTLKIKIQPITYQLHIENGSYDVFTRKATNKYPTIANDNTQKGMVSQKKELISKFLDCAVGLRNNLDEAQKLSMQKKWENLKDSIAKTSAGNQGIESETEKGKITKQEQSDNLDSSTASVLPASITTVPQDDNIETTGNTESSDKGAKIQ

Entity 2 polymer

描述 description	Transcriptional regulatory protein RCO1
分子量 formula_weight	78951.3 kDa
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	E,F

MDTSKKDTTRSPSHSNSSSPSSSSLSSSSSKEKKRPKRLSSQNVNYDLKRRKIITSEGIERSFKNEHSNLAVEDNIPEEEPKELLEKDSKGNIIKLNEPSTISEDSKVSVTGLPLNKGPSEKIKRESLWNYRKNLGGQSNNSEMTLVPSKRFTQVPKNFQDLNRNDLKTFLTENMTEESNIRSTIGWNGDIINRTRDREPESDRDNKKLSNIRTKIILSTNATYDSKSKLFGQNSIKSTSNASEKIFRDKNNSTIDFENEDFCSACNQSGSFLCCDTCPKSFHFLCLDPPIDPNNLPKGDWHCNECKFKIFINNSMATLKKIESNFIKQNNNVKIFAKLLFNIDSHNPKQFQLPNYIKETFPAVKTGSRGQYSDENDKIPLTDRQLFNTSYGQSITKLDSYNPDTHIDSNSGKFLICYKCNQTRLGSWSHPENSRLIMTCDYCQTPWHLDCVPRASFKNLGSKWKCPLHSPTKVYKKIHHCQEDNSVNYKVWKKQRLINKKNQLYYEPLQKIGYQNNGNIQIIPTTSHTDYDFNQDFKITQIDENSIKYDFFDKIYKSKMVQKRKLFQFQESLIDKLVSNGSQNGNSEDNMVKDIASLIYFQVSNNDKSSNNKSASKSNNLRKLWDLKELTNVVVPNELDSIQFNDFSSDEIKHLLYLKKIIESKPKEELLKFLNIENPENQSE

Entity 3 polymer

描述 description	Histone deacetylase RPD3
分子量 formula_weight	48962.0 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	B

MVYEATPFDPITVKPSDKRRVAYFYDADVGNYAYGAGHPMKPHRIRMAHSLIMNYGLYKKMEIYRAKPATKQEMCQFHTDEYIDFLSRVTPDNLEMFKRESVKFNVGDDCPVFDGLYEYCSISGGGSMEGAARLNRGKCDVAVNYAGGLHHAKKSEASGFCYLNDIVLGIIELLRYHPRVLYIDIDVHHGDGVEEAFYTTDRVMTCSFHKYGEFFPGTGELRDIGVGAGKNYAVNVPLRDGIDDATYRSVFEPVIKKIMEWYQPSAVVLQCGGDSLSGDRLGCFNLSMEGHANCVNYVKSFGIPMMVVGGGGYTMRNVARTWCFETGLLNNVVLDKDLPYNEYYEYYGPDYKLSVRPSNMFNVNTPEYLDKVMTNIFANLENTKYAPSVQLNHTPRDAEDLGDVEEDSAEAKDTKGGSQYARDLHVEHDNEFY

Entity 4 polymer

描述 description	Chromatin modification-related protein EAF3
分子量 formula_weight	45266.4 kDa
来源方法 src_method	nat
拷贝数 entity_count	3

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	C,D,G

MVDLEQEFALGGRCLAFHGPLMYEAKILKIWDPSSKMYTSIPNDKPGGSSQATKEIKPQKLGEDESIPEEIINGKCFFIHYQGWKSSWDEWVGYDRIRAYNEENIAMKKRLANEAKEAKKSLLEQQKKKKLSTSLGGPSNGGKRKGDSRSNASISKSTSQSFLTSSVSGRKSGRSSANSLHPGSSLRSSSDQNGNDDRRRSSSLSPNMLHHIAGYPTPKISLQIPIKLKSVLVDDWEYVTKDKKICRLPADVTVEMVLNKYEHEVSQELESPGSQSQLSEYCAGLKLYFDKCLGNMLLYRLERLQYDELLKKSSKDQKPLVPIRIYGAIHLLRLISVLPELISSTTMDLQSCQLLIKQTEDFLVWLLMHVDEYFNDKDPNRSDDALYVNTSSQYEGVALGM

Entity 5 polymer

描述 description	Histone H3.1
分子量 formula_weight	15437.2 kDa
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,e

MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA

Entity 6 polymer

描述 description	Histone H4
分子量 formula_weight	11394.4 kDa
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	b,f

MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Entity 7 polymer

描述 description	Histone H2A type 1-B/E
分子量 formula_weight	14165.6 kDa
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	c,g

MSGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPKKTESHHKAKGK

Entity 8 polymer

描述 description	Histone H2B type 1-K
分子量 formula_weight	13921.2 kDa
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	d,h

MPEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSVYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK

Entity 9 polymer

描述 description	5-DNA
分子量 formula_weight	45368.1 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polydeoxyribonucleotide
链编号 strand_id	i

ATCAATATCCACCTGCAGATACTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGCATGTTCAGCTGGAATCCAGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTTGGTAGTATCTGCAGGTGGATATTGAT

Entity 10 polymer

描述 description	3-DNA
分子量 formula_weight	45359.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polydeoxyribonucleotide
链编号 strand_id	j

ATCAATATCCACCTGCAGATACTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGCATGTTCAGCTGGATTCCAGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTTGGTAGTATCTGCAGGTGGATATTGAT

Entity 11 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	7

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7. 引用文献 (1)

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分辨率 resolution	4.40 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	213127

fit	/app/data/saxs_computation/w9/8w9f/8w9f.fit
pddf	/app/data/pr_computation/w9/8w9f/8w9f.pr.out
profile	/app/data/saxs_computation/w9/8w9f/8w9f.dat

Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 3

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

冷冻电镜 EM 3D

5. 实体与聚合体信息 (11)

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 non-polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)