SAXSdb — 8i02

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8i02
沉积日期 deposition_date	2023-01-10
结构标题 title	Cryo-EM structure of the SIN3S complex from S. pombe
关键词 keywords	SIN3, SIN3S, Pst2, Clr6, deacetylase, DNA BINDING PROTEIN; DNA BINDING PROTEIN
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	52.23 Å
回转半径 Rg (电子) rg_electron	51.68 Å
零角强度 I(0) i0	1131210000.00
分子量 molecular_weight	282150.0 kDa
排除体积 excluded_volume	353370 Å³
包络体积 envelope_volume	513420 Å³
水化壳体积 shell_volume	83709 Å³
包络直径 envelope_diameter	187.1 Å
壳层 Rg shell_rg	54.05 Å
包络 Rg envelope_rg	50.92 Å
形状 Rg shape_rg	51.70 Å
总 Rg total_rg	51.69 Å
总原子数 total_atoms	19876
残基数 n_residues	2457
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	174.7 Å
Rg (实空间) rg_real	52.19 Å
Rg 误差 (实空间) rg_real_error	1.98 Å
I(0) (实空间) i0_real	1.1310e+09
I(0) 误差 (实空间) i0_real_error	2.3610e+07
Rg (倒空间) rg_reciprocal	52.25 Å
I(0) (倒空间) i0_reciprocal	1131000000.0000
解质量估计 total_estimate	0.8975
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	64.1 Å
偏度 Skewness skewness	0.225
峰度 Kurtosis kurtosis	-0.566
角度范围 angular_range	— – 0.1500 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	83860000.0000
实空间数据点数 n_real_points	31
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.916; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.916

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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 (8)

Entity 1 polymer

描述 description	Cph1
分子量 formula_weight	45046.1 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	F
原子数 atom_count	19876

MASSINNSSQPTVPSISNNSHGDSFVNEGPPSNFKNNSLTSSTHSSTDHVNVLPISQDKEMDISSPVKKQKASYSNKSPNKAPIQKSRGSSLKSHLETESQQTPVKRRRRKATIRNVDYCSACGGRGLFICCEGCPCSFHLSCLEPPLTPENIPEGSWFCVTCSIKSHHPPKHPLSIWSQLYDWIDSQNPSQYRLPDDLVHYFHGISRGDTGAYKETEGEMDTDEFSALPTGSSITNLAYCGYCSKPSMGACWVYGCQLCDTFYHKNCKEHAKKCSHDSIGKKGMRVPKNAVVIRTPLVLDTTSNTLNPKVMISGWQFLMGEFPSDELLYFPRLPVSCLYKVSEDGLIKDFLYAIGIEAKKFNNERKKRELEVIPPDVKSALLPARTHPNLPIALRTLFNKART

Entity 2 polymer

描述 description	Paired amphipathic helix protein pst2
分子量 formula_weight	125011.6 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	A

MEQTLAILKNDNSTLVAEMQNQLVHDFSPNGTALPELDIKAFVQKLGQRLCHRPYVYSAFMDVVKALHNEIVDFPGFIERISVILRDYPDLLEYLNIFLPSSYKYLLSNSGANFTLQFTTPSGPVSTPSTYVATYNDLPCTYHRAIGFVSRVRRALLSNPEQFFKLQDSLRKFKNSECSLSELQTIVTSLLAEHPSLAHEFHNFLPSSIFFGSKPPLGSFPLRGIQSSQFTLSNISDLLSQSRPDNLSPFSHLSNESSDFFKNVKNVLTDVETYHEFLKLLNLYVQGIIDRNILVSRGFGFLKSNSGLWRSFLSLTSLSPEEFLSVYNSACSDFPECGPSYRLLPVEERNISCSGRDDFAWGILNDDWVSHPTWASEESGFIVQRKTPYEEAMTKLEEERYEFDRHIEATSWTIKSLKKIQNRINELPEEERETYTLEEGLGLPSKSIYKKTIKLVYTSEHAEEMFKALERMPCLTLPLVISRLEEKNEEWKSVKRSLQPGWRSIEFKNYDKSLDSQCVYFKARDKKNVSSKFLLAEADILRSQAKLHFPLRSRSAFEFSFVYDNEIVLFDTCYMVCTYIVCNSPSGLKKVEHFFKNILPLHFGLEKDKFSIFLDQVFRGPDYDVNAPNIVGNKPVRRKRSNSITQLTEFVKQPKINGQRESRSAAAARKKEESGNKSQSNSQNSLSDESGNVTPVSKKQLSQPAAAIKASLKYPSHPDSLLEHQDHAGDTENEMHDDVDKEQFGYSSMYVFFRLFNLLYERLYELQRLEDQVSIIQQRIIPNPVSQKQKIWRDRWNDLSDVPDEKTHYENTYVMILRLIYGIVDQSAFEDYLRFYYGNKAYKIYTIDKLVWSAAKQVHHIVSDGKYKFVTSLVEQNSSASPKKNYDDFLYRLEIEKLLNPDEILFRFCWINKFKSFGIKIMKRANLIVDQSLDTQRRVWKKYVQNYRIQKLTEEISYKNYRCPFLCRNIEKERTVEQLVSRLQTKLLRSAELVSGLQAKLCLDSFKLLYLPRTEDSYIDASYLRLRDTDFLDCQNKRKQRWRNRWESLLKSVRGTSDNTAEVNFDADINALFIP

Entity 3 polymer

描述 description	Histone deacetylase clr6
分子量 formula_weight	46165.8 kDa
EC 编号 ec_number	3.5.1.98
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

MGFGKKKVSYFYDEDVGNYHYGPQHPMKPHRVRMVHNLVVNYNLYEKLNVITPVRATRNDMTRCHTDEYIEFLWRVTPDTMEKFQPHQLKFNVGDDCPVFDGLYEFCSISAGGSIGAAQELNSGNAEIAINWAGGLHHAKKREASGFCYVNDIALAALELLKYHQRVLYIDIDVHHGDGVEEFFYTTDRVMTCSFHKFGEYFPGTGHIKDTGIGTGKNYAVNVPLRDGIDDESYESVFKPVISHIMQWFRPEAVILQCGTDSLAGDRLGCFNLSMKGHSMCVDFVKSFNLPMICVGGGGYTVRNVARVWTYETGLLAGEELDENLPYNDYLQYYGPDYKLNVLSNNMENHNTRQYLDSITSEIIENLRNLSFAPSVQMHKTPGDFTFENAEKQNIAKEEIMDERV

Entity 4 polymer

描述 description	RbAp48-related WD40 repeat-containing protein prw1
分子量 formula_weight	48528.9 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	C

MAVSAVPHPSKQAQASEEGINQEKCINEEYKIWKKNSPFLYDLIITRALEWPCMSLQWYPEQQIFAEHGYTEQKMFLGVRADVGKYLLAVASIQLPYLNQTVPPTTMEGASAGDESSLRVNISNLYSHPESVCSAKLMPQDDSCVATVGNYHNDVLVFDKESFESYSSASESPLKPKYRLTKHTQPCTSVCWNFLSKGTLVSGSQDATLSCWDLNAYNESDSASVLKVHISSHEKQVSDVRFHYKHQDLLASVSYDQYLHVHDIRRPDASTKPARSVHAHSGPIHSVAFNPHNDFILATCSTDKTIALWDLRNLNQRLHTLEGHEDIVTKISFSPHEEPILASTSADRRTLVWDLSRIGEDQPAEEAQDGPPELLFMHGGHTSCTIDMDWCPNYNWTMATAAEDNILQIWTPSRSIWGNEQLEEDATAYLS

Entity 5 polymer

描述 description	Chromatin modification-related protein eaf3
分子量 formula_weight	39191.2 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,E

MAVSYKVNERVLCFHGPLLYEAKIVDTEMKGDVTTYLIHYKGWKNSWDEWVEQDRILQWTEENLKTQKELKNAAISTRQKPTSKKSASSTSKHDSTGVKTSGKRSRESSTVTVDGDSHELPSRIKTQKSESPIPQQVKRDGTTDAKNEETTKPENNEKDDFEEEPPLPKHKISVPDVLKLWLVDDWENITKNQQLIAIPRNPTVRAAIAAFRESKISHLNNEIDVDVFEQAMAGLVIYFNKCLGNMLLYRFERQQYLEIRQQYPDTEMCDLYGVEHLIRLFVSLPELIDRTNMDSQSIECLLNYIEEFLKYLVLHKDEYFIKEYQNAPPNYRSLVGV

Entity 6 polymer

描述 description	Uncharacterized protein C2F7.07c
分子量 formula_weight	68871.7 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	G

MDAKPWNHTSEAFQASILEDLKIIQKAGAERNAKSSHGSINSRSASPNKATSRRNRAQNGNSNGRASVDNSDDGSKDDLDYSPSVKRKHVNGEGAEKGDHDTSNNGPSITKLRRKVRRTYDTKDGFVAWNTLDDDFRPIVPDQERSRKINPQKGNNNNLLKENKSLKTTAKDLSDISSSSMKKANNSSKPLFSGKLTFKANIPVPTSEVVTENNVTRNVTVYSNQKHLGNESENFNDMEGRAEDISSNELLPTPEEYPYRYNNDYCSACHGPGNFLCCETCPNSFHFTCIDPPIEEKNLPDDAWYCNECKHHSLYNELDEQEELESNVKEEGTMVDVWMQLCTYIDSHNPIQFHLPHSISSFFRGVGSGVMGEYIETDVLKHLKSSRRSNGEERDPLLLKSKSGTPILCFRCHKSALVSQSILACDYCNSYWHPDCLNPPLATLPSNLRKWKCPNHSDHVTPRYRLPEKAKVIRVGLPRGFKNKGNIVIDENEDEPSVQTIQLQGKIRVVPSKPFKLNFLEQIRDNVINLRKMVEQDEQLCIETFSKFDFYATRDCELPLRILCDVANDNLENDDYVLALRDLLRISKWDPNQPVPAPFDLANLLSY

Entity 7 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 8 non-polymer

描述 description	POTASSIUM ION
分子量 formula_weight	39.1 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) 1 domains

CATH v4.4 (1 domains)

结构域编号 domain_id	8i02B01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	800 — Arginase; Chain A
同源超家族 H-superfamily homologous superfamily	20 — Histone deacetylase domain

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7. 引用文献 (1)

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分辨率 resolution	2.90 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	777199

fit	/app/data/saxs_computation/i0/8i02/8i02.fit
pddf	/app/data/pr_computation/i0/8i02/8i02.pr.out
profile	/app/data/saxs_computation/i0/8i02/8i02.dat

Cryo-EM structure of the SIN3S complex from S. pombe

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 (8)

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 non-polymer

Entity 8 non-polymer

6. 折叠分类 (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)