8i03

Cryo-EM structure of the SIN3L complex from S. pombe

Method: ELECTRON MICROSCOPY D_max: 211.2 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	8i03
沉积日期 deposition_date	2023-01-10
结构标题 title	Cryo-EM structure of the SIN3L complex from S. pombe
关键词 keywords	SIN3, SIN3L, Pst1, Pst3, 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	70.96 Å
回转半径 Rg (电子) rg_electron	71.13 Å
零角强度 I(0) i0	2485390000.00
分子量 molecular_weight	418020.0 kDa
排除体积 excluded_volume	521670 Å³
包络体积 envelope_volume	872310 Å³
水化壳体积 shell_volume	106770 Å³
包络直径 envelope_diameter	290.4 Å
壳层 Rg shell_rg	64.97 Å
包络 Rg envelope_rg	70.43 Å
形状 Rg shape_rg	71.18 Å
总 Rg total_rg	70.83 Å
总原子数 total_atoms	29430
残基数 n_residues	3634
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	211.2 Å
Rg (实空间) rg_real	70.34 Å
Rg 误差 (实空间) rg_real_error	1.31 Å
I(0) (实空间) i0_real	2.4740e+09
I(0) 误差 (实空间) i0_real_error	4.9080e+07
Rg (倒空间) rg_reciprocal	69.74 Å
I(0) (倒空间) i0_reciprocal	2478000000.0000
解质量估计 total_estimate	0.8394
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	96.0 Å
偏度 Skewness skewness	0.328
峰度 Kurtosis kurtosis	-0.591
角度范围 angular_range	— – 0.1100 Å⁻¹
当前正则化参数 α current_alpha	0.0192
最高正则化参数 α highest_alpha	118300000.0000
实空间数据点数 n_real_points	23
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.970; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.007

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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	Paired amphipathic helix protein pst1
分子量 formula_weight	171667.1 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	A
原子数 atom_count	29430

MAKDWQDARLGQCHRLEDYSNVAINYTGPYLTPSGTMAYHPGNAPLFTQAPPHTNPQGPPPFPLFNSISPVYDPATGRLLYRNVNTQVSHTAIPNPANGYAAVYGGPPSQLPPPPQPQSHPNVTVISASPARAIEQQPTILSSTDSNIPRPGTVKSSASPFVPNQNPSAPPPPPQEYRQLNVTDALSYLDLVKLQFHQEPEIYNEFLDIMKEFKSQAIETPEVITRVSKLFAGYPNLIQGFNTFLPPGYSIEISSADPGSLAGIHITTPQGPLMINDLGKTTAPPPPHGSTTPLPAAASYTSMNMKQSSASHPVLQPPAPSTLQFNPSPSPAAPSYPPVDASVKQAADLDQAINFVNNVKNRFSHKPEAYNSFLDILKSYQHDQRPIQLVYFQVSQLFAEAPDLLEEFKRFLPDVSVNAPAETQDKSTVVPQESATATPKRSPSATPTSALPPIGKFAPPTTAKAQPAPEKRRGEPAVQTRNHSKRTRTATSSVEETTPRAFNVPIAQNKNPSELEFLEHARQYLANESKYNEFIKLLELYSQEVFDKNALVERCYVFFGSNEHLMNWLKDLVKYNPANPIPVPRPRVDLTQCKSCGPSYRLLPKIELLLPCSGRDDLCWTILNDAWVSFPTLASEDSGFIAHRKNQFEENLHKLEEERYEYDRHIGANMRFIELLQIHADKMLKMSEVEKANWTLPSNLGGKSVSIYHKVIKKVYGKEHAQQIIENLQKNPSVTIPIVLERLKKKDREWRSLQNHWNELWHDIEEKNFYRSLDHQGVSFKSVDKKSTTPKFLISELRNLAQQQKVELSEGKVTPSHQFLFSYKDPNIITDIARLFGVFLIHGSTHSAEDNEKMSNFLRSFLSLFFDVPYDSFIPYLPTHFNEEESDIDSLSSSLIEKPRASSSPIHHANNNGLRLLKDVLKKTYRGARENRSSVKEDYVSESTERTPDASEIDEHISEHEENDDESSSVFSTGEVWVNCKFTDTDGSLLDDGTKLSDRSVYNLFGNMSLYCFFRLFHTLYSRLEEIKNLEQMAYSKQHDVKSNPVAVELGLVRHPSERLGFALPTADTVYEQAIQLCERLMEGEIDQNGFEDALRCLYGIHAFRLYTVEKLVTSIIKQLHSVTTNRRLAQVFMYYEKDRVQRRTSPRQQIMYRIQTETAFGPDENLCCIDWNSQTRQSAIRLMGREDLTMGTLKSDAEKWCYYIGSYIMSSPTEGILPEHVRIPFLRKCLPSDEGNEDDESSSVVKSANAIITSFLESGLALTIPINTVKIRYENGTEDVFARNSEQVYNGPYDKIRDYRQSKWREWLNSDEGWTQGLSKDKVRRIKPCTIESLFNESTLRSGKAERFSENAGVESIGKKGKNLLNESGNGKKLDKGLPPKVNGKSSVTRGNKTNLKARNGRNNDDSSNKINLSEKEKEKESIEDEEKNREGSMSPVAKHASDVEDDHDVAKSTAPDFETSSHRPERSSEKKSPSPVFTSVKQTAENDADNEDDKTDMDDQTEETLDADNTMEEEPSKDDL

Entity 2 polymer

描述 description	Paired amphipathic helix protein pst3
分子量 formula_weight	133049.8 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

MDVMNVPVDSERDNPGDKVETQSDKNHLPKASPSQSQSPVNTSLHNGDGKDNGVATEPVENKQILSERSVTRDDYEKGKTIVSSLALSSISGKDGSISSQNAEGLSSSSNRPLDVNDALSYLELVKYYFSERREIYNRFLEIMRDFKSQALDTLGVINRVSELFNGYPQLIEGFNTFLPSGYKIEVQLDSSNTSVVRVGTPMHPLPQQGVQSTLPVAPSNEDQRTMESTSPTDSQPQPSAPNLVSSTENEKPRVDFNYAIAYMNKVKARYPPNSDTYMEFLGVLRTYQKAQKSIFEVRARVAEIFKDSPDLLEEFKLFLPDNVDSTEPSTPNVQKSPNRLPPVGNFSLPPSAPVREKRNRPAHSAQISRSISKTSRMYRQTAEEPLNSYSLHVYPQKITAPTSPYAATQEELLAFTTIRQHLPDTLAFHKFLELLHLYREKLLDKTELLNSFSKLVRNDNLTLWFSEFIRWSDNPILVKNEPVDERVYLPETFECISLTYRKLPDSWKQDKCSGRDDLDNSVLNDDYISVAPKPSHVKNIMHHENQYLQALQLVEDERYDYDRVLNTTESAIKILANFCEPTIHEHLETALQELERSKRIIKNALIIVYGKEHANLALDTLFKKLPTAAPVLLKRIKTKDQEWRRSKREWSKIWRQIEKKNAQAAFDDRYCRIEGRDRRGLSYSRILRDIDDIYQRQKHRIDGAKLGFQFTQVLCDSLIFLNILRLSDAQLTNSSFYSYADKGRISAVLKALLSQFFGIPLPREALETNLASENIESVKKHRDGLSKIFIRPESADNSNNTNVSFQTDETQTEDETMSDIHPDDVENHSKSKFLGEESKNIIGYNFFGNATMYVLFRLICVCYSRLEHIKLFVESSTIYASSTGGYENILNICEKYLKGSCSRLEFRKYLQKFNNETCYMICSIERLLKVIFYRIHEILLDPKLGQLLLLFESDGANSVTTPREQMVYRNHVESILAPESKIFNMRWYPLEKRLCIQQLLPADLTMHDFENPAKAFMYYVDSYAISHITEGVDLMQVKMPFLRRSLQRISQQGYLAGRGSGRLHSLFNEHFCKSNLQLFFSTDTYVIFFEPNTENVYINSYNLWVDQSSQSKKQNRTTNWRRWLESDEGWRKSKANTDIKFFSETTLDQCIEAM

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	2

聚合体 Polymer

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

MGFGKKKVSYFYDEDVGNYHYGPQHPMKPHRVRMVHNLVVNYNLYEKLNVITPVRATRNDMTRCHTDEYIEFLWRVTPDTMEKFQPHQLKFNVGDDCPVFDGLYEFCSISAGGSIGAAQELNSGNAEIAINWAGGLHHAKKREASGFCYVNDIALAALELLKYHQRVLYIDIDVHHGDGVEEFFYTTDRVMTCSFHKFGEYFPGTGHIKDTGIGTGKNYAVNVPLRDGIDDESYESVFKPVISHIMQWFRPEAVILQCGTDSLAGDRLGCFNLSMKGHSMCVDFVKSFNLPMICVGGGGYTVRNVARVWTYETGLLAGEELDENLPYNDYLQYYGPDYKLNVLSNNMENHNTRQYLDSITSEIIENLRNLSFAPSVQMHKTPGDFTFENAEKQNIAKEEIMDERV

Entity 4 polymer

描述 description	Transcriptional regulatory protein dep1
分子量 formula_weight	55701.5 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	E

MTENLQSESIPHEILPKEPFDLPMNNLKSSPKNKDSEKRINNSIAESEQVVDSALSNPETNANEDIIAPQLPSQNSEIIEKNSPVNKLNSSTSLTTHQLASLPKLEVTDHDNVSEAETVVLNEDEEKETSLVGSVSVTEDLGDSSAIGRTILVNNSVEPQMENTANITIVSPSLKESDFESEEKATNDNNGLIETNHNSKLEESSEHEEEEDEESNIERTEDSDHQIPQRGGTLEAPRKGGPRSGVGSRKRKRATVSRKWSTNSESKIKRVALETSQEESDREIADRRSASEQAHEADDEKAIKRKEAFDALLNIETEFTFLRNRLYGKKLLKLNEHEEMIQNETHERFNACIDLITERRDDRVRLATENLMKQLGNIKNVMDYVTKQRKYQLLFDKRRIRQALLTKIATKCFQLLNKQKSVHDPTYITQKTMSYRQSALLQKQRIEYEAAVLCELNSFAGFPTAPIIETASFDDIRNDLLEMGCLSENQD

Entity 5 polymer

描述 description	Transcriptional regulatory protein rxt2
分子量 formula_weight	27429.3 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

MKQFEEQIERFKQALFEDSDASDSDSSIGEALTNRGLKRKKGSKNVYYGCVGNSSGSSIDIDYYNIGNTKRGVVSHFRRRIDPEWLDHDNPYNDINIAEIMSPLTKPQDLLTHPAISSIFEQNYLSILASSALEIISAEHKYTAHLEQLMVALLGDDPSLPGPPHEVFGISPEQCRELTITVQEALEKSKEFIRCWTNVRMDLLRAIRFKNKVIAYCQGEDYNGNTQVLSKNESDGKPNS

Entity 6 polymer

描述 description	Transcriptional regulatory protein sds3
分子量 formula_weight	30800.6 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	G

MDVLSRVFDNEKEELDPLLNNPLTASEFRAKKAELEAELESIRNGTCKTLLDLADELRRSRDEELEIAERWRTFLVNRAQEEYEVEMKAAKEEYEYRCKTLKEMVLSHLNEKKRKIYEAKDMFDIGSESSTLLLHDASSQFIDRRKLRHRRNAGNQQNTQQLPSLNFFDDYLLFPTDETAVIPQSVKNAVRNSVNSVKPTSAEASLFSPLLSMANANPTNGRERDPRASERAERDREKAVEKGLSGATEEDIQSDLQLLKKELAKKK

Entity 7 polymer

描述 description	Chromatin modification-related protein png2
分子量 formula_weight	34925.9 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	H

MGTSGIEIFAALNDFTDAIVSVPESVCGKFTSLKEIDAQVRDIRQNVIQEIGVVLKNEKNDELSGEERCERLQKTLKEILPYSDSKICLATDAMNNIKSCIDRLDAGFEYVELEIPQQLRLGYPDDRALMNYHSTVTPQTSERRRETRRHQNNQHSQQYSSQERSSSYNNFEDASSPQSSYHTPTKRRKNAVPRKSSSPPLSSTKHAPQSTERRPVRRSESRLKQTNGEPLVKHDTLDSSDISREGEQLYCYCQQVSYGQMIGCDNENCKREWFHLPCVGLVEPPKGIWYCKECEELAKSSESRQ

Entity 8 polymer

描述 description	Transcriptional regulatory protein rxt3
分子量 formula_weight	39464.2 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

MEEKTPENEQSKKTFDPKDSMKIEETSTNGSSQPSQPSNIKLSIGSILESSNDNGDPEYSENGMGNMNMNTLPMATSTPMSYTKQPSEAKYPNSVWERKGVSDQEENTSSVKRQKTLPTQSSGEEEAKYSHPGAPTATSADSISMESRPSNLSTSLSKTTSYPQFQVRQFVSPIISIDNSALEPFLNRYPASESLFPVTEYEYTPWLEFPLLYSSIGKFVRVTIDIKWLNAAINPRLCRREIWGTDVYTDDSDIATILAHCGCFSLLKPVRKIAVVDLYILPPLVHYKGTRKNQIESRSWSSRQDGISLKIKEVTWKPACASIFENSIHTLTLEERLQARLELSRSSTFKI

Entity 9 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	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	J,K

MAVSAVPHPSKQAQASEEGINQEKCINEEYKIWKKNSPFLYDLIITRALEWPCMSLQWYPEQQIFAEHGYTEQKMFLGVRADVGKYLLAVASIQLPYLNQTVPPTTMEGASAGDESSLRVNISNLYSHPESVCSAKLMPQDDSCVATVGNYHNDVLVFDKESFESYSSASESPLKPKYRLTKHTQPCTSVCWNFLSKGTLVSGSQDATLSCWDLNAYNESDSASVLKVHISSHEKQVSDVRFHYKHQDLLASVSYDQYLHVHDIRRPDASTKPARSVHAHSGPIHSVAFNPHNDFILATCSTDKTIALWDLRNLNQRLHTLEGHEDIVTKISFSPHEEPILASTSADRRTLVWDLSRIGEDQPAEEAQDGPPELLFMHGGHTSCTIDMDWCPNYNWTMATAAEDNILQIWTPSRSIWGNEQLEEDATAYLS

Entity 10 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

Entity 11 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	4

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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	8i03C01
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

结构域编号 domain_id	8i03D01
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	3.200 Å
最低分辨率 resolution_low	— Å
R 因子 r_factor	—
R_work r_work	—
R_free r_free	—

分辨率 resolution	3.20 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	389222

fit	/app/data/saxs_computation/i0/8i03/8i03.fit
pddf	/app/data/pr_computation/i0/8i03/8i03.pr.out
profile	/app/data/saxs_computation/i0/8i03/8i03.dat

Cryo-EM structure of the SIN3L 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

精修参数 Refinement

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 non-polymer

Entity 11 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)