8ifg

Cryo-EM structure of the Clr6S (Clr6-HDAC) complex from S. pombe

Method: ELECTRON MICROSCOPY D_max: 172.9 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	8ifg
沉积日期 deposition_date	2023-02-17
结构标题 title	Cryo-EM structure of the Clr6S (Clr6-HDAC) complex from S. pombe
关键词 keywords	Rpd3S, Histone deacetylase, HDAC, Clr6, Rpd3, Clr6S, Clr6 HDAC, 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	50.16 Å
回转半径 Rg (电子) rg_electron	49.91 Å
零角强度 I(0) i0	1035430000.00
分子量 molecular_weight	270420.0 kDa
排除体积 excluded_volume	339290 Å³
包络体积 envelope_volume	478820 Å³
水化壳体积 shell_volume	81544 Å³
包络直径 envelope_diameter	185.9 Å
壳层 Rg shell_rg	52.37 Å
包络 Rg envelope_rg	49.05 Å
形状 Rg shape_rg	49.91 Å
总 Rg total_rg	50.00 Å
总原子数 total_atoms	19067
残基数 n_residues	2338
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	172.9 Å
Rg (实空间) rg_real	50.17 Å
Rg 误差 (实空间) rg_real_error	2.21 Å
I(0) (实空间) i0_real	1.0350e+09
I(0) 误差 (实空间) i0_real_error	2.2060e+07
Rg (倒空间) rg_reciprocal	50.13 Å
I(0) (倒空间) i0_reciprocal	1035000000.0000
解质量估计 total_estimate	0.8811
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	61.3 Å
偏度 Skewness skewness	0.315
峰度 Kurtosis kurtosis	-0.393
角度范围 angular_range	— – 0.1550 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	91850000.0000
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: 0.863; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.976; Smooth: 0.885

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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	RbAp48-related WD40 repeat-containing protein prw1
分子量 formula_weight	48528.9 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	B
原子数 atom_count	19068

MAVSAVPHPSKQAQASEEGINQEKCINEEYKIWKKNSPFLYDLIITRALEWPCMSLQWYPEQQIFAEHGYTEQKMFLGVRADVGKYLLAVASIQLPYLNQTVPPTTMEGASAGDESSLRVNISNLYSHPESVCSAKLMPQDDSCVATVGNYHNDVLVFDKESFESYSSASESPLKPKYRLTKHTQPCTSVCWNFLSKGTLVSGSQDATLSCWDLNAYNESDSASVLKVHISSHEKQVSDVRFHYKHQDLLASVSYDQYLHVHDIRRPDASTKPARSVHAHSGPIHSVAFNPHNDFILATCSTDKTIALWDLRNLNQRLHTLEGHEDIVTKISFSPHEEPILASTSADRRTLVWDLSRIGEDQPAEEAQDGPPELLFMHGGHTSCTIDMDWCPNYNWTMATAAEDNILQIWTPSRSIWGNEQLEEDATAYLS

来源 Source

来源生物 organism	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
NCBI 分类编号 ncbi_taxonomy_id	284812
宿主生物 host_organism	Trichoplusia ni

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	man
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

来源 Source

来源生物 organism	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
NCBI 分类编号 ncbi_taxonomy_id	284812
宿主生物 host_organism	Trichoplusia ni

Entity 3 polymer

描述 description	Histone deacetylase clr6
分子量 formula_weight	45773.4 kDa
EC 编号 ec_number	3.5.1.98
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

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

KKKVSYFYDEDVGNYHYGPQHPMKPHRVRMVHNLVVNYNLYEKLNVITPVRATRNDMTRCHTDEYIEFLWRVTPDTMEKFQPHQLKFNVGDDCPVFDGLYEFCSISAGGSIGAAQELNSGNAEIAINWAGGLHHAKKREASGFCYVNDIALAALELLKYHQRVLYIDIDVHHGDGVEEFFYTTDRVMTCSFHKFGEYFPGTGHIKDTGIGTGKNYAVNVPLRDGIDDESYESVFKPVISHIMQWFRPEAVILQCGTDSLAGDRLGCFNLSMKGHSMCVDFVKSFNLPMICVGGGGYTVRNVARVWTYETGLLAGEELDENLPYNDYLQYYGPDYKLNVLSNNMENHNTRQYLDSITSEIIENLRNLSFAPSVQMHKTPGDFTFENAEKQNIAKEEIMDERV

来源 Source

来源生物 organism	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
NCBI 分类编号 ncbi_taxonomy_id	284812
宿主生物 host_organism	Trichoplusia ni

Entity 4 polymer

描述 description	Chromatin modification-related protein eaf3
分子量 formula_weight	39191.2 kDa
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

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

MAVSYKVNERVLCFHGPLLYEAKIVDTEMKGDVTTYLIHYKGWKNSWDEWVEQDRILQWTEENLKTQKELKNAAISTRQKPTSKKSASSTSKHDSTGVKTSGKRSRESSTVTVDGDSHELPSRIKTQKSESPIPQQVKRDGTTDAKNEETTKPENNEKDDFEEEPPLPKHKISVPDVLKLWLVDDWENITKNQQLIAIPRNPTVRAAIAAFRESKISHLNNEIDVDVFEQAMAGLVIYFNKCLGNMLLYRFERQQYLEIRQQYPDTEMCDLYGVEHLIRLFVSLPELIDRTNMDSQSIECLLNYIEEFLKYLVLHKDEYFIKEYQNAPPNYRSLVGV

来源 Source

来源生物 organism	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
NCBI 分类编号 ncbi_taxonomy_id	284812
宿主生物 host_organism	Trichoplusia ni

Entity 5 polymer

描述 description	Cph1
分子量 formula_weight	45046.1 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	F

MASSINNSSQPTVPSISNNSHGDSFVNEGPPSNFKNNSLTSSTHSSTDHVNVLPISQDKEMDISSPVKKQKASYSNKSPNKAPIQKSRGSSLKSHLETESQQTPVKRRRRKATIRNVDYCSACGGRGLFICCEGCPCSFHLSCLEPPLTPENIPEGSWFCVTCSIKSHHPPKHPLSIWSQLYDWIDSQNPSQYRLPDDLVHYFHGISRGDTGAYKETEGEMDTDEFSALPTGSSITNLAYCGYCSKPSMGACWVYGCQLCDTFYHKNCKEHAKKCSHDSIGKKGMRVPKNAVVIRTPLVLDTTSNTLNPKVMISGWQFLMGEFPSDELLYFPRLPVSCLYKVSEDGLIKDFLYAIGIEAKKFNNERKKRELEVIPPDVKSALLPARTHPNLPIALRTLFNKART

来源 Source

来源生物 organism	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
NCBI 分类编号 ncbi_taxonomy_id	284812
宿主生物 host_organism	Trichoplusia ni

Entity 6 polymer

描述 description	Cph2
分子量 formula_weight	68871.7 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	P

MDAKPWNHTSEAFQASILEDLKIIQKAGAERNAKSSHGSINSRSASPNKATSRRNRAQNGNSNGRASVDNSDDGSKDDLDYSPSVKRKHVNGEGAEKGDHDTSNNGPSITKLRRKVRRTYDTKDGFVAWNTLDDDFRPIVPDQERSRKINPQKGNNNNLLKENKSLKTTAKDLSDISSSSMKKANNSSKPLFSGKLTFKANIPVPTSEVVTENNVTRNVTVYSNQKHLGNESENFNDMEGRAEDISSNELLPTPEEYPYRYNNDYCSACHGPGNFLCCETCPNSFHFTCIDPPIEEKNLPDDAWYCNECKHHSLYNELDEQEELESNVKEEGTMVDVWMQLCTYIDSHNPIQFHLPHSISSFFRGVGSGVMGEYIETDVLKHLKSSRRSNGEERDPLLLKSKSGTPILCFRCHKSALVSQSILACDYCNSYWHPDCLNPPLATLPSNLRKWKCPNHSDHVTPRYRLPEKAKVIRVGLPRGFKNKGNIVIDENEDEPSVQTIQLQGKIRVVPSKPFKLNFLEQIRDNVINLRKMVEQDEQLCIETFSKFDFYATRDCELPLRILCDVANDNLENDDYVLALRDLLRISKWDPNQPVPAPFDLANLLSY

来源 Source

来源生物 organism	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
NCBI 分类编号 ncbi_taxonomy_id	284812
宿主生物 host_organism	Trichoplusia ni

Entity 7 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	nat
拷贝数 entity_count	3

Entity 8 water

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
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	—

分辨率 resolution	3.20 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	721645

fit	/app/data/saxs_computation/if/8ifg/8ifg.fit
pddf	/app/data/pr_computation/if/8ifg/8ifg.pr.out
profile	/app/data/saxs_computation/if/8ifg/8ifg.dat

Cryo-EM structure of the Clr6S (Clr6-HDAC) 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

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 (8)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 polymer

聚合体 Polymer

来源 Source

Entity 4 polymer

聚合体 Polymer

来源 Source

Entity 5 polymer

聚合体 Polymer

来源 Source

Entity 6 polymer

聚合体 Polymer

来源 Source

Entity 7 non-polymer

Entity 8 water

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)