8zpk

Cryo-EM structure of origin recognition complex (Orc6 with residues 1 to 270 deleted) with ARS1 DNA bound

Method: ELECTRON MICROSCOPY D_max: 164.0 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	8zpk
沉积日期 deposition_date	2024-05-30
最后修订 last_revision	2025-04-16
结构标题 title	Cryo-EM structure of origin recognition complex (Orc6 with residues 1 to 270 deleted) with ARS1 DNA bound
关键词 keywords	REPLICATION; REPLICATION
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	47.58 Å
回转半径 Rg (电子) rg_electron	47.61 Å
零角强度 I(0) i0	1491670000.00
分子量 molecular_weight	314400.0 kDa
排除体积 excluded_volume	390640 Å³
包络体积 envelope_volume	562620 Å³
水化壳体积 shell_volume	96120 Å³
包络直径 envelope_diameter	177.7 Å
壳层 Rg shell_rg	53.47 Å
包络 Rg envelope_rg	47.13 Å
形状 Rg shape_rg	47.63 Å
总 Rg total_rg	47.75 Å
总原子数 total_atoms	22033
残基数 n_residues	2572
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	164.0 Å
Rg (实空间) rg_real	47.48 Å
Rg 误差 (实空间) rg_real_error	1.38 Å
I(0) (实空间) i0_real	1.4920e+09
I(0) 误差 (实空间) i0_real_error	2.8220e+07
Rg (倒空间) rg_reciprocal	47.58 Å
I(0) (倒空间) i0_reciprocal	1492000000.0000
解质量估计 total_estimate	0.8666
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	54.7 Å
偏度 Skewness skewness	0.335
峰度 Kurtosis kurtosis	-0.247
角度范围 angular_range	— – 0.1650 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	265700000.0000
实空间数据点数 n_real_points	34
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.779; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.934

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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 (10)

Entity 1 polymer

描述 description	Origin recognition complex subunit 2
分子量 formula_weight	71342.2 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	22033

MLNGEDFVEHNDILSSPAKSRNVTPKRVDPHGERQLRRIHSSKKNLLERISLVGNERKNTSPDPALKPKTPSKAPRKRGRPRKIQEELTDRIKKDEKDTISSKKKRKLDKDTSGNVNEESKTSNNKQVMEKTGIKEKREREKIQVATTTYEDNVTPQTDDNFVSNSPEPPEPATPSKKSLTTNHDFTSPLKQIIMNNLKEYKDSTSPGKLTLSRNFTPTPVPKNKKLYQTSETKSASSFLDTFEGYFDQRKIVRTNAKSRHTMSMAPDVTREEFSLVSNFFNENFQKRPRQKLFEIQKKMFPQYWFELTQGFSLLFYGVGSKRNFLEEFAIDYLSPKIAYSQLAYENELQQNKPVNSIPCLILNGYNPSCNYRDVFKEITDLLVPAELTRSETKYWGNHVILQIQKMIDFYKNQPLDIKLILVVHNLDGPSIRKNTFQTMLSFLSVIRQIAIVASTDHIYAPLLWDNMKAQNYNFVFHDISNFEPSTVESTFQDVMKMGKSDTSSGAEGAKYVLQSLTVNSKKMYKLLIETQMQNMGNLSANTGPKRGTQRTGVELKLFNHLCAADFIASNEIALRSMLREFIEHKMANITKNNSGMEIIWVPYTYAELEKLLKTVLNTL

来源 Source

来源生物 organism	Saccharomyces cerevisiae S288C
NCBI 分类编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	Saccharomyces cerevisiae

Entity 2 polymer

描述 description	Origin recognition complex subunit 5
分子量 formula_weight	55347.2 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	E

MNVTTPEVAFREYQTNCLASYISADPDITPSNLILQGYSGTGKTYTLKKYFNANPNLHAVWLEPVELVSWKPLLQAIARTVQYKLKTLYPNIPTTDYDPLQVEEPFLLVKTLHNIFVQYESLQEKTCLFLILDGFDSLQDLDAALFNKYIKLNELLPKDSKINIKFIYTMLETSFLQRYSTHCIPTVMFPRYNVDEVSTILVMSRCGELMEDSCLRKRIIEEQITDCTDDQFQNVAANFIHLIVQAFHSYTGNDIFALNDLIDFKWPKYVSRITKENIFEPLALYKSAIKLFLSTDDNLSENGQGESAITTNRDDLENSQTYDLSIISKYLLIASYICSYLEPRYDASIFSRKTRIIQGRAAYGRRKKKEVNPRYLQPSLFAIERLLAIFQAIFPIQGKAESGSLSALREESLMKANIEVFQNLSELHTLKLIATTMNKNIDYLSPKVRWKVNVPWEIIKEISESVHFNISDYFSDIHE

来源 Source

来源生物 organism	Saccharomyces cerevisiae S288C
NCBI 分类编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	Saccharomyces cerevisiae

Entity 3 polymer

描述 description	Origin recognition complex subunit 6
分子量 formula_weight	21192.7 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	F

MSLLVKKYCKMTTEEIIRLCNDFELPREVAYKIVDEYNINASRLVCPWQLVCGLVLNCTFIVFNERRRKDPRIDHFIVSKMCSLMLTSKVDDVIECVKLVKELIIGEKWFRDLQIRYDDFDGIRYDEIIFRKLGSMLQTTNILVTDDQYNIWKKRIEMDLALTEPLGSGSDYKDDDDKI

来源 Source

来源生物 organism	Saccharomyces cerevisiae S288C
NCBI 分类编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	Saccharomyces cerevisiae

Entity 4 polymer

描述 description	DNA (38-MER)
分子量 formula_weight	23708.3 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	G

TACAGATTTTATGTTTAGATCTTTTATGCTTGCTTTTCAAAAGGCCTGCAGGCAAGTGCACAAACAATACTTAAATA

Entity 5 polymer

描述 description	DNA (40-MER)
分子量 formula_weight	23766.3 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	H

TATTTAAGTATTGTTTGTGCACTTGCCTGCAGGCCTTTTGAAAAGCAAGCATAAAAGATCTAAACATAAAATCTGTA

Entity 6 polymer

描述 description	Origin recognition complex subunit 1
分子量 formula_weight	104546.2 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

MAKTLKDLQGWEIITTDEQGNIIDGGQKRLRRRGAKTEHYLKRSSDGIKLGRGDSVVMHNEAAGTYSVYMIQELRLNTLNNVVELWALTYLRWFEVNPLAHYRQFNPDANILNRPLNYYNKLFSETANKNELYLTAELAELQLFNFIRVANVMDGSKWEVLKGNVDPERDFTVRYICEPTGEKFVDINIEDVKAYIKKVEPREAQEYLKDLTLPSKKKEIKRGPQKKDKATQTAQISDAETRATDITDNEDGNEDESSDYESPSDIDVSEDMDSGEISADELEEEEDEEEDEDEEEKEARHTNSPRKRGRKIKLGKDDIDASVQPPPKKRGRKPKDPSKPRQMLLISSCRANNTPVIRKFTKKNVARAKKKYTPFSKRFKSIAAIPDLTSLPEFYGNSSELMASRFENKLKTTQKHQIVETIFSKVKKQLNSSYVKEEILKSANFQDYLPARENEFASIYLSAYSAIESDSATTIYVAGTPGVGKTLTVREVVKELLSSSAQREIPDFLYVEINGLKMVKPTDCYETLWNKVSGERLTWAASMESLEFYFKRVPKNKKKTIVVLLDELDAMVTKSQDIMYNFFNWTTYENAKLIVIAVANTMDLPERQLGNKITSRIGFTRIMFTGYTHEELKNIIDLRLKGLNDSFFYVDTKTGNAILIDAAGNDTTVKQTLPEDVRKVRLRMSADAIEIASRKVASVSGDARRALKVCKRAAEIAEKHYMAKHGYGYDGKTVIEDENEEQIYDDEDKDLIESNKAKDDNDDDDDNDGVQTVHITHVMKALNETLNSHVITFMTRLSFTAKLFIYALLNLMKKNGSQEQELGDIVDEIKLLIEVNGSNKFVMEIAKTLFQQGSDNISEQLRIISWDFVLNQLLDAGILFKQTMKNDRICCVKLNISVEEAKRAMNEDETLRNL

来源 Source

来源生物 organism	Saccharomyces cerevisiae S288C
NCBI 分类编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	Saccharomyces cerevisiae

Entity 7 polymer

描述 description	Origin recognition complex subunit 3
分子量 formula_weight	72161.8 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	C

MSDLNQSKKMNVSEFADAQRSHYTVYPSLPQSNKNDKHIPFVKLLSGKESEVNVEKRWELYHQLHSHFHDQVDHIIDNIEADLKAEISDLLYSETTQKRRCFNTIFLLGSDSTTKIELKDESSRYNVLIELTPKESPNVRMMLRRSMYKLYSAADAEEHPTIKYEDINDEDGDFTEQNNDVSYDLSLVENFKRLFGKDLAMVFNFKDVDSINFNTLDNFIILLKSAFKYDHVKISLIFNINTNLSNIEKNLRQSTIRLLKRNYHKLDVSSNKGFKYGNQIFQSFLDTVDGKLNLSDRFVEFILSKMANNTNHNLQLLTKMLDYSLMSYFFQNAFSVFIDPVNVDFLNDDYLKILSRCPTFMFFVEGLIKQHAPADEILSLLTNKNRGLEEFFVEFLVRENPINGHAKFVARFLEEELNITNFNLIELYHNLLIGKLDSYLDRWSACKEYKDRLHFEPIDTIFQELFTLDNRSGLLTQSIFPSYKSNIEDNLLSWEQVLPSLDKENYDTLSGDLDKIMAPVLGQLFKLYREANMTINIYDFYIAFRETLPKEEILNFIRKDPSNTKLLELAETPDAFDKVALILFMQAIFAFENMGLIKFQSTKSYDLVEKCVWRGI

来源 Source

来源生物 organism	Saccharomyces cerevisiae S288C
NCBI 分类编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	Saccharomyces cerevisiae

Entity 8 polymer

描述 description	Origin recognition complex subunit 4
分子量 formula_weight	60772.2 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	D

MTISEARLSPQVNLLPIKRHSNEEVEETAAILKKRTIDNEKCKDSDPGFGSLQRRLLQQLYGTLPTDEKIIFTYLQDCQQEIDRIIKQSIIQKESHSVILVGPRQSYKTYLLDYELSLLQQSYKEQFITIRLNGFIHSEQTAINGIATQLEQQLQKIHGSEEKIDDTSLETISSGSLTEVFEKILLLLDSTTKTRNEDSGEVDRESITKITVVFIFDEIDTFAGPVRQTLLYNLFDMVEHSRVPVCIFGCTTKLNILEYLEKRVKSRFSQRVIYMPQIQNLDDMVDAVRNLLTVRSEISPWVSQWNETLEKELSDPRSNLNRHIRMNFETFRSLPTLKNSIIPLVATSKNFGSLCTAIKSCSFLDIYNKNQLSNNLTGRLQSLSDLELAILISAARVALRAKDGSFNFNLAYAEYEKMIKAINSRIPTVAPTTNVGTGQSTFSIDNTIKLWLKKDVKNVWENLVQLDFFTEKSAVGLRDNATAAFYASNYQFQGTMIPFDLRSYQMQIILQELRRIIPKSNMYYSWTQL

来源 Source

来源生物 organism	Saccharomyces cerevisiae S288C
NCBI 分类编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	Saccharomyces cerevisiae

Entity 9 non-polymer

描述 description	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
分子量 formula_weight	523.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 10 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	3

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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	3.210 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	3.21 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	146160

fit	/app/data/saxs_computation/zp/8zpk/8zpk.fit
pddf	/app/data/pr_computation/zp/8zpk/8zpk.pr.out
profile	/app/data/saxs_computation/zp/8zpk/8zpk.dat

Cryo-EM structure of origin recognition complex (Orc6 with residues 1 to 270 deleted) with ARS1 DNA bound

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

精修参数 Refinement

冷冻电镜 EM 3D

5. 实体与聚合体信息 (10)

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

Entity 5 polymer

聚合体 Polymer

Entity 6 polymer

聚合体 Polymer

来源 Source

Entity 7 polymer

聚合体 Polymer

来源 Source

Entity 8 polymer

聚合体 Polymer

来源 Source

Entity 9 non-polymer

Entity 10 non-polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)