9cop

Yeast RAVE bound to V-ATPase V1 complex

Method: ELECTRON MICROSCOPY D_max: 224.6 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	9cop
沉积日期 deposition_date	2024-07-17
结构标题 title	Yeast RAVE bound to V-ATPase V1 complex
关键词 keywords	V-ATPase, RAVE, assembly, HYDROLASE; HYDROLASE
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	74.85 Å
回转半径 Rg (电子) rg_electron	74.16 Å
零角强度 I(0) i0	3841770000.00
分子量 molecular_weight	516930.0 kDa
排除体积 excluded_volume	643550 Å³
包络体积 envelope_volume	1116200 Å³
水化壳体积 shell_volume	128010 Å³
包络直径 envelope_diameter	258.0 Å
壳层 Rg shell_rg	67.78 Å
包络 Rg envelope_rg	75.38 Å
形状 Rg shape_rg	74.35 Å
总 Rg total_rg	73.37 Å
总原子数 total_atoms	70017
残基数 n_residues	5041
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	224.6 Å
Rg (实空间) rg_real	74.84 Å
Rg 误差 (实空间) rg_real_error	1.48 Å
I(0) (实空间) i0_real	3.8340e+09
I(0) 误差 (实空间) i0_real_error	8.1710e+07
Rg (倒空间) rg_reciprocal	73.44 Å
I(0) (倒空间) i0_reciprocal	3828000000.0000
解质量估计 total_estimate	0.8352
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	64.2 Å
偏度 Skewness skewness	0.349
峰度 Kurtosis kurtosis	-0.697
角度范围 angular_range	— – 0.1050 Å⁻¹
当前正则化参数 α current_alpha	0.0189
最高正则化参数 α highest_alpha	156200000.0000
实空间数据点数 n_real_points	22
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.956; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.981; Smooth: 0.001

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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 (12)

Entity 1 polymer

描述 description	V-type proton ATPase catalytic subunit A
分子量 formula_weight	118782.5 kDa
EC 编号 ec_number	7.1.2.2
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
原子数 atom_count	70017

MAGAIENARKEIKRISLEDHAESEYGAIYSVSGPVVIAENMIGCAMYELVKVGHDNLVGEVIRIDGDKATIQVYEETAGLTVGDPVLRTGKPLSVELGPGLMETIYDGIQRPLKAIKEESQSIYIPRGIDTPALDRTIKWQFTPGKFQVGDHISGGDIYGSVFENSLISSHKILLPPRSRGTITWIAPAGEYTLDEKILEVEFDGKKSDFTLYHTWPVRVPRPVTEKLSADYPLLTGQRVLDALFPCVQGGTTCIPGAFGCGKTVISQSLSKYSNSDAIIYVGCFAKGTNVLMADGSIECIENIEVGNKVMGKDGRPREVIKLPRGRETMYSVVQKSQHRAHKSDSSREVPELLKFTCNATHELVVRTPRSVRRLSRTIKGVEYFEVITFEMGQKKAPDGRIVELVKEVSKSYPISEGPERANELVESYRKASNKAYFEWTIEARDLSLLGSHVRKATYQTYAPILYENDHFFDYMQKSKFHLTIEGPKVLAYLLGLWIGDGLSDRATFSVDSRDTSLMERVTEYAEKLNLCAEYKDRKEPQVAKTVNLYSKVVRGNGIRNNLNTENPLWDAIVGLGFLKDGVKNIPSFLSTDNIGTRETFLAGLIDSDGYVTDEHGIKATIKTIHTSVRDGLVSLARSLGLVVSVNAEPAKVDMNGTKHKISYAIYMSGGDVLLNVLSKCAGSKKFRPAPAAAFARECRGFYFELQELKEDDYYGITLSDDSDHQFLLANQVVVHNCGERGNEMAEVLMEFPELYTEMSGTKEPIMKRTTLVANTSNMPVAAREASIYTGITLAEYFRDQGKNVSMIADSSSRWAEALREISGRLGEMPADQGFPAYLGAKLASFYERAGKAVALGSPDRTGSVSIVAAVSPAGGDFSDPVTTATLGITQVFWGLDKKLAQRKHFPSINTSVSYSKYTNVLNKFYDSNYPEFPVLRDRMKEILSNAEELEQVVQLVGKSALSDSDKITLDVATLIKEDFLQQNGYSTYDAFCPIWKTFDMMRAFISYHDEAQKAVANGANWSKLADSTGDVKHAVSSSKFFEPSRGEKEVHGEFEKLLSTMQERFAESTD

Entity 2 polymer

描述 description	V-type proton ATPase subunit B
分子量 formula_weight	57815.0 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

MVLSDKELFAINKKAVEQGFNVKPRLNYNTVSGVNGPLVILEKVKFPRYNEIVNLTLPDGTVRQGQVLEIRGDRAIVQVFEGTSGIDVKKTTVEFTGESLRIPVSEDMLGRIFDGSGRPIDNGPKVFAEDYLDINGSPINPYARIYPEEMISTGVSAIDTMNSIARGQKIPIFSASGLPHNEIAAQICRQAGLVRPTKDVHDGHEENFSIVFAAMGVNLETARFFKQDFEENGSLERTSLFLNLANDPTIERIITPRLALTTAEYLAYQTERHVLTILTDMSSYADALREVSAAREEVPGRRGYPGYMYTDLSTIYERAGRVEGRNGSITQIPILTMPNDDITHPIPDLTGYITEGQIFVDRQLHNKGIYPPINVLPSLSRLMKSAIGEGMTRKDHGDVSNQLYAKYAIGKDAAAMKAVVGEEALSIEDKLSLEFLEKFEKTFITQGAYEDRTVFESLDQAWSLLRIYPKEMLNRISPKILDEFYDRARDDADEDEEDPDTRSSGKKKDASQEESLI

Entity 3 polymer

描述 description	V-type proton ATPase subunit E
分子量 formula_weight	26508.4 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	I,K

MSSAITALTPNQVNDELNKMQAFIRKEAEEKAKEIQLKADQEYEIEKTNIVRNETNNIDGNFKSKLKKAMLSQQITKSTIANKMRLKVLSAREQSLDGIFEETKEKLSGIANNRDEYKPILQSLIVEALLKLLEPKAIVKALERDVDLIESMKDDIMREYGEKAQRAPLEEIVISNDYLNKDLVSGGVVVSNASDKIEINNTLEERLKLLSEEALPAIRLELYGPSKTRKFFD

Entity 4 polymer

描述 description	V-type proton ATPase subunit G
分子量 formula_weight	12738.7 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,L

MSQKNGIATLLQAEKEAHEIVSKARKYRQDKLKQAKTDAAKEIDSYKIQKDKELKEFEQKNAGGVGELEKKAEAGVQGELAEIKKIAEKKKDDVVKILIETVIKPSAEVHINAL

Entity 5 polymer

描述 description	V-type proton ATPase subunit D
分子量 formula_weight	29235.0 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	M

MSGNREQVFPTRMTLGLMKTKLKGANQGYSLLKRKSEALTKRFRDITKRIDDAKQKMGRVMQTAAFSLAEVSYATGENIGYQVQESVSTARFKVRARQENVSGVYLSQFESYIDPEINDFRLTGLGRGGQQVQRAKEIYSRAVETLVELASLQTAFIILDEVIKVTNRRVNAIEHVIIPRTENTIAYINSELDELDREEFYRLKKVQEKKQNETAKLDAEMKLKRDRAEQDASEVAADEEPQGETLVADQEDDVIF

Entity 6 polymer

描述 description	V-type proton ATPase subunit F
分子量 formula_weight	13348.0 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	N

AEKRTLIAVIADEDTTTGLLLAGIGQITPETQEKNFFVYQEGKTTKEEITDKFNHFTEERDDIAILLINQHIAENIRARVDSFTNAFPAILEIPSKDHPYDPEKDSVLKRVRKLFGE

Entity 7 polymer

描述 description	V-type proton ATPase subunit H
分子量 formula_weight	54482.6 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	P

MGATKILMDSTHFNEIRSIIRSRSVAWDALARSEELSEIDASTAKALESILVKKNIGDGLSSSNNAHSGFKVNGKTLIPLIHLLSTSDNEDCKKSVQNLIAELLSSDKYGDDTVKFFQEDPKQLEQLFDVSLKGDFQTVLISGFNVVSLLVQNGLHNVKLVEKLLKNNNLINILQNIEQMDTCYVCIRLLQELAVIPEYRDVIWLHEKKFMPTLFKILQRATDSQLATRIVATNSNHLGIQLQYHSLLLIWLLTFNPVFANELVQKYLSDFLDLLKLVKITIKEKVSRLCISIILQCCSTRVKQHKKVIKQLLLLGNALPTVQSLSERKYSDEELRQDISNLKEILENEYQELTSFDEYVAELDSKLLCWSPPHVDNGFWSDNIDEFKKDNYKIFRQLIELLQAKVRNGDVNAKQEKIIIQVALNDITHVVELLPESIDVLDKTGGKADIMELLNHSDSRVKYEALKATQAIIGYTFK

Entity 8 polymer

描述 description	Regulator of V-ATPase in vacuolar membrane protein 1
分子量 formula_weight	155127.3 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	x

MSLNFLPGRPNATPQTACQATWQNHTIFAYCSGNNLIILTNKFTRLQTIYTQSDCTAVDINSQNGFIALSFHNRVLIYKPIHQIMQNPKWTQCCQLFHDDTPVNCLRWSSDNELAIGSDFLSFWKIKDNFGVYQPILQWNQKQPKPVYNVIISQDSQLIVSIGKYDCNAKLWKRVSIVGEQAIFNLTMLPHPKPITAMRWKKEPDQVSKNNTASHALYTLCEDKVLRIWSCFEMEKNHTVQIWGEVPLSPTQKFCVIIDNWIIRQTLSVKDSEIFDISDSDIVILGSMTGEMEVLALNNLSQDPPKPMTKKTISHKKVKKATMLNDTRYLYLPEIQPYDNVKGKLSFLVHDLQGVIRHLLIDILQLINNKTEDLSAALEHKFTGHNKSVQKLVRSSDGEALLTTSRFSENGVWYPQKLNHGVSLRLQNTIQTESPIKFAVVHELGKQVICLLENGALQAWECPTNRKEDSEQKQSYLRVETRLKEEKKIHPIVMLNTPEPKHSHERHFTALIFSDGSIKAFEVSLTRGIFEVKSDSLDIDGDDIYKISIIDPVHQTFVSNRPLISLITKKGLTRTYKAIVNYNDRHVQWIKACEINTGIMNCTCIRGSSTGKLCIVNSTGKVMSLWDLNRGVLEYEETFHNPIEDIDWTSTEYGQSIVSIGFTGYALLYTQLRYDYTNNTPSYLPIEKIDITAHTAHNIGDSVWMKNGTFVVASGNQFYIKDKSLDLTDPFTYQSIGSRKILSNDILHLSSVLNGPLPVYHPQFLIQAIYANKLQLVKELLLRLFLALRKLDFESQDVSNLDSNLGMDPLKYFIAKDRDYPVESFPDPYPCFNKTVSLALTEQLTKTTLPYLTRHQQITLITVIEAVDEVTKNENIVDYNGVRFLLGVKLFLSHKNIQKSILMRDVSWALHSDNKEILLSSIDRHITSWNRAREYRIAYWIKEQDLVKKFEDIAKYEFSKDDKRDPSRCAIFYLALKKKQILLSLWKMAIGHPEQQKMVRFISNDFTVPRWRTAALKNAFVLLSKHRYMDAAVFFLLTDSLKDCVNVLCKQVHDMDLAIGVCRVYEGDNGPVLGELLTAQMLPETIKENDRWKASFIYWKLRKQEVAIKALLTAPIDLENNSSIVDKEVCVNRSFLVEDPALLYLYNHLRNRNLKYFIGSLNVEAKIECTLILRVTDILCRMGCNYLAVSLVKNWKFIERNSIPVQKLLKSPTKDRAYSAIGAMASEPISTARMRPSLFDKFGSPSASDIESPNPKLPNSLLDDFLQPPPNSTSSNSLAQSSSSAPRSILDEFVSPSYSQHKENLTPKAPNDSVGETDNSENRKDKLSKDILDDLSSQKPQKPKKSAITKNLLDDFV

Entity 9 polymer

描述 description	Regulator of V-ATPase in vacuolar membrane protein 2
分子量 formula_weight	40061.0 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	y

MSVDLFPNDRFGAEDKYDNFKDAVKECSWLIEEIVKPQLPNIIDNFSKCLEMLESDQIFKMPVSNGIPNESNKQNDSPTVKGVITRQGQYIVDFHIVVRFPQFQRGKQVMFRMNTGLNFLLIQFSKIMTHLKNILEILNQLQVATDVSEFVSKFGVAMELLNHSLILLQNPPRDLVFPEDNNFAMKEMFQDCYSVCESTAHILGLELTLCRNELCIELRNLIKVTKKPWCEIDSKTGRSFCDQIRNQVTNERNKTLSKILSENGVQVQDSTLLNHIISSFQSEAITLPEAQELLRRGVTFDNRVVMECEKLIVSTSDPTLISISAKLNSLKASMANHQANLVASKQLSTYK

Entity 10 polymer

描述 description	Suppressor of kinetochore protein 1
分子量 formula_weight	22357.3 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	z

MVTSNVVLVSGEGERFTVDKKIAERSLLLKNYLNDMHDSNLQNNSDSESDSDSETNHKSKDNNNGDDDDEDDDEIVMPVPNVRSSVLQKVIEWAEHHRDSNFPDEDDDDSRKSAPVDSWDREFLKVDQEMLYEIILAANYLNIKPLLDAGCKVVAEMIRGRSPEEIRRTFNIVNDFTPEEEAAIRRENEWAEDR

Entity 11 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	2

Entity 12 non-polymer

描述 description	ADENOSINE-5'-DIPHOSPHATE
分子量 formula_weight	427.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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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	2.70 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	71341

fit	/app/data/saxs_computation/co/9cop/9cop.fit
pddf	/app/data/pr_computation/co/9cop/9cop.pr.out
profile	/app/data/saxs_computation/co/9cop/9cop.dat

Yeast RAVE bound to V-ATPase V1 complex

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 (12)

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

Entity 12 non-polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)