8hex

C5 portal vertex in HCMV B-capsid

Method: ELECTRON MICROSCOPY D_max: 271.1 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	8hex
沉积日期 deposition_date	2022-11-08
结构标题 title	C5 portal vertex in HCMV B-capsid
关键词 keywords	B-capsid, C5 portal vertex, in-situ structure, VIRUS, VIRAL PROTEIN; VIRAL 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	76.54 Å
回转半径 Rg (电子) rg_electron	76.49 Å
零角强度 I(0) i0	18648000000.00
分子量 molecular_weight	1176800.0 kDa
排除体积 excluded_volume	1478900 Å³
包络体积 envelope_volume	2227100 Å³
水化壳体积 shell_volume	235050 Å³
包络直径 envelope_diameter	277.1 Å
壳层 Rg shell_rg	80.77 Å
包络 Rg envelope_rg	75.53 Å
形状 Rg shape_rg	76.49 Å
总 Rg total_rg	76.51 Å
总原子数 total_atoms	82790
残基数 n_residues	10455
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	271.1 Å
Rg (实空间) rg_real	79.73 Å
Rg 误差 (实空间) rg_real_error	1.61 Å
I(0) (实空间) i0_real	1.8660e+10
I(0) 误差 (实空间) i0_real_error	3.8180e+08
Rg (倒空间) rg_reciprocal	76.54 Å
I(0) (倒空间) i0_reciprocal	18650000000.0000
解质量估计 total_estimate	0.8792
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	94.9 Å
偏度 Skewness skewness	0.513
峰度 Kurtosis kurtosis	-0.013
角度范围 angular_range	— – 0.1000 Å⁻¹
当前正则化参数 α current_alpha	1.1040
最高正则化参数 α highest_alpha	1442000000.0000
实空间数据点数 n_real_points	21
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.804; Stabil: 0.883; Sysdev: 1.000; Positv: 1.000; Valcen: 0.978; Smooth: 0.412

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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 (9)

Entity 1 polymer

描述 description	Triplex capsid protein 2
分子量 formula_weight	34635.8 kDa
来源方法 src_method	nat
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	h,I,n,o
原子数 atom_count	82790

MAAMEANIFCTFDHKLSIADVGKLTKLVAAVVPIPQRLHLIKHYQLGLHQFVDHTRGYVRLRGLLRNMTLTLMRRVEGNQILLHVPTHGLLYTVLNTGPVTWEKGDALCVLPPLFHGPLARENLLTLGQWELVLPWIVPMPLALEINQRLLIMGLFSLDRSYEEVKAAVQQLQTITFRDATFTIPDPVIDQHLLIDMKTACLSMSMVANLASELTMTYVRKLALEDSSMLLVKCQELLMRLDRERSVGEPRTPARPQHVSPDDEIARLSALFVMLRQLDDLIREQVVFTVCDVSPDNKSATCIFKG

Entity 2 polymer

描述 description	Triplex capsid protein 1
分子量 formula_weight	33071.3 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	g,m

MDARAVAKRPRDPADEDNELVTALKAKREVNTISVRYLYHADHQALTARFFVPEGLVEFEAQPGALLIRMETGCDSPRHLYISLYLLGIRASNVSASTRCLLESVYTASAARAALQWLDLGPHLLHRRLETLGCVKTVSLGITSLLTCVMRGYLYNTLKTEVFALMIPKDMYLTWEETRGRLQYVYLIIVYDYDGPETRPGIYVLTSSIAHWQTLVDVARGKFARERCSFVNRRITRPRQIPLCTGVIQKLGWCLADDIHTSFLVHKELKLSVVRLDNFSVELGDFREFV

Entity 3 polymer

描述 description	Capsid vertex component 1
分子量 formula_weight	68567.2 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	M

METHLYSDLAFEARFADDEQLPLHLVLDQEVLSNEEAETLRYVYYRNVDSAGRSTGRAPGGDEDDAPASDDAEDAVGGDRAFDRERRTWQRACFRVLPRPLELLDYLRQSGLTVTLEKEQRVRMFYAVFTTLGLRCPDNRLSGAQTLHLRLVWPDGSYRDWEFLARDLLREEMEANKRDRQHQLATTTNHRRRGGLRNNLDNGSDRRLPEAAVASLETAVSTPFFEIPNGAGTSSANGDGRFSNLEQRVARLLRGDEEFIYHAGPLEPPSKIRGHELVQLRLDVNPDLMYATDPHDRDEVARTDEWKGAGVSRLREVWDVQHRVRLRVLWYVNSFWRSRELSYDDHEVELYRALDAYRARIAVEYVLIRAVRDEIYAVLRRDGGALPQRFACHVSRNMSWRVVWELCRHALALWMDWADVRSCIIKALTPRLSRGAAAAAQRARRQRERSAPKPQELLFGPRNESGPPAEQTWYADVVRCVRAQVDLGVEVRAARCPRTGLWIVRDRRGRLRRWLSQPEVCVLYVTPDLDFYWVLPGGFAVSSRVTLHGLAQRALRDRFQNFEAVLARGMHVEAGRQEPETPRVSGRRLPFDDL

Entity 4 polymer

描述 description	Capsid vertex component 2
分子量 formula_weight	71269.6 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	N,O

MSLLHTFWRLPVAVFFEPHEENVLRCPERVLRRLLEDAAVTMRGGGWREDVLMDRVRKRYLRQELRDLGHRVQTYCEDLEGRVSEAEALLNQQCELDEGPSPRTLLQPPCRPRSSSPGTGVAGASAVPHGLYSRHDAITGPAAAPSDVVAPSDAVAASAAAGASSTWLAQCAERPLPGNVPSYFGITQNDPFIRFHTDFRGEVVNTMFENASTWTFSFGIWYYRLKRGLYTQPRWKRVYHLAQMDNFSISQELLLGVVNALENVTVYPTYDCVLSDLEAAACLLAAYGHALWEGRDPPDSVATVLGELPQLLPRLADDVSREIAAWEGPVAAGNNYYAYRDSPDLRYYMPLSGGRHYHPGTFDRHVLVRLFHKRGVIQHLPGYGTITEELVQERLSGQVRDDVLSLWSRRLLVGKLGRDVPVFVHEQQYLRSGLTCLAGLLLLWKVTNADSVFAPRTGKFTLADLLGSDAVAGGGLPGGRAGGEEEGYGGRHGRVRNFEFLVRYYIGPWYARDPAVTLSQLFPGLALLAVTESVRSGWDPSRREDSAGGGDGGGAVLMQLSKSNPVADYMFAQSSKQYGDLRRLEVHDALLFHYEHGLGRLLSVTLPRHRVSTLGSSLFNVNDIYELLYFLVLGFLPSVAVL

Entity 5 polymer

描述 description	Small capsomere-interacting protein
分子量 formula_weight	8495.9 kDa
来源方法 src_method	nat
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	R,S,i,j

MSNTAPGPTVANKRDEKHRHVVNVVLELPTEISEATHPVLATMLSKYTRMSSLFNDKCAFKLDLLRMVAVSRTRR

Entity 6 polymer

描述 description	Major capsid protein
分子量 formula_weight	154048.9 kDa
来源方法 src_method	nat
拷贝数 entity_count	6

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	a,B,C,D,Y,Z

MENWSALELLPKVGIPTDFLTHVKTSAGEEMFEALRIYYGDDPERYNIHFEAIFGTFCNRLEWVYFLTSGLAAAAHAIKFHDLNKLTTGKMLFHVQVPRVASGAGLPTSRQTTIMVTKYSEKSPITIPFELSAACLTYLRETFEGTILDKILNVEAMHTVLRALKNTADAMERGLIHSFLQTLLRKAPPYFVVQTLVENATLARQALNRIQRSNILQSFKAKMLATLFLLNRTRDRDYVLKFLTRLAEAATDSILDNPTTYTTSSGAKISGVMVSTANVMQIIMSLLSSHITKETVSAPATYGNFVLSPENAVTAISYHSILADFNSYKAHLTSGQPHLPNDSLSQAGAHSLTPLSMDVIRLGEKTVIMENLRRVYKNTDTKDPLERNVDLTFFFPVGLYLPEDRGYTTVESKVKLNDTVRNALPTTAYLLNRDRAVQKIDFVDALKTLCHPVLHEPAPCLQTFTERGPPSEPAMQRLLECRFQQEPMGGAARRIPHFYRVRREVPRTVNEMKQDFVVTDFYKVGNITLYTELHPFFDFTHCQENSETVALCTPRIVIGNLPDGLAPGPFHELRTWEIMEHMRLRPPPDYEETLRLFKTTVTSPNYPELCYLVDVLVHGNVDAFLLIRTFVARCIVNMFHTRQLLVFAHSYALVTLIAEHLADGALPPQLLFHYRNLVAVLRLVTRISALPGLNNGQLAEEPLSAYVNALHDHRLWPPFVTHLPRNMEGVQVVADRQPLNPANIEARHHGVSDVPRLGAMDADEPLFVDDYRATDDEWTLQKVFYLCLMPAMTNNRACGLGLNLKTLLVDLFYRPAFLLMPAATAVSTSGTTSKESTSGVTPEDSIAAQRQAVGEMLTELVEDVATDAHTPLLQACRELFLAVQFVGEHVKVLEVRAPLDHAQRQGLPDFISRQHVLYNGCCVVTAPKTLIEYSLPVPFHRFYSNPTICAALSDDIKRYVTEFPHYHRHDGGFPLPTAFAHEYHNWLRSPFSRYSATCPNVLHSVMTLAAMLYKISPVSLVLQTKAHIHPGFALTAVRTDTFEVDMLLYSGKSCTSVIINNPIVTKEERDISTTYHVTQNINTVDMGLGYTSNTCVAYVNRVRTDMGVRVQDLFRVFPMNVYRHDEVDRWIRHAAGVERPQLLDTETISMLTFGSMSERNAAATVHGQKAACELILTPVTMDVNYFKIPNNPRGRASCMLAVDPYDTEAATKAIYDHREADAQTFAATHNPWASQAGCLSDVLYNTRHRERLGYNSKFYSPCAQYFNTEEIIAANKTLFKTIDEYLLRAKDCIRGDTDTQYVCVEGTEQLIENPCRLTQEALPILSTTTLALMETKLKGGAGAFATSETHFGNYVVGEIIPLQQSMLFNS

Entity 7 polymer

描述 description	portal protein
分子量 formula_weight	3592.4 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	A,E

XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Entity 8 polymer

描述 description	portal protein
分子量 formula_weight	1294.6 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	F

XXXXXXXXXXXXXXX

Entity 9 polymer

描述 description	portal protein
分子量 formula_weight	1124.4 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

XXXXXXXXXXXXX

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7. 引用文献 (1)

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分辨率 resolution	4.00 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	26181

fit	/app/data/saxs_computation/he/8hex/8hex.fit
pddf	/app/data/pr_computation/he/8hex/8hex.pr.out
profile	/app/data/saxs_computation/he/8hex/8hex.dat

C5 portal vertex in HCMV B-capsid

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 (9)

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

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)