9c3c

Cryo-EM structure of native dystrophin-glycoprotein complex (DGC)

Method: ELECTRON MICROSCOPY D_max: 237.9 Å Quality: REASONABLE

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	9c3c
沉积日期 deposition_date	2024-05-31
结构标题 title	Cryo-EM structure of native dystrophin-glycoprotein complex (DGC)
关键词 keywords	beta-helix, sarcolemma, glycosylation, muscular dystrophy, membrane protein; MEMBRANE 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	83.47 Å
回转半径 Rg (电子) rg_electron	84.60 Å
零角强度 I(0) i0	1069370000.00
分子量 molecular_weight	277520.0 kDa
排除体积 excluded_volume	348540 Å³
包络体积 envelope_volume	637120 Å³
水化壳体积 shell_volume	72258 Å³
包络直径 envelope_diameter	280.4 Å
壳层 Rg shell_rg	58.99 Å
包络 Rg envelope_rg	82.41 Å
形状 Rg shape_rg	84.58 Å
总 Rg total_rg	84.15 Å
总原子数 total_atoms	19475
残基数 n_residues	2458
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	237.9 Å
Rg (实空间) rg_real	82.97 Å
Rg 误差 (实空间) rg_real_error	1.64 Å
I(0) (实空间) i0_real	1.0590e+09
I(0) 误差 (实空间) i0_real_error	2.2530e+07
Rg (倒空间) rg_reciprocal	77.62 Å
I(0) (倒空间) i0_reciprocal	1052000000.0000
解质量估计 total_estimate	0.6712
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	50.1 Å
偏度 Skewness skewness	0.439
峰度 Kurtosis kurtosis	-1.007
角度范围 angular_range	— – 0.0950 Å⁻¹
当前正则化参数 α current_alpha	0.0516
最高正则化参数 α highest_alpha	32490000.0000
实空间数据点数 n_real_points	20
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.452; Stabil: 0.984; Sysdev: 1.000; Positv: 1.000; Valcen: 0.348; Smooth: 0.006

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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	Alpha-dystroglycan
分子量 formula_weight	67623.7 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	19475

HWPSEPSEAVRDWENQLEASMHSVLSDLHEALPTVVGIPDGTAVVGRSFRVTIPTDLIGSSGEVIKVSTAGKEVLPSWLHWDPQSHTLEGLPLDTDKGVHYISVSAAQLDANGSHIPQTSSVFSIEVYPEDHSEPQSVRAASPDLGEAAASACAAEEPVTVLTVILDADLTKMTPKQRIDLLHRMQSFSEVELHNMKLVPVVNNRLFDMSAFMAGPGNAKKVVENGALLSWKLGCSLNQNSVPDIRGVEAPAREGTMSAQLGYPVVGWHIANKKPPLPKRIRRQIHATPTPVTAIGPPTTAIQEPPSRIVPTPTSPAIAPPTETMAPPVRDPVPGKPTVTTRTRGAIIQTPTLGPIQPTRVSDAGTVVSGQIRATVTIPGYVEPTAVATPPTTTTKKPRVSTPKPATPSTDSSATTTRRPTKKPRTPRPVPRVTTKAPITRLETASPPTRIRTTTSGVPRGGEPNQRPELKNHIDRVDAWVGTYFEVKIPSDTFYDKEDTTTDKLKLTLKLREQQLVGEKSWVQFNSNSQLMYGLPDSSHVGKHEYFMHATDKGGLSAVDAFEIHVHKRPQGDKAPARFKAKFVGDPAPVVNDIHKKIALVKKLAFAFGDRNCSTVTLQNITRG

Entity 2 polymer

描述 description	Beta-dystroglycan
分子量 formula_weight	15714.1 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	B

SIVVEWTNNTLPLEPCPKEQITGLSRRIAEDNGQPRPAFTNALEPDFKATSIAITGSGSCRHLQFIPVAPPGIPSSVTPPTEVPDRDPEKSSEDDVYLHTVIPAVVVAAILLIAGIIAMICYRKKRKGKLTLEDQATFIKKGVPI

Entity 3 polymer

描述 description	Dystrophin
分子量 formula_weight	427942.8 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	D

MLWWEEVEDCYEREDVQKKTFTKWINAQFSKFGKQHIENLFSDLQDGRRLLDLLEGLTGQQLPKEKGSTRVHALNNVNKALRVLQKNNVDLVNIGSTDIVDGNHKLTLGLIWNIILHWQVKNVMKNIMAGLQQTNSEKILLSWVRQSTRNYSQVNVINFTTSWSDGLALNALIHSHRPDLFDWNSVVCQQSATQRLEHAFNIAKCQLGIEKLLDPEDVATTYPDKKSILMYITSLFQVLPQQVSIEAIQEVELLPRPSKVTREEHFQLHHQMHYSQQITVSLAQGYERTSSPKPRFKSYAYTQAAYVSTSDPTRSPFPSQHLEAPGDKSFGSSLMETEVSLDSYQTALEEVLSWLLSAEDTLQAQKEISSDVEEVKEQFHTHEGYMMDLTSHQGRVGNVLQLGSQLIRTGKLSEEEETEVQEQMNLLNSRWECLRVASMEKQSNLHKVLMDLQNQKLKELNDWLTKTEERTRKMEEEPLGPDLEDLKRQVQQHKVLQEDLEQEQVRVNSLTHMVVVVDESSGEHATAALEEQLKVLGDRWANICRWTEDRWVLLQDILLKWQRFTEEQCLFSTWLSEKEDAVNKIHTTGFKDQNEMLSSLHKLTVLKTDLEKKKQSMDKLSSLNQALLSTLKNKSVTQKMEAWLENFALRWDNLVQKLEKSSAQISQAVTTTQPSLTQTTVMETVTMVTTREQILVKHAQEELPPPPPQKKRQIIVDSEIRKRLDVDITELHSWITRSEAVLQSPEFAIYRKEGNFSDLKEKVNAIEREKAEKFRKLQDASRSAQALVEQMVNEGVNADSIKQALEQLNSRWIEFCQLLSERLHWLEYQNSIITFYNQLQQLEQMITTAENWLKTQPTTASEPTAIKSQLKMCKDEVNRLSALQPQIERLKIQSTALKEKGQGPMFLDADFVAFTNHFNQVFADAQAREKELQTIFDTLPPTRYQETISTIRTWIQQSEPKLSIPQLSVTEYEIMEQRLGELQALQSSLQEQQSGLTYLSTTVKEMAKKAPSEISRKYQSEFEEIEGHWKKLSYQLVDHCQKLEEQMNKLRKIQNHIKTLKKWMAEVDVFLKEEWPALGDSEILKKQLKQCRLLVNDIQTIQPSLNSVNESGQKIKNEAEPEFASRLETELRELNSQWDHMCRQVYTRKDALKAGLDKTLSLQKDLSEMHEWMTQAEEEYLERDFEYKTPDELQTAVEEMKRAKEEAQQKESKVKLLTESVNSVIAQAPPAAQEALKKELDTLTTNYQWLCTRLNGKCKTLEEVWACWHELLSYLEKANKWLNEVEVKLKTTETLPGGAEEISEVLDSLENLMQHSEDNPNQIRILAQTLTDGGVMDELINEELETFNSRWRELHEEAVRRQKLLEQSIQSAQEIEKSLHLIQESLAFIDKQLAAYIADKVDAAQMPQEAQKIQSDLTSHEISLEEMKKHNQGKEAAQRVLSQIDVAQKKLQDVSMKFRLFQKPANFEQRLEESKMILDEVKMHLPALETKSVEQEVVQSQLNHCVNLYKSLSEVKSEVEMVIKTGRQIVQKKQTENPKELDERVTALKLHYNELGAKVTERKQQLEKCLKLSRKMRKEMNALTEWLAATDMELTKRSAVEGMPSNLDAEIAWGKATQKEVEKQKAHLKSVIELGEALKTVLGKKETLVEDKLSLLNSNWVAVTSRAEEWLNLLLEYQKHMETFDQNVDHITKWIIQADTLLDESEKKKPQQKEDVLKRLKAEMNDIRPKVDSIRDQAANLMANRGDHCRKVVEPKISELNHRFAAISHRIKTGKASIPLKELEQFNSDIQKLLEPLEAEIQQGVNLKEEDFNKDMSEDNEGTVKELLQRGDNLHERITDERKREEIKIKQQLLQTKHNALKDLRSQRRKKALEISHQWYQYKRQADDLLKCLDDIEKKLASLPDPKDERKIKEIDRELQKKKEELNAVHRQAEGLSEDGAAMAVEPIQIQLSKRWREIESKFAQFRRLNFAQIHTVREETMVVMTEDMPLEISYVPSTYLTEITHVSQALSEVDQLLNAPDLSAKDFEDLFKQEESLKNIKECMQQISGRIDVIHNKKAAALQSATAAERVKLQEALAQLDSQWEKVNKMYKDRQGRFDRSVEKWRRFHYDMKIFNQWLTEAEQFLKKTQIPENWEHAKYKWYLKELQDGIGQRQTVVRTLNTTGEEIIQQSSKTDANILQEKLGNLNLRWQEVCKQLAERRKRLEEQKNILSEFQRDLNEFVLWLEEADNITSIPLEPGNEQQLKEKLEQVKLLAEELPLRQGILKQLNEAGGTALVSAPISPEEQDKLENKLKQTNLQWIKVSKALPEKQEEIVAHVKELGQLEEQLNHLLLWLTPIRNQLEIYNQPNQTGPFDIKETEVAVQAKQPDVERILSKGQHLYKEKPATQPVKRKLEDLSSEWKVVNYLLQELRAKRPDLPPGPATIGASPSQTVTLVTQTVVTKEISLSELEMPSSLLLEVPALADFNRAWTELTDWLSLLDRVLKSQQVIVGDLEDINEMIIKQKATLQELEQRRPQLEELITAAQNLKNKTSNQEARTIITDRIERIQNQWDEVQEHLQNRRQQLNEMLKDSTQWLEAKEEAEQVLGQARAKLESWKEGPYTMDALQKKIEETKQLAKDLRQWQINVDVANDLALKLLRDYSADDTRKVHMITENINASWGSIHKRVNEREATLEEAYRLLQQFPLDLEKFLAWLTEAETTANVLQDATHKERLPEDSKGVRELMKQWQDLQGEIEAHTDIYHNLDENGQKILRSLEGSDEAVLLQRRLDNMNFKWSELRKKSLNIRSHLEASSDQWKRLHLSLQELLVWLQLKDDELNRQAPVGGDFPAVQKQNDVHRAFKRELKTKEPVIMSTLETVRIFLTEQPLGGLEKLYQEPRELPPDERAQNVTRLLRKQAEEVNAEWEKLNLHSTDWQRKLDEALERLQELQEATDELDLKLRQAEVIKGSWQPVGDLLIDSLQDHLEKVKALRGEIAPLKENVSHVNDLGRQLTTLGIQLSPYNLSTLEDLNTRWKLLQVAVEDRIRQLHEAHRDFGPASQHFLSTSVQGPWERAISPNKVPYYINHETQTTCWDHPKMTELYQSLADLNNVRFSAYRTAMKLRRLQKALCLDLLTLSAACDALDQHNLKQNDQPMDILQIINCLTTVYDRLEQEHNNLVNVPLCVDMCLNWLLNVYDTGRTGRIRVLSFKTGIISLCKAHLEDKYRYLFKQVASSTGFCDQRRLGLLLHDSIQIPRQLGEVASFGGSNIEPSVRSCFQFANNKPEIEAALFLDWMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRVAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAKHPRMGYLPVQTVLEGDNMETPVTLINFWPVDSAPASSPQLSHDDTHSRIEHYASRLAEMENSNGSYLNDSISPNESIDDEHLLIQHYCQSLNQDSPLSQPRSPAQILISLESEERGELERILADLEEENRNLQAEYDRLKQQHEHKGLSPLPSPPEMMPTSPQSPRDAELIAEAKLLRQHKGRLEARMQILEDHNKQLESQLHRLRQLLEQPQAEAKVNGTTVSSPSTSLQRSDSSQPMLLRVVGSQTSESMGEEDLPSPPQDTSTGLEEVMEQLNNSFPSSRGHNVGSLFHMADDLGRAMESLVSVMTDEEGAE

Entity 4 polymer

描述 description	Alpha-sarcoglycan
分子量 formula_weight	35969.0 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	a

QQTTLYPLVGRVFVHTLEPASFLHLPEHAAPATIPVTYHAHLQGHPDLPRWLRYTQRSPHHPGFLYGAATPEDRGRQVIEVTAYNRDSFDTAGQSLVLLIRDPEGSPLPYQTEFLVRSHDVEEVLPPTPASHFLTALAGLWEPGELKLLNITSALDRGGRVPLPIGGQKEGVYIKVGSASPFSTCLKMVASPDSHARCARGQPPLLSCYDTLAPHFRVDWCNVSLVDTSVPEPVDEVPTPGDGILEHDPFFCPPTEATARDFLADALVTLLVPLLVALLLALLLAYIMCCRREGRLKRDLATSDIQMVHHCTIHENTEELRQMAAS

Entity 5 polymer

描述 description	Beta-sarcoglycan
分子量 formula_weight	34768.7 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

MAAAAAAAAEQQSSNGPVKKSMREKAVERRNVNKEHNSNFKAGYIPIDEDRLHKTGLRGRKGNLAICVIVLLFLLAVINLIITLVIWAVIRIGPNGCDSMEFHESGLLRFKQVSDMGVIHPLYKSTVGGRRNENLVITGNNQPIVFQQGTTKLSVEKNKTSITSDIGMQFFDPRTQNILFSTDYETHEFHLPSGVKSLNVQKASTERITSNATSDLNIKVDGRAIVRGNEGVFIMGKTIEFHMGGNMELKAENSIILNGTVMVSTTRLPSSSSADQLGGGDWVRYKLCMCADGTLFKVQVTGQNVGCQVSDNPCGNTH

Entity 6 polymer

描述 description	Sarcoglycan delta
分子量 formula_weight	32142.3 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	d

MPQEQYTHHRSTMPSAEGPQVYKVGIYGWRKRCLYFFVLLLMILILVNLAMTIWILKVMNFTIDGMGNLRITEKGLKLEGDSEFLQPLYAKEIQSRPGNALYFKSARNVTVNILNDQTKVLTQLITGPKAVEAYGKKFEVKTVSGKLLFSADDNEVVVGAERLRVLGAEGTVFPKSIETPNVRADPFKELRLESPTRALVMEAPKGVEINAEAGNMEATCRTELRLESKDGEIKLDAAKIKLPRLPHGSYTPTGTRQKVFEICVCANGRLFLSQAGTGSTCQINTSVCL

Entity 7 polymer

描述 description	Gamma-sarcoglycan
分子量 formula_weight	32005.5 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	g

MAGEQYLTATEGTHIERPENQCVYKIGIYGWRKRCLYLLVLLLLIILVVNLALTIWILKVMWFSPTGMGHLHVTKDGLRLEGESEFLFPLYAKEIHSRVDSSLLLQSTQNVTVNARNSDGEVTGRLKVGPQMVEVQSQQFQINSREGKSLFTVDEEEVVVGTDRLRVTGPEGALFEHSVETPLVTADPFQDLRLESPTRSLSMDAPRGVHIEAHAGEVEALSQMDIVLHSSDGTLVLDAETVCLPKLLQGTQAASGSSQGLYEICVCPDGKLYLSVAGAGTTCQEHSHICL

Entity 8 polymer

描述 description	Sarcospan
分子量 formula_weight	26058.6 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	n

MGKDRQPRGQQRQGDAAGPDDPGPKKGAGTREQRGEEEAQTCCGCRFPLLLALLQLALGVAVTVVGFLMASVSSSLLVRATPYWAGIIVCVVAYLGLFMLCVSYQVDERTCIQFSMKLLYFVLSALGLVVCVLAVAFAAHHYSLLTHLTCENAPDSCQCKLPSSEPLSRTFVYRDVTDCTSITGTFQVFLLVQMVLNLVCGLVCLVACFVMWKHRYQVFYVGVRMCPLSASEGQQQKV

Entity 9 polymer

描述 description	Dystrobrevin
分子量 formula_weight	92647.1 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	V

MIEDSGKRGNTMAERRQLFAEMRAQDLDRIRLSTYRTACKLRFVQKKCNLHLVDIWNVIEALRENALNNLDPNTELNVARLEAVLSTIFYQLNKRMPTTHQIHVEQSISLLLNFLLAAFDPEGHGKISVFAVKMALATLCGGKIMDKLRYIFSMISDSSGVMVYGRYDQFLREVLKLPTAVFEGPSFGYTEQSARSCFSQQKKVTLNGFLDTLMSDPPPQCLVWLPLLHRLANVENVFHPVECSYCHSESMMGFRYRCQQCHNYQLCQDCFWRGHAGGSHSNQHQMKEYTSWKSPAKKLTNALSKSLSCASSREPLHPMFPDQPEKPLNLAHIVPPRPVTSMNDTLFSHSVPSSGSPFITRRLPEGISAASPVAEEHSLIKLYVNQLDHGARSPPKDSEVEQNKMLARAAPAFLKGKGIQYSLNVADRLADEHVLIGLYVNMLRNNPSCMLESSNRLDEEHRLIARYAARLAAESSSSQPTQQRSAPDISFTIDANKQQRQLIAELENKNREILQEIQRLRLEHEQASQPAPEKAQQNPTLLAELRLLRQRKDELEQRMSALQESRRELMVQLEGLMKLLKEEELKQGTQGASSPRSSPSHTISRPIPMPIRSASACSTPTHTPQDSLTGVGGDVQEAFAQSSRRNLRNDLLVAADSITNTMSSLVKELNSEVGSETESNVDSEFTRTQFEDLVPSPTSEKAFLAQIQARKPGYIHSGATTSTVRSDMVTEDGDSYVRPEDENYDSDSVRQLENELKMEEYLKQKLQDEAYQLHVSTETRLKHPCPVTETKWHVLFWVFVFFGGLLSLALQIYFWGLF

Entity 10 branched

描述 description	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	586.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	7

Entity 11 branched

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	424.4 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 12 non-polymer

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	221.2 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	4.30 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	134481

fit	/app/data/saxs_computation/c3/9c3c/9c3c.fit
pddf	/app/data/pr_computation/c3/9c3c/9c3c.pr.out
profile	/app/data/saxs_computation/c3/9c3c/9c3c.dat

Cryo-EM structure of native dystrophin-glycoprotein complex (DGC)

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 branched

Entity 11 branched

Entity 12 non-polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)