8jut

rat megalin RAP complex

Method: ELECTRON MICROSCOPY D_max: 353.0 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	8jut
沉积日期 deposition_date	2023-06-27
结构标题 title	rat megalin RAP complex
关键词 keywords	endocytosis receptor, ENDOCYTOSIS; ENDOCYTOSIS
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	94.13 Å
回转半径 Rg (电子) rg_electron	94.03 Å
零角强度 I(0) i0	17688400000.00
分子量 molecular_weight	1051100.0 kDa
排除体积 excluded_volume	1279400 Å³
包络体积 envelope_volume	2671900 Å³
水化壳体积 shell_volume	241460 Å³
包络直径 envelope_diameter	276.5 Å
壳层 Rg shell_rg	89.43 Å
包络 Rg envelope_rg	87.26 Å
形状 Rg shape_rg	94.04 Å
总 Rg total_rg	93.97 Å
总原子数 total_atoms	73258
残基数 n_residues	9040
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	353.0 Å
Rg (实空间) rg_real	100.40 Å
Rg 误差 (实空间) rg_real_error	3.10 Å
I(0) (实空间) i0_real	1.7860e+10
I(0) 误差 (实空间) i0_real_error	4.1320e+08
Rg (倒空间) rg_reciprocal	94.61 Å
I(0) (倒空间) i0_reciprocal	17710000000.0000
解质量估计 total_estimate	0.8824
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	110.3 Å
偏度 Skewness skewness	0.525
峰度 Kurtosis kurtosis	0.167
角度范围 angular_range	— – 0.0800 Å⁻¹
当前正则化参数 α current_alpha	1.0630
最高正则化参数 α highest_alpha	732000000.0000
实空间数据点数 n_real_points	17
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.817; Stabil: 0.800; Sysdev: 1.000; Positv: 1.000; Valcen: 0.972; Smooth: 0.665

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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 (20)

Entity 1 polymer

描述 description	LDL receptor related protein 2
分子量 formula_weight	519871.4 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,B
原子数 atom_count	73258

MERGAAAAAWMLLLAIAACLEPVSSQECGSGNFRCDNGYCIPASWRCDGTRDCLDDTDEIGCPPRSCESGLFLCPAEGTCIPSSWVCDEDKDCSDGADEQQNCAGTTCSAQQMTCSNGQCIPSEYRCDHVSDCPDGSDERNCHYPTCDQLTCANGACYNTSQRCDQKVDCRDSSDEANCTTLCSQKEFECGSGECILRAYVCDHDNDCEDNSDERNCNYDTCGGHQFTCSNGQCINQNWVCDGDDDCQDSGDEDGCESNQSHHRCYPREWACPGSGRCISIDKVCDGVPDCPEGDDENNVTSGRTCGMGVCSVLNCEYQCHQTPFGGECFCPPGHIINSNDSRTCIDFDDCQIWGICDQKCENRQGRHQCLCEEGYILERGQHCKSSDSFSAASVIFSNGRDLLVGDLHGRNFRILAESKNRGMVMGVDFHYQKHRVFWTDPMQEKVFSTDINGLNTQEILNVSVDTPENLAVDWINNKLYLVETKVNRIDVVNLEGNQRVTLITENLGHPRGIALDPTVGYLFFSDWGSLSGQPKVERAFMDGSNRKDLVTTKVGWPAGITLDLVSKRVYWVDSRYDYIETVTYDGIQRKTVARGGSLVPHPFGISLFEEHVFFTDWTKMAVMKASKFTETNPQVYHQSSLRPHGVTVYHALRQPNATNPCGSNNGGCAQVCVLSHRTDNGGLGYRCKCEFGFELDDDEHRCVAVKNFLLFSSKTAVRGIPFTLSTQEDVMVPVTGSPSFFVGIDFDAQHSTVFYSDLSKDIIYKQKIDGTGKEVITANRLESVECLTFDWISRNLYWTDGGLKSVTVLRLADKSRRQIISNLNNPRSIVVHPTAGYMFLSDWFRPAKIMRAWSDGSHLMPIVNTSLGWPNGLAIDWSASRLYWVDAFFDKIEHSTLDGLDRKRLGHVDQMTHPFGLTVFKDNVFITDWRLGAIIRVRKSDGGDMTVIRRGISSVMHVKAYDADLQTGSNYCSQTTHANGDCSHFCFPVPNFQRVCGCPYGMKLQRDQMTCEGDPAREPPTQQCGSLSFPCNNGKCVPSFFRCDGVDDCHDNSDEHQCGVFNNTCSPSAFACVRGGQCIPGQWHCDRQNDCLDGSDEQNCPTHATSSTCPSTSFTCDNHVCIPKDWVCDTDNDCSDGSDEKNCQASGTCQPTQFRCPDHRCISPLYVCDGDKDCADGSDEAGCVLNCTSAQFKCADGSSCINSRYRCDGVYDCRDNSDEAGCPTRPPGMCHLDEFQCQGDGTCIPNTWECDGHPDCIHGSDEHTGCVPKTCSPTHFLCDNGNCIYKAWICDGDNDCRDMSDEKDCPTQPFHCPSTQWQCPGYSTCINLSALCDGVFDCPNGTDESPLCNQDSCSHFNGGCTHQCMQGPFGATCLCPLGYQLANDTKTCEDINECDIPGFCSQHCVNMRGSFRCACDPEYTLESDGRTCKVTGSENPLLVVASRDKIIVDNITAHTHNLYSLVQDVSFVVALDFDSVTGRVFWSDLLQGKTWSVFQNGTDKRVVHDSGLSVTEMIAVDWIGRNLYWTDYALETIEVSKIDGSHRTVLISKNVTKPRGLALDPRMGDNVMFWSDWGHHPRIERASMDGTMRTVIVQEKIYWPCGLSIDYPNRLIYFMDAYLDYIEFCDYDGHNRRQVIASDLVLHHPHALTLFEDFVYWTDRGTRQVMQANKWHGGNQSVVMYSVHQPLGITAIHPSRQPPSRNPCASASCSHLCLLSAQAPRHYSCACPSGWNLSDDSVNCVRGDQPFLMSVRDNIIFGISLDPEVKSNDAMVPISGIQHGYDVEFDDSEQFIYWVENPGEIHRVKTDGSNRTVFAPLSLLGSSLGLALDWVSRNIYYTTPASRSIEVLTLKGDTRYGKTLIANDGTPLGVGFPVGIAVDPARGKLYWSDHGTDSGVPAKIASANMDGTSLKILFTGNLQHLEVVTLDIQEQKLYWAVTSRGVIERGNVDGTERMILVHHLAHPWGLVVYGSFLYYSDEQYEVIERVDKSSGNNKVVLRDNVPYLRGLRVYHRRNAADSSNGCSNNPNACQQICLPVPGGMFSCACASGFKLSPDGRSCSPYNSFMVVSMLPAVRGFSLELSDHSEAMVPVAGQGRNVLHADVDVANGFIYWCDFSSSVRSSNGIRRIKPDGSNFTNVVTYGIGANGIRGVALDWAAGNLYFTNAFVYETLIEVLRINTTYRRVLLKVSVDMPRHIIVDPKHRYLFWADYGQKPKIERSFLDCTNRTVLVSEGIVTPRGLAMDHDTGYIYWVDDSLDLIARIHLDGGESQVVRYGSRYPTPYGITVFGESIIWVDRNLKKVFQASKQPGNTDPPVVIRDKINLLRDVTIFDEHAQPLSPAELNNNPCLQSNGGCSHFCFALPELPTPRCGCAFGTLGNDGKSCATSQEDFLIYSLNNSLRSLHFDPRDHSLPFQVISVAGTAIALDYDRRNNRIFFTQKLNSLRGQISYVSLYSGSSSPTVLLSNIGVTDGIAFDWINRRIYYSDFSNQTINSMAEDGSNRAVIARVSKPRAIVLDPCRGYMYWTDWGTNAKIERATLGGNFRVPIVNTSLVWPNGLALDLETDLLYWADASLQKIERSTLTGTNREVVVSTAFHSFGLTVYGQYIYWTDLYTRKIYRANKYDGSDLVAMTTRLPTQPSGISTVVKTQRQQCSNPCDQFNGGCSHICAPGPNGAECQCPHEGNWYLANDNKYCVVDTGTRCNQLQFTCLNGHCINQDWKCDNDNDCGDGSDELPTVCAFHTCRSTAFTCGNGRCVPYHYRCDYYNDCGDNSDEAGCLFRNCNSTTEFTCSNGRCIPLSYVCNGINNCHDNDTSDEKNCPPHTCPPDFTKCQTTNICVPRAFLCDGDNDCGDGSDENPIYCASHTCRSNEFQCLSPQRCIPSYWFCDGEADCADGSDEPDTCGHSVNTCRASQFQCDNGRCISGNWVCDGDNDCGDMSDEDQRHHCELQNCSSTQFTCVNSRPPNRRCIPQYWVCDGDADCSDALDELQNCTMRTCSAGEFSCANGRCVRQSFRCDRRNDCGDYSDERGCSYPPCHANQFTCQNGRCIPRFFVCDEDNDCGDGSDEQEHLCHTPEPTCPLHQFRCDNGHCIEMGRVCNHVDDCSDNSDEKGCGINECLDSSISRCDHNCTDTITSFYCSCLPGYKLMSDKRSCVDIDECKESPQLCSQKCENVVGSYICKCAPGYIREPDGKSCRQNSNIEPYLIFSNRYYIRNLTTDGSSYSLILQGLGNVVALDFDRVEKRLYWIDAEKQIIERMFLNKTNRETIINHRLRRAESLAVDWVSRKLYWLDAILDCLFVSDLEGRHRKMIAQHCVDANNTFCFEHPRGIVLHPQRGHVYWADWGVHAYIGRIGMDGTNKSVIISTKIEWPNAITIDYTNDLLYWADAHLGYIEFSDLEGHHRHTVYDGSLPHPFALTIFEDTVFWTDWNTRTVEKGNKYDGSGRVVLVNTTHKPFDIHVYHPYRQPIMSNPCGTNNGGCSHLCLIKAGGRGFTCACPDDFQTVQLRDRTLCMPMCSSTQFLCGNNEKCIPIWWKCDGQKDCSDGSDEPDLCPHRFCRLGQFQCRDGNCTSPQALCNARQDCADGSDEDRVLCEHHRCESNEWQCANKRCIPQSWQCDSVNDCLDNSDEDTSHCASRTCRPGQFKCNNGRCIPQSWKCDVDNDCGDYSDEPIDECTTAAYNCDNHTEFSCKTNYRCIPQWAVCNGFDDCRDNSDEQGCESVPCHPSGDFRCANHHCIPLRWKCDGTDDCGDNSDEENCVPRECSESEFRCADQQCIPSRWVCDQENDCGDNSDERDCEMKTCHPEHFQCTSGHCVPKALACDGRADCLDASDESACPTRFPNGTYCPAAMFECKNHVCIQSFWICDGENDCVDGSDEEIHLCFNIPCESPQRFRCDNSRCVYGHQLCNGVDDCGDGSDEKEEHCRKPTHKPCTDTEYKCSNGNCISQHYVCDNVNDCGDLSDETGCNLGDNRTCAENICEQNCTQLSSGGFICSCRPGFKPSTLDKNSCQDINECEEFGICPQSCRNSKGSYECFCVDGFKSMSTHYGERCAADGSPPLLLLPENVRIRKYNTSSEKFSEYLEEEEHIQTIDYDWDPEHIGLSVVYYTVLAQGSQFGAIKRAYIPNFESGSNNPIREVDLGLKYLMQPDGLAVDWVGRHIYWSDAKSQRIEVATLDGRYRKWLITTQLDQPAAIAVNPKLGLMFWTDQGKQPKIESAWMNGEHRSVLVSENLGWPNGLSIDYLNDDRVYWSDSKEDVIEAIKYDGTDRRLIINEAMKPFSLDIFEDKLYWVAKEKGEVWRQNKFGKENKEKVLVVNPWLTQVRIFHQLRYNQSVSNPCKQVCSHLCLLRPGGYSCACPQGSDFVTGSTVQCDAASELPVTMPPPCRCMHGGNCYFDENELPKCKCSSGYSGEYCEVGLSRGIPPGTTMAVLLTFVIVIIVGALVLVGLFHYRKTGSLLPTLPKLPSLSSLAKPSENGNGVTFRSGADVNMDIGVSPFGPETIIDRSMAMNEHFVMEVGKQPVIFENPMYAAKDNTSKVALAVQGPSTGAQVTVPENVENQNYGRPIDPSEIVPEPKPASPGADEIQGKKWNIFKRKPKQTTNFENPIYAEMDSEVKDAVAVAPPPSPSLPAKASKRNLTPGYTATEDTFKDTANLVKEDSDV

Entity 2 polymer

描述 description	Alpha-2-macroglobulin receptor-associated protein
分子量 formula_weight	42112.8 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	C,D

MAPLRDRVSTLPRLQLLVLLLLPLLLVPQPIAGHGGKYSREKNEPEMAAKRESGEEFRMEKLNQLWEKAKRLHLSPVRLAELHSDLKIQERDELNWKKLKVEGLDGDGEKEAKLVHNLNVILARYGLDGRKDTQTVHSNALNEDTQDELGDPRLEKLWHKAKTSGKFSSEELDKLWREFLHYKEKIHEYNVLLDTLSRAEEGYENLLSPSDMTHIKSDTLASKHSELKDRLRSINQGLDRLRKVSHQGYGPATEFEEPRVIDLWDLAQSANFTEKELESFREELKHFEAKIEKHNHYQKQLEISHQKLKHVESIGDPEHISRNKEKYVLLEEKTKELGYKVKKHLQDLSSRVSRARHNEL

来源 Source

来源生物 organism	Rattus norvegicus
通用名 common_name	Norway rat
NCBI 分类编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Escherichia coli

Entity 3 polymer

描述 description	unclear peptide
分子量 formula_weight	528.6 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	G,N

XXXXXX

Entity 4 polymer

描述 description	unclear peptide
分子量 formula_weight	472.5 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	H,O

XNXXX

Entity 5 polymer

描述 description	unclear peptide
分子量 formula_weight	556.7 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	I,P

XXLXXX

Entity 6 polymer

描述 description	unclear peptide
分子量 formula_weight	291.4 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	J,Q

XCX

Entity 7 polymer

描述 description	unclear peptide
分子量 formula_weight	531.6 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	K,R

XEEXX

Entity 8 polymer

描述 description	unclear peptide
分子量 formula_weight	472.5 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	L,M,S,T

XXNXX

Entity 9 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	syn
拷贝数 entity_count	13

Entity 10 branched

描述 description	;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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	910.8 kDa
来源方法 src_method	syn
拷贝数 entity_count	12

Entity 11 branched

描述 description	;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	910.8 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 12 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	man
拷贝数 entity_count	10

Entity 13 branched

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	424.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 14 branched

描述 description	;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	910.8 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 15 branched

描述 description	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	586.5 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 16 branched

描述 description	beta-D-mannopyranose-(1-3)-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	man
拷贝数 entity_count	2

Entity 17 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	22

Entity 18 non-polymer

描述 description	2-acetamido-2-deoxy-alpha-D-galactopyranose
分子量 formula_weight	221.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	24

Entity 19 non-polymer

描述 description	CALCIUM ION
分子量 formula_weight	40.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	88

Entity 20 non-polymer

描述 description	NICKEL (II) ION
分子量 formula_weight	58.7 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	4.20 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	67775

fit	/app/data/saxs_computation/ju/8jut/8jut.fit
pddf	/app/data/pr_computation/ju/8jut/8jut.pr.out
profile	/app/data/saxs_computation/ju/8jut/8jut.dat

rat megalin RAP 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 (20)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

来源 Source

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 branched

Entity 10 branched

Entity 11 branched

Entity 12 branched

Entity 13 branched

Entity 14 branched

Entity 15 branched

Entity 16 branched

Entity 17 non-polymer

Entity 18 non-polymer

Entity 19 non-polymer

Entity 20 non-polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)