8ugp

In-situ structure of typeA supercomplex in respiratory chain ( local refined map focused on CI iron-sulfur cluster regions )

Method: ELECTRON MICROSCOPY D_max: 69.5 Å Quality: EXCELLENT

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	8ugp
沉积日期 deposition_date	2023-10-05
结构标题 title	In-situ structure of typeA supercomplex in respiratory chain ( local refined map focused on CI iron-sulfur cluster regions )
关键词 keywords	in-situ cryo-EM structure, mammalian, mitochondria, respiratory supercomplex, proton pumping, membrane protein, electron transport; ELECTRON TRANSPORT
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	23.96 Å
回转半径 Rg (电子) rg_electron	23.06 Å
零角强度 I(0) i0	100011000.00
分子量 molecular_weight	76665.0 kDa
排除体积 excluded_volume	94483 Å³
包络体积 envelope_volume	104920 Å³
水化壳体积 shell_volume	35396 Å³
包络直径 envelope_diameter	68.5 Å
壳层 Rg shell_rg	31.86 Å
包络 Rg envelope_rg	23.12 Å
形状 Rg shape_rg	22.87 Å
总 Rg total_rg	24.40 Å
总原子数 total_atoms	5129
残基数 n_residues	706
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	69.5 Å
Rg (实空间) rg_real	23.75 Å
Rg 误差 (实空间) rg_real_error	0.24 Å
I(0) (实空间) i0_real	1.0000e+08
I(0) 误差 (实空间) i0_real_error	1.1680e+06
Rg (倒空间) rg_reciprocal	23.80 Å
I(0) (倒空间) i0_reciprocal	100000000.0000
解质量估计 total_estimate	0.9069
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	68.4 Å
偏度 Skewness skewness	0.092
峰度 Kurtosis kurtosis	-0.517
角度范围 angular_range	— – 0.3300 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	50240000.0000
实空间数据点数 n_real_points	65
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.955; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.968; Smooth: 0.952

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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 (14)

Entity 1 polymer

描述 description	NADH-ubiquinone oxidoreductase chain 3
分子量 formula_weight	12998.4 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	1A
原子数 atom_count	5152

MNIMLTLLTNVTLASLLVLIAFWLPQLNAYSEKTSPYECGFDPMGSARLPFSMKFFLVAITFLLFDLEIALLLPLPWASQTNNLKTMLTMALFLLILLAASLAYEWTQKGLEWAE

Entity 2 polymer

描述 description	NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial
分子量 formula_weight	28500.2 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	1B

MRNVSTQVPVSAHRPSRFGQRPRIPGALQRTDRRGCLKAEAEMAALAASGLLRPILALRSSMGAAVQVRFVHPSAATDSPSSSQPAVSQAGAVVSKPTTLPSSRGEYVVAKLDDLVNWARRSSLWPMTFGLACCAVEMMHMAAPRYDMDRFGVVFRASPRQSDVMIVAGTLTNKMAPALRKVYDQMPEPRYVVSMGSCANGGGYYHYSYSVVRGCDRIVPVDIYVPGCPPTAEALLYGILQLQRKIKREKRLRIWYRR

Entity 3 polymer

描述 description	NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial
分子量 formula_weight	30154.3 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	1C

MAAAAAARGCWRGLVGPAAVARVSGRPSVLLLPVRKESAAADTRPTIRPRNDVVHKQLSAFGQYVAEILPKYVQQVQVSCFNELEIFIHPDGVIPVLTFLRDHTNAQFKSLADLTAVDVPTRQNRFEIVYNLLSLRFNSQIRVKTYTDELTPIESSVTVYKAANWYEREIWDMFGVFFANHPDLRRILTGYGFEGHPFRKDFPLSGYVELRYDDEVKRVVAEPVELAQEFRKFDLNSPWEAFPAYRQPPEDLKLEAGDKKPETK

Entity 4 polymer

描述 description	NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial
分子量 formula_weight	54168.1 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	1D

MAALRALCSLRGVAAQVLRPGAGARLPIQPSRGARQWQPDVEWAEQFGGAVMYPTKETAHWKPPPWNGNYYWPNYFPLLSDVDPPKDTLVSNLTLNFGPQHPAAHGVLRLVMELSGEMVRKCDPHIGLLHRGTEKLIEYKTYLQALPYFDRLDYVSMMCNEQAYSLAVEKLLNIQPPPRAQWIRVLFGEITRLLNHIMAVTTHALDIGAMTPFFWMFEEREKMFEFYERVSGARMHAAYIRPGGVHQDLPLGLLDDIYEFSKNFSFRIDELEEMLTNNRIWRNRTVDIGVVTAEDALNYGFSGVMLRGSGIQWDLRKTQPYDVYDQVEFDVPIGSRGDCYDRYLCRVEEMRQSLRIISQCLNKMPPGEIKVDDAKVSPPKRAEMKTSMESLIHHFKLYTEGYQVPPGATYTAIEAPKGEFGVYLVSDGSSRPYRCKIKAPGFAHLAGLDKMSKGHMLADVVAIIGTQDIVFGEVDR

Entity 5 polymer

描述 description	NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
分子量 formula_weight	79627.4 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	1G

MLRIPVTRALIGLSKSPKGCVRTTATAASNLIEVFVDGQSVMVEPGTTVLQACEKVGMQIPRFCYHERLSVAGNCRMCLVEIEKAPKVVAACAMPVMKGWNILTNSEKSKKAREGVMEFLLANHPLDCPICDQGGECDLQDQSMMFGSDRSRFLEGKRAVEDKNIGPLVKTIMTRCIQCTRCIRFASEIAGVDDLGTTGRGNDMQVGTYIEKMFMSELSGNIIDICPVGALTSKPYAFTARPWETRKTESIDVMDAVGSNIVVSTRTGEVMRILPRMHEDINEEWISDKTRFAYDGLKRQRLTQPMIRNEKGLLTYTTWEDALSRVAGMLQSFQGNDVAAIAGGLVDAEALVALKDLLNRVDSDSLCTEEVFPTAGAGTDLRSNYLLNTTIAGVEEADVILLVGTNPRFEAPLFNARIRKSWLHNDLKVALIGSPVDLTYRYDHLGDSPKILQDIASGNHPFSQILKEAKKPMVVLGSSALQRSDGTAILAAVSNIAQNIRLSSGVTGDWKVMNILHRIASQVAALDLGYKPGVEAIRKNPPKVLFLLGADGGCITRQDLPKDCFIIYQGHHGDVGAPMADVILPGAAYTEKSATYVNTEGRAQQTKVAVTPPGLAREDWKIIRALSEIAGMTLPYDTLDQVRSRLEEVSPNLVRYDDVEGANYFQQANELSKLVNQQLLADPLVPPQLTIKDFYMTDSISRASQTMAKCVKAVTEGIQAVEEPSIC

Entity 6 polymer

描述 description	NADH-ubiquinone oxidoreductase chain 1
分子量 formula_weight	35591.4 kDa
EC 编号 ec_number	7.1.1.2
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	1H

MFMINILSLIIPILLAVAFLTLVERKVLGYMQLRKGPNVVGPYGLLQPIADALKLVTKEPLRPGTSSISMFIIAPILGLSLALTMWVPLPMPYPLINMNLGVLFMLAMSSLAVYSILWSGWASNSKYALIGALRAVAQTISYEVTLAIILLSVLLMNGSYTLSTLITTQEHIWMIFTSWPLAMMWFISTLAETNRAPFDLTEGESELVSGFNVEYAAGPFAMFFMAEYANIIMMNAFTAILFLGASHDPHTPELYTINFVLKTLALTITFLWIRASYPRFRYDQLMHLLWKSFLPLTLALCMWHISLPIMTASIPPQS

Entity 7 polymer

描述 description	NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial
分子量 formula_weight	27135.0 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	1I

MEASQECRLRLSVDRPPPHGKERQRFKMRCLSTPMLLRALAQAQAAHAGHPSARTLHSSAVAATYKFVNMREPSMDMKSVTDRAAQTLLWTELVRGLGMTLSYLFREPATINYPFEKGPLSPRFRGEHALRRYPSGEERCIACKLCEAVCPAQAITIEAEPRADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEFSTETHEELLYNKEKLLNNGDKWEAEIAANIQADYLYR

Entity 8 polymer

描述 description	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial
分子量 formula_weight	42606.3 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	1P

MAAAVHPRVVRAVPMSRSCLAAVATSVSYGPPQRQLHHALIPHGKGGRSSVSGIVATVFGATGFLGRYVVNHLGRMGSQVIVPYRCEPYDTMHLRPMGDLGQIIFMEWNGKDKDSIRKVVEHSNVVINLVGREWETKNFDFEDVFVKIPHAIAQVSKEAGVEKLIHISHLNADIKSPSRYLRSKAVGEKEVRAAFPEATIIKPSDIFGREDRFLNYFASMRWFGGVPLISLGKETVKQPVYIVDVSKGIINAIKDPDAKGKTFAFVGPNRYLLFDLVQYIFAVAYRPFLPYPLPHFAYRWVGRLFEVSPFEPWTTRDKVERVHMSDMTLPHLPGLEDLGIQATPLELKAIEVLRRHRTYRWLTSEMEDVKPAKTVNI

Entity 9 polymer

描述 description	NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
分子量 formula_weight	19746.5 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	1Q

MAAVSMSVALKQALWGRRAAAVGAVSVSKVPTRLLSTSTWRLAQDQTQDTQLIAVDEKLDITTLTGVPEEHIKTRKVRIFVPARNNMQSGVNNTKKWKMEFDTRERWENPLMGWSSTADPLSNLVLTFSTKEDAVAFAEKNGWSFDVEERKVPKPKSKSYGANFSWNKRTRVSTK

Entity 10 polymer

描述 description	NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
分子量 formula_weight	13349.0 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	1R

MAAVTFLRLLGRSGAGARNLLGGSRCFGVRTSPTGEKVTHTGQAYDDGDYRRVRFSDRQKEVNENFAIDLIAEQPVSEVGSRVISCDGGGGALGHPRVYINLDKETKTGTCGYCGLQFRQPHH

Entity 11 polymer

描述 description	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6
分子量 formula_weight	14953.3 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	1W

MAASGLPRAAAAAGTSVKPIFSRDMNEAKRRVRELYRAWYREVPNTVHLFQLDISVKQGRDKVREMFMKNAHVTDPRVVDLLVIKGKMELEETINVWKQRTHIMRFFHETEAPRPTDFLSKFYVGHDP

Entity 12 polymer

描述 description	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
分子量 formula_weight	17162.4 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	1q

MELVQVLRRGLQQVSGHGGLRGYLRVLFRANDVRVGTLVGEDKYGNKYYEDNKQFFGRHRWVIYTTEMNGRDTFWDVDGSMVPPEWHRWLHCMTDDPPTTKPPTARKYIWTNHKFNVSGTPQQYVPYSTTRKKIQEWVPPSTPYK

Entity 13 non-polymer

描述 description	IRON/SULFUR CLUSTER
分子量 formula_weight	351.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 14 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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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	2.00 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	60000

fit	/app/data/saxs_computation/ug/8ugp/8ugp.fit
pddf	/app/data/pr_computation/ug/8ugp/8ugp.pr.out
profile	/app/data/saxs_computation/ug/8ugp/8ugp.dat

In-situ structure of typeA supercomplex in respiratory chain ( local refined map focused on CI iron-sulfur cluster regions )

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 (14)

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 polymer

聚合体 Polymer

Entity 12 polymer

聚合体 Polymer

Entity 13 non-polymer

Entity 14 non-polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)