9gbk

Blm10-20S proteasome complex from pre1-1

Method: ELECTRON MICROSCOPY D_max: 207.8 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	9gbk
沉积日期 deposition_date	2024-07-31
结构标题 title	Blm10-20S proteasome complex from pre1-1
关键词 keywords	proteasome biogenesis, Ump1, pre1-1, cryo-EM, propertied maturation, 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	71.59 Å
回转半径 Rg (电子) rg_electron	71.72 Å
零角强度 I(0) i0	10595800000.00
分子量 molecular_weight	886660.0 kDa
排除体积 excluded_volume	1114900 Å³
包络体积 envelope_volume	1725000 Å³
水化壳体积 shell_volume	199660 Å³
包络直径 envelope_diameter	238.1 Å
壳层 Rg shell_rg	73.82 Å
包络 Rg envelope_rg	69.28 Å
形状 Rg shape_rg	71.72 Å
总 Rg total_rg	71.76 Å
总原子数 total_atoms	62494
残基数 n_residues	7941
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	207.8 Å
Rg (实空间) rg_real	71.33 Å
Rg 误差 (实空间) rg_real_error	0.68 Å
I(0) (实空间) i0_real	1.0550e+10
I(0) 误差 (实空间) i0_real_error	1.8450e+08
Rg (倒空间) rg_reciprocal	71.19 Å
I(0) (倒空间) i0_reciprocal	10590000000.0000
解质量估计 total_estimate	0.6087
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	75.6 Å
偏度 Skewness skewness	0.440
峰度 Kurtosis kurtosis	-0.302
角度范围 angular_range	— – 0.1100 Å⁻¹
当前正则化参数 α current_alpha	0.0724
最高正则化参数 α highest_alpha	1559000000.0000
实空间数据点数 n_real_points	23
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.928; Stabil: 0.999; Sysdev: 0.006; Positv: 1.000; Valcen: 0.995; Smooth: 0.109

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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 (16)

Entity 1 polymer

描述 description	Proteasome subunit beta type-6
分子量 formula_weight	24883.9 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	1,M
原子数 atom_count	64984

QFNPYGDNGGTILGIAGEDFAVLAGDTRNITDYSINSRYEPKVFDCGDNIVMSANGFAADGDALVKRFKNSVKWYHFDHNDKKLSINSAARNIQHLLYGKRFFPYYVHTIIAGLDEDGKGAVYSFDPVGSYEREQCRAGGAAASLIMPFLDNQVNFKNQYEPGTNGKVKKPLKYLSVEEVIKLVRDSFTSATERHIQVGDGLEILIVTKDGVRKEFYELKRD

Entity 2 polymer

描述 description	Proteasome subunit beta type-7
分子量 formula_weight	25945.5 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	2,N

TQQPIVTGTSVISMKYDNGVIIAADNLGSYGSLLRFNGVERLIPVGDNTVVGISGDISDMQHIERLLKDLVTENAYDNPLADAEEALEPSYIFEYLATVMYQRRSKMNPLWNAIIVAGVQSNGDQFLRYVNLLGVTYSSPTLATGFGAHMANPLLRKVVDRESDIPKTTVQVAEEAIVNAMRVLYYRDARSSRNFSLAIIDKNTGLTFKKNLQVENMKWDFAKDIKGYGTQKI

Entity 3 polymer

描述 description	Proteasome activator BLM10
分子量 formula_weight	246282.4 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	3

MTANNDDDIKSPIPITNKTLSQLKRFERSPGRPSSSQGEIKRKKSRLYAADGRPHSPLRARSATPTLQDQKLFNGMDSTSLLNERLQHYTLDYVSDRAQHMKNIYDPSSRWFSRSVRPEFPIEEFLPYKTESHEDQAKYLCHVLVNLYIAISSLDIQGLISISSKDLADLKKEVDDLALKTDLFRLSNNTAENDLLGNDIADYDDAEGLEDELDEYFDLAGPDFNATGKITAKSATIVNVNHWTNELKNCLHFDFPVALRKSLATVYYYLSLVQGQKVYRQMHVDMFERLVSLDDDRTNFTELLQKQGLLLDHQIMLNFLCEFLPYPDPDYARYELSSKEDLQLFRLLLKHAHNAKPFFDKSKESLLVDTMNFLLSSLAPSTMMAVMPIVTSVVPYHYHIHSKIIDYFPFCYSIWSSVSANVAIDTHMYDFVGSISKDVHNKILSSEHEKDVVGVEFGEFGIFTDDQMTFMFNRLQGHLRTDGQIHSYSRTVKPFVYAINGSKKDRFFEKLVSLAKAIETFIHPSNNGFWTKPNAKFVHAFIKSYHGRVKYEEDICARGVTNGICLTSFCHEEIVEIFLNIISLGSQNKNPDIANYYISCFAYLLELDPSNAYLIYDKILIDLYDTLADQFINSRHRIISSLKQFTRVIRFIVMDKLYRVHITNVLSMLVSKLDMNDTNLTSNLINGIVSIAAFIPIQDLTGEDDYISFESDTLPLVQQHFYHIKCGESSKTFRVDDELLNNAFKASTTVFQSMLKVYVEKIFQLVDVDLEDSLVTKINQTTMILQESMDDKIFNYFASLLQRNFWSNDSFKEKDPNYELVTIPLAALVRRNNGLSKELVRTLLFHIKEQIKRGAGSVRSTSEIQQRDVKLVLYLTALNDVLRQCHESLLEYSDELITFMKYLYDNVTNPPLDVITSIVIHSALATLCTTEITDCRLFPEDSKIPEKDRWGGLQFDPRRFDKQHLSFQWHVPSSDEITLSISILESLSEYCINNVEELMKAPRHDSEYGDMIQKYVLVMTHTLSGSSLLFDPDFNKYRTQSNLSYREKLILLKNIRENNCDPQELDIDIEQIRSGKDDEDYIESKDIEAGLNAGVSDVVQLRDEFPDELIVDEEVVSEMPSGVNTPIAGTHGTDNSAMSSDLAFRDLDIYTCNYYFGNTTEEKLQNPQYLQVHRVRARIGHFFHKLYVFLSTNFENNTNMFQILLHGLKVWFTDLGQETVFNEDPNAFIDVDFLENVQSLSHVNEPFTRTNFAIRANSLHQSRVLLHSTNRKASKLENLLLVDIIQLATSLYPDIYKPAQGTLVHCMKQLVGSYGVVINKIIPSLEKAIKDHDYMKIQVILNVLLIKKIHRKLMTDYKDIGRLIFLLIECCRVNELEIGMYADKILTDIVIGIKIPSSVCVISDQAFLPLAPPDGTINLQVEAVKLAKKKKREYYLSLLVDLQDKLLDKLDNEKDMGWKIRMFILRFVTQIQSNLESKPDKRAVFSIISQISTKHPEIIHLVVKSLLSTCNKIISLSDYEYDITRAYKNEFNPSFVEILDTSTTSFPKTFTEEMNNFDNPKYFIDLRAYVGWLCWGRLMYVMSPKALKLNLRENELEVLKTAGHLLTREFLRDVTMNLVQDNETRGVFSSGNVSFFSLVILLISSGFCELNMSDLFELCESYYNKDDKASMIMSVEIVAGLVCGSKFMSVSDLDKRDTFIENFLAKCLDYELNHDAFEIWSTLAWWLPAVVDLRRSKTFFCHFINADGMFDRESDAATHQTSKIYMLRSILMSMEFRAPDVGKLFDELVFDHPYDQVRQAVAKLLTTLVQNQSNPSISDPTTLLEAERNDPDGLGLPLKSVPEKVDAYIKKQFEIIKNLEDSVVGLNPQQFIKTDYFYRTSTIFYWIKEMARGPNKVLLVPYLVDYVLPFLIGLVKHKDVCALASLDPVRLYAGLGYMPIRKNHVAAIVDYVCSSNVALSSNQTKLQLAFIQHFLSAELLQLTEEEKNKILEFVVSNLYNEQFVEVRVRAASILSDIVHNWKEEQPLLSLIERFAKGLDVNKYTSKERQKLSKTDIKIHGNVLGLGAIISAFPYVFPLPPWIPKQLSNLSSWARTSGMTGQAAKNTISEFKKVRADTWKFDRASFNTEELEDLEGVLWRSYYA

Entity 4 polymer

描述 description	Proteasome subunit alpha type-1
分子量 formula_weight	28033.8 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,O

MSGAAAASAAGYDRHITIFSPEGRLYQVEYAFKATNQTNINSLAVRGKDCTVVISQKKVPDKLLDPTTVSYIFCISRTIGMVVNGPIPDARNAALRAKAEAAEFRYKYGYDMPCDVLAKRMANLSQIYTQRAYMRPLGVILTFVSVDEELGPSIYKTDPAGYYVGYKATATGPKQQEITTNLENHFKKSKIDHINEESWEKVVEFAITHMIDALGTEFSKNDLEVGVATKDKFFTLSAENIEERLVAIAEQD

Entity 5 polymer

描述 description	Proteasome subunit alpha type-2
分子量 formula_weight	27191.8 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,P

MTDRYSFSLTTFSPSGKLGQIDYALTAVKQGVTSLGIKATNGVVIATEKKSSSPLAMSETLSKVSLLTPDIGAVYSGMGPDYRVLVDKSRKVAHTSYKRIYGEYPPTKLLVSEVAKIMQEATQSGGVRPFGVSLLIAGHDEFNGFSLYQVDPSGSYFPWKATAIGKGSVAAKTFLEKRWNDELELEDAIHIALLTLKESVEGEFNGDTIELAIIGDENPDLLGYTGIPTDKGPRFRKLTSQEINDRLEAL

Entity 6 polymer

描述 description	Proteasome subunit alpha type-3
分子量 formula_weight	28748.2 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	C,Q

MGSRRYDSRTTIFSPEGRLYQVEYALESISHAGTAIGIMASDGIVLAAERKVTSTLLEQDTSTEKLYKLNDKIAVAVAGLTADAEILINTARIHAQNYLKTYNEDIPVEILVRRLSDIKQGYTQHGGLRPFGVSFIYAGYDDRYGYQLYTSNPSGNYTGWKAISVGANTSAAQTLLQMDYKDDMKVDDAIELALKTLSKTTDSSALTYDRLEFATIRKGANDGEVYQKIFKPQEIKDILVKTGITKKDEDEEADEDMK

Entity 7 polymer

描述 description	Proteasome subunit alpha type-4
分子量 formula_weight	28478.1 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	D,R

MSGYDRALSIFSPDGHIFQVEYALEAVKRGTCAVGVKGKNCVVLGCERRSTLKLQDTRITPSKVSKIDSHVVLSFSGLNADSRILIEKARVEAQSHRLTLEDPVTVEYLTRYVAGVQQRYTQSGGVRPFGVSTLIAGFDPRDDEPKLYQTEPSGIYSSWSAQTIGRNSKTVREFLEKNYDRKEPPATVEECVKLTVRSLLEVVQTGAKNIEITVVKPDSDIVALSSEEINQYVTQIEQEKQEQQEQDKKKKSNH

Entity 8 polymer

描述 description	Proteasome subunit alpha type-5
分子量 formula_weight	28649.1 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	E,S

MFLTRSEYDRGVSTFSPEGRLFQVEYSLEAIKLGSTAIGIATKEGVVLGVEKRATSPLLESDSIEKIVEIDRHIGCAMSGLTADARSMIEHARTAAVTHNLYYDEDINVESLTQSVCDLALRFGEGASGEERLMSRPFGVALLIAGHDADDGYQLFHAEPSGTFYRYNAKAIGSGSEGAQAELLNEWHSSLTLKEAELLVLKILKQVMEEKLDENNAQLSCITKQDGFKIYDNEKTAELIKELKEKEAAESPEEADVEMS

Entity 9 polymer

描述 description	Proteasome subunit alpha type-6
分子量 formula_weight	25634.0 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	F,T

MFRNNYDGDTVTFSPTGRLFQVEYALEAIKQGSVTVGLRSNTHAVLVALKRNADELSSYQKKIIKCDEHMGLSLAGLAPDARVLSNYLRQQCNYSSLVFNRKLAVERAGHLLCDKAQKNTQSYGGRPYGVGLLIIGYDKSGAHLLEFQPSGNVTELYGTAIGARSQGAKTYLERTLDTFIKIDGNPDELIKAGVEAISQSLRDESLTVDNLSIAIVGKDTPFTIYDGEAVAKYI

Entity 10 polymer

描述 description	Probable proteasome subunit alpha type-7
分子量 formula_weight	31575.1 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,U

MTSIGTGYDLSNSVFSPDGRNFQVEYAVKAVENGTTSIGIKCNDGVVFAVEKLITSKLLVPQKNVKIQVVDRHIGCVYSGLIPDGRHLVNRGREEAASFKKLYKTPIPIPAFADRLGQYVQAHTLYNSVRPFGVSTIFGGVDKNGAHLYMLEPSGSYWGYKGAATGKGRQSAKAELEKLVDHHPEGLSAREAVKQAAKIIYLAHEDNKEKDFELEISWCSLSETNGLHKFVKGDLLQEAIDFAQKEINGDDDEDEDDSDNVMSSDDENAPVATNANATTDQEGDIHLE

Entity 11 polymer

描述 description	Proteasome subunit beta type-1
分子量 formula_weight	21517.2 kDa
EC 编号 ec_number	3.4.25.1
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,V

TSIMAVTFKDGVILGADSRTTTGAYIANRVTDKLTRVHDKIWCCRSGSAADTQAIADIVQYHLELYTSQYGTPSTETAASVFKELCYENKDNLTAGIIVAGYDDKNKGEVYTIPLGGSVHKLPYAIAGSGSTFIYGYCDKNFRENMSKEETVDFIKHSLSQAIKWDGSSGGVIRMVVLTAAGVERLIFYPDEYEQL

Entity 12 polymer

描述 description	Proteasome subunit beta type-2
分子量 formula_weight	25114.5 kDa
EC 编号 ec_number	3.4.25.1
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,W

TTIVGVKFNNGVVIAADTRSTQGPIVADKNCAKLHRISPKIWCAGAGTAADTEAVTQLIGSNIELHSLYTSREPRVVSALQMLKQHLFKYQGHIGAYLIVAGVDPTGSHLFSIHAHGSTDVGYYLSLGSGSLAAMAVLESHWKQDLTKEEAIKLASDAIQAGIWNDLGSGSNVDVCVMEIGKDAEYLRNYLTPNVREEKQKSYKFPRGTTAVLKESIVNICDIQEEQVDITA

Entity 13 polymer

描述 description	Proteasome subunit beta type-3
分子量 formula_weight	22627.8 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,X

MSDPSSINGGIVVAMTGKDCVAIACDLRLGSQSLGVSNKFEKIFHYGHVFLGITGLATDVTTLNEMFRYKTNLYKLKEERAIEPETFTQLVSSSLYERRFGPYFVGPVVAGINSKSGKPFIAGFDLIGCIDEAKDFIVSGTASDQLFGMCESLYEPNLEPEDLFETISQALLNAADRDALSGWGAVVYIIKKDEVVKRYLKMRQD

Entity 14 polymer

描述 description	Proteasome subunit beta type-4
分子量 formula_weight	24431.6 kDa
突变 mutation	S142F
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	K,Y

MDIILGIRVQDSVILASSKAVTRGISVLKDSDDKTRQLSPHTLMSFAGEAGDTVQFAEYIQANIQLYSIREDYELSPQAVSSFVRQELAKSIRSRRPYQVNVLIGGYDKKKNKPELYQIDYLGTKVELPYGAHGYSGFYTFFLLDHHYRPDMTTEEGLDLLKLCVQELEKRMPMDFKGVIVKIVDKDGIRQVDDFQAQDYKDDDDKHHHHHH

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;brewer's yeast ;
NCBI 分类编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Saccharomyces cerevisiae

Entity 15 polymer

描述 description	Proteasome subunit beta type-5
分子量 formula_weight	23325.2 kDa
EC 编号 ec_number	3.4.25.1
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	L,Z

TTTLAFRFQGGIIVAVDSRATAGNWVASQTVKKVIEINPFLLGTMAGGAADCQFWETWLGSQCRLHELREKERISVAAASKILSNLVYQYKGAGLSMGTMICGYTRKEGPTIYYVDSDGTRLKGDIFCVGSGQTFAYGVLDSNYKWDLSVEDALYLGKRSILAAAHRDAYSGGSVNLYHVTEDGWIYHGNHDVGELFWKVKEEEGSFNNVIG

Entity 16 water

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	2483

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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	triclinic

分辨率 resolution	2.39 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	129737

fit	/app/data/saxs_computation/gb/9gbk/9gbk.fit
pddf	/app/data/pr_computation/gb/9gbk/9gbk.pr.out
profile	/app/data/saxs_computation/gb/9gbk/9gbk.dat

Blm10-20S proteasome complex from pre1-1

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 (16)

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 polymer

聚合体 Polymer

Entity 14 polymer

聚合体 Polymer

来源 Source

Entity 15 polymer

聚合体 Polymer

Entity 16 water

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)