8r57

CryoEM structure of wheat 40S ribosomal subunit, head domain

Method: ELECTRON MICROSCOPY D_max: 154.3 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	8r57
沉积日期 deposition_date	2023-11-16
结构标题 title	CryoEM structure of wheat 40S ribosomal subunit, head domain
关键词 keywords	small ribosomal subunit, wheat, eukaryotes, 40S, RIBOSOME; RIBOSOME
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	44.76 Å
回转半径 Rg (电子) rg_electron	46.37 Å
零角强度 I(0) i0	3196820000.00
分子量 molecular_weight	361210.0 kDa
排除体积 excluded_volume	406110 Å³
包络体积 envelope_volume	563890 Å³
水化壳体积 shell_volume	98033 Å³
包络直径 envelope_diameter	170.6 Å
壳层 Rg shell_rg	52.85 Å
包络 Rg envelope_rg	46.65 Å
形状 Rg shape_rg	46.46 Å
总 Rg total_rg	46.35 Å
总原子数 total_atoms	24691
残基数 n_residues	2307
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	154.3 Å
Rg (实空间) rg_real	44.75 Å
Rg 误差 (实空间) rg_real_error	1.32 Å
I(0) (实空间) i0_real	3.1970e+09
I(0) 误差 (实空间) i0_real_error	5.4290e+07
Rg (倒空间) rg_reciprocal	44.76 Å
I(0) (倒空间) i0_reciprocal	3197000000.0000
解质量估计 total_estimate	0.8570
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	52.9 Å
偏度 Skewness skewness	0.421
峰度 Kurtosis kurtosis	-0.109
角度范围 angular_range	— – 0.1750 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	416000000.0000
实空间数据点数 n_real_points	36
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.757; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.870

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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	Plectin/eS10 N-terminal domain-containing protein
分子量 formula_weight	20464.0 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	K
原子数 atom_count	25048

MIISKKNRNEICKYLFQEGVLYAKKDYNLAKHPQIDVPNLQVIKLMQSFKSKEYVRETFSWQHYYWYLTNDGIEFLRNFLNLPSEIVPATLKKSARPPGRPLGSGPPGDRPRGPPRFEGDRPRYGDRDGYRGGPRGAPGDFGGEKGGAPAEFQPSFRSSGGGGFGRGGGGGFGRGGGGGGGFGASPME

Entity 2 polymer

描述 description	40S ribosomal protein S12
分子量 formula_weight	15364.8 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	M

MAEENAPVEVAAPVAAPTPVLGEPMDLMTALQLVMKKSSAHDGLVKGLREAAKAIEKHAAQICVLAEDCDQPDYVKLVKALCAEHNVHLVTVPSAKTLGEWAGLCKIDSEGKARKVVGCSCVVVKDYGEDSEGLHIVQEYVKSH

Entity 3 polymer

描述 description	40S ribosomal protein S3
分子量 formula_weight	25398.7 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	F

MATQISKKKKFVSDGVFYAELNEMLTRELAEDGYSGVEVRVTPMRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFNFPENGVELYAEKVVNRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFVMESGAKGCEVIVSGKLRAQRAKSMKFKDGYMISSGQPVNEYIDAAVRHVLLRQGVLGIKVKIMLDWDPKGKLGPTTPLPDLVTIHPPKEEDELRPPALVEV

Entity 4 polymer

描述 description	Small ribosomal subunit protein uS7c
分子量 formula_weight	22350.9 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	P

MAVVEPVPGGDVKLFNRWTFEDVQVSDISLNDYLAVTSMKHYTFLPHSAGRYSAKRFRKAQCPIIERLTNSLMMHGRNNGKKIMAVRIIKHTMEIIHLLTDANPIQIIVDAIINSGPREDATRIGSAGVVRRQAVDISPLRRVNQAIYLLTTGARESAFRNVKTIAECLADELINAAKGSSNSYAIKKKDEIERVAKANR

Entity 5 polymer

描述 description	40S ribosomal protein S16
分子量 formula_weight	16857.0 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	Q

MAAVLTRPTPGTVQCFGRKKTAVAVAYCKPGRGLIKVNGAPIELIRPEMLRLKAFEPILLAGRSRFKDIDMRIRVRGGGKTSQIYSIRQAIAKSLVAYYQKYVDEAAKKEVKEIFGRYDRTLLVADPRRCEPKKFGGRGARARFQKSYR

Entity 6 polymer

描述 description	Ribosomal protein S20
分子量 formula_weight	14128.4 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	U

MATELAYAPPMKSGKLGFEGTQEVQHRIRITLSSKSVKNLEKVCSDLVKGAKEKQLKVKGPVRMPTKVLNITTRKSPCGEGTNTWDRFEMRVHKRVIDLVSSPDVVKQITSITIEPGVEVEVTISDQ

Entity 7 polymer

描述 description	40S ribosomal protein S19
分子量 formula_weight	17097.6 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	T

MATVPAPAAETAASTARTVKDVNPHEFVKAYSAHLKRSGKMELPEWVDIVKTARFKELPPSDADWYYIRAASMARKIYLRQGIGIGGFQKIYGGRQRNGSRPPHFCKSSGAVSRNILQELQKMGIIDVDPKGGRLITSQGRRDLDQVAGTVPAEF

Entity 8 polymer

描述 description	40S ribosomal protein S25
分子量 formula_weight	12094.2 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	Z

MAPKKEKAPAASSKPAKSGGGKQKKKKWSKGKQKEKVNNAVLFDQATYDKLLTEVPKYKQITPSVLSERLRINGSLARRAIKDLMERGLIRMVSIHSSQQIFTRATNT

Entity 9 polymer

描述 description	40S ribosomal protein S28
分子量 formula_weight	7477.8 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	c

MDTQVKLAVVVKVMGRTGSRGQVTQVRVKFLDDQNRLIMRNVKGPVREGDILTLLESEREARRLR

Entity 10 polymer

描述 description	Small ribosomal subunit protein uS14
分子量 formula_weight	6392.4 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	d

MGHSNVWNSHPKNYGAGSRVCRVCGNSHGLIRKYGLMCCRQCFRSDAKDIGFIKYR

Entity 11 polymer

描述 description	Ribosomal protein RACK1 subfamily. WD repeat G protein beta family
分子量 formula_weight	36200.5 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

MAGAQESLVYAGVMRGHNDVVTAIATPIDNSPFIVSSSRDKSLLVWDLTNPIQATQDSSSEYGVPFRRLTGHGHFVQDVVLSSDGQFALSGSWDGELRLWDLSTGVTTRRFVGHEKDVLSVAFSIDNRQIVSASRDRTIKLWNTLGECKYTIGGDLGGGEGHTGWVSCVRFSPNNFAPTIVSGSWDRSVKVWNLTNCKLRCTLDGHGGYVSAVAVSPDGSLCASGGKDGVTLLWDLTEGKRLYSLDAGSIINSLCFSPNRYWLCAATQDSIKIWDLESKHIVQDLRPEVPVSTKQMLYCTCLSWSADGSTLYAGYTDGTIRIYKISGFSYSS

Entity 12 polymer

描述 description	Putative ribosomal protein S18
分子量 formula_weight	17702.7 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	S

MSLIAGEEFQHILRVLNTNVDGKQKIMFALTSIKGVGRRFSNIVCKKADIDMNKRAGELSAEEMDRLMAVVHNPRQFKVPDWFLNRKKDYKDGRFSQVVSNAVDMKLRDDLERLKKIRNHRGLRHYWGVRVRGQHTKTTGRRGKTVGVSKKR

Entity 13 polymer

描述 description	40S ribosomal protein S15
分子量 formula_weight	17295.4 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	R

MADVDVDPEVAAAGPKKRTFRKFSYRGVDLDALLDMSTEDLVQLFPARPRRRFSRGLKRKPMALVKKLRKAKSEAPAGEKPEQVRTHLRNMIIMPEMIGSVVGIYNGKCFNQVEIKPEMIGHYLAEFSLSYKPVKHGRPGIGATHSSRFIPLK

Entity 14 polymer

描述 description	40S ribosomal protein S17
分子量 formula_weight	16479.1 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	h

MGRVRTKTVKKTSRQVIEKYYSRMTLDFHTNKKVLEEVSILQSKRLRNKVAGFTTHLMRRIQRGPVRGISLKLQEEERERRMDFVPEKSALEVDEIRVDKETMDMLAFLGMADLPGVERAPEATSAAAPYRQPFNGPRGGNRA

Entity 15 polymer

描述 description	RNA (458-MER)
分子量 formula_weight	584382.8 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polyribonucleotide
链编号 strand_id	A

UACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUGCAAGUAUGAACCAAUUUGAACUGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUAGUUUGUUUGAUGGUACGUGCUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCAACAAACCCCGACUUCUGGGAGGGGCGCAUUUAUUAGAUAAAAGGCUGACGCGGGCUCUGCUCGCUGAUCCGAUGAUUCAUGAUAACUCGACGGAUCGCACGGCCUUCGUGCCGGCGACGCAUCAUUCAAAUUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGGGGCCUACCAUGGUGGUGACGGGUGACGGAGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACGGGGAGGUAGUGACAAUAAAUAACAAUACCGGGCGCAUUAGUGUCUGGUAAUUGGAAUGAGUACAAUCUAAAUCCCUUAACGAGGAUCCAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAXAUUUAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGACCUUGGGCCGGGUCGGCCGGUCCGCCUCACGGCGAGCACCGACCUACUCGACCCUUCGGCCGGCAUCGCGCUCCUAGCCUUAAUUGGCCGGGUCGUGUUUCCGGCAUCGUUACUUUGAAGAAAUUAGAGUGCUCAAAGCAAGCCAUCGCUCUGGAUACAUUAGCAUGGGAUAACAUCAUAGGAUUCCGGUCCUAUUGUGUUGGCCUUCGGGAUCGGAGUAAUGAUUAAUAGGGACAGUCGGGGGCAUUCGUAUUUCAUAGUCAGAGGUGAAAUUCUUGGAUUUAUGAAAGACGAACAACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUGGGGGCUCGAAGACGAUCAGAUACCGUCCUAGUCUCAACCAUAAACGAUGCCGACCAGGGAUCGGCGGAUGUUGCUUAUAGGACUCCGCCGGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGCACCACCAGGCGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCAGACAUAGCAAGGAUUGACAGACUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCNGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUCAGCCUGCUAACUAGCUAUGCGGAGCCAUCCCUCCGCAGCUAGCUUCUUAGAGGGACUAUCGCCGUUUAGGCGACGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAUGUAUUCAACGAGUAUAUAGCCUUGGCCGACAGGCCCGGGUAAUCUUGGGAAAUUUCAUCGUGAUGGGGAUAGAUCAUUGCAAUUGUUGGUCUUCAACGAGGAAUGCCUAGUAAGCGCGAGUCAUCAGCUCGCGUUGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAAUGGUCCGGUGAAGUGUUCGGAUCGCGGCGACGGGGGCGGUUCGCCGCCCCCGACGUCGCGAGAAGUCCAUUGAACCUUAUCAUUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCNGUAGGUGAACCUGCGGAAGGAUCAUUG

Entity 16 polymer

描述 description	Ubiquitin-like domain-containing protein
分子量 formula_weight	17692.6 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

MQIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGAKKRKKKTYTKPKKQKHKHKKVKLAVLQFYKVDDATGKVTRLRKECPNADCGAGTFMANHFDRHYCGKCGLTYVYNQKA

Entity 17 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	20

Entity 18 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

Entity 19 non-polymer

描述 description	POTASSIUM ION
分子量 formula_weight	39.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

Entity 20 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	357

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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	2.55 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	256000

fit	/app/data/saxs_computation/r5/8r57/8r57.fit
pddf	/app/data/pr_computation/r5/8r57/8r57.pr.out
profile	/app/data/saxs_computation/r5/8r57/8r57.dat

CryoEM structure of wheat 40S ribosomal subunit, head domain

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

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

Entity 15 polymer

聚合体 Polymer

Entity 16 polymer

聚合体 Polymer

Entity 17 non-polymer

Entity 18 non-polymer

Entity 19 non-polymer

Entity 20 water

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)