8yfr

Cryo EM structure of Komagataella phaffii Rat1-Rai1 complex bound within the RNAPII cleft

Method: ELECTRON MICROSCOPY D_max: 188.1 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	8yfr
沉积日期 deposition_date	2024-02-25
结构标题 title	Cryo EM structure of Komagataella phaffii Rat1-Rai1 complex bound within the RNAPII cleft
关键词 keywords	transcription termination, RNA polymerase II, TRANSCRIPTION; TRANSCRIPTION
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	57.89 Å
回转半径 Rg (电子) rg_electron	57.34 Å
零角强度 I(0) i0	4395050000.00
分子量 molecular_weight	560300.0 kDa
排除体积 excluded_volume	702190 Å³
包络体积 envelope_volume	1065600 Å³
水化壳体积 shell_volume	149130 Å³
包络直径 envelope_diameter	195.2 Å
壳层 Rg shell_rg	65.66 Å
包络 Rg envelope_rg	55.25 Å
形状 Rg shape_rg	57.37 Å
总 Rg total_rg	57.43 Å
总原子数 total_atoms	39350
残基数 n_residues	4905
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	188.1 Å
Rg (实空间) rg_real	57.57 Å
Rg 误差 (实空间) rg_real_error	1.27 Å
I(0) (实空间) i0_real	4.3950e+09
I(0) 误差 (实空间) i0_real_error	8.0400e+07
Rg (倒空间) rg_reciprocal	58.15 Å
I(0) (倒空间) i0_reciprocal	4399000000.0000
解质量估计 total_estimate	0.8733
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	76.7 Å
偏度 Skewness skewness	0.128
峰度 Kurtosis kurtosis	-0.410
角度范围 angular_range	— – 0.1350 Å⁻¹
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	471400000.0000
实空间数据点数 n_real_points	28
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.844; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.970; Smooth: 0.846

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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	DNA-directed RNA polymerase subunit
分子量 formula_weight	194107.4 kDa
EC 编号 ec_number	2.7.7.6
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	39350

MSQFPYSSAPLRSVKEVQFGLLSPEEIRAISVVKIEYPEIMDESRQRPREGGLNDPKLGSIDRNFKCQTCGEGMAECPGHFGHMELAKPVFHIGFIPKIKKVCECICMNCGKLLLDETNPTMAQAIRIRDPKKRFNAVWQLCKTKMVCEADAPVDEYSEQKVVSRGGCGNTQPVVRKDGMKLWGTWKKSGFSDRDAQPERKLLTPGEILNVFKHISPEDCFRLGFNEDYARPEWMIITVLPVPPPQVRPSIAMDETTQGQDDLTHKLSDILKANINVQKLEMDGSPQHIINEVEQLLQFHVATYMDNDIAGQPQALQKSGRPVKAIRARLKGKEGRLRGNLMGKRVDFSARTVISGDPNLELDQVGVPISIAKTLSYPETVTQYNIHRLTEYVRNGPNEHPGAKYVIRDNGDRIDLRYHKRAGDIVLQYGWKVERHLMDDDPVLFNRQPSLHKMSMMAHRVKVMPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEETRAELSQLCAVPLQIVSPQSNKPVMGIVQDTLCGVRKMTLRDTFIEYEQVMNMLFWVPSWDGVVPQPAILKPKPLWTGKQLLSIAIPSGIHLQRTDGGNSLLSPKDNGMLIVDGKVMFGVVDKKTVGSGGGGLIHTVMREKGPKICAELFGNIQKVVNYWLLHNGFSIGIGDAIADASTMKEITHAISSAKEQVQEIIYKAQHNELELKPGMTLRESFEGEVSRTLNDARDSAGRSAEMNLKDLNNVKQMVSAGSKGSFINIAQMSACVGQQMVEGKRIAFGFADRSLPHFTKDDFSPESKGFVENSYLRGLTPQEFFFHAMAGREGLIDTAVKTAETGYIQRRLVKALEDIMVHYDGTTRNSLGDIIQFLYGEDGLDGTQVERQTIDTIPGSDKAFHKRYYVDLMDEKNSIKPDVIEYAADILGDVELQKELNSEYEQLVSDRKFLREIVFVNGDHNWPLPVNLRRIIQNAQQIFHLDRAKASDLTIPEIIHGVRDLCKKLFVLRGENELIKEAQQNATSLFQCLVRARLATRRILEEFRLNRDAFEWVLGTIEAQFQRSLVHPGEMVGVIAAQSIGEPATQMTLNTFHYAGVSSKNVTLGVPRLKEILNVAKNIKTPALTVYLDREIALDIEKAKVIQSSIEYTTLKNVTSATEIYYDPDPTSTVIEEDFDTVEAYFSIPDEKVEETIDKQSPWLLRLELDRARMLDKQLTMNQVADKISEVFSDDLFVMWSEDNADKLIIRCRVIRDPKAMDEELEAEEDQMLKRIEAHMLDLIALRGIPGISKVYMVKHKVSVPDESGEYKNEELWALETDGINLAEVMAVPGVDSSRTYSNSFVEILSVLGIEATRSSLYKEILNVIAFDGSYVNYRHMALLVDVMTSRGYLMAITRHGINRADTGALMRCSFEETVEILFEAGAAAELDDCRGVSENVMLGQLAPMGTGAFDVMIDEKLLTSLPADYAPTMPLFKGKATQGSATPYDNNAQYDDEFNHDDVADVMFSPMAETGSGDDRSGGLTEYAGIQSPYQPTSPGLSATSPGFAPTSPGFAPTSPRYSPTSPGYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPQYSPTSPQYSPTSPQYSPTSPQYSPTSPQYSPTSPQYSPTSPQYSPTSPQYSPTSPQYSPTSPQYSPTSPQYSPTSPQYSPTSPQYSPTSPQYSPASPQYSPSRHSPNGESKEGE

Entity 2 polymer

描述 description	DNA-directed RNA polymerase subunit beta
分子量 formula_weight	139746.1 kDa
EC 编号 ec_number	2.7.7.6
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

MSYDPYSIDDTITTEDCWTVISAFFEEKGLVSQQLDSFDEFMETSIQDLVWEEPRLILDQPAQHTNEKDNINKRYEIRFGKIYLSRPTMTEADGTTHAMFPQEARLRNLTYSSPVYLDMEKSMFTSIDDEGNPNATLDWQQVHEPIKDGVEEGNKVHIGKVPIMLRSKFCSLRTLDEVDLYKMKECPYDMGGYFVINGSEKVLIAQERSAANIVQVFKKAAPSPISHVAEIRSALEKGSRLISTMQIKLYGREDKGTGRTIKATLPYVKQDIPIVIVFRALGVVPDGEILQHICYDENDWQMLEMLKPCIEEGFVIQDKEVALDFIGRRGSAALGIRREKRIQYAKDILQKELLPHITQEEGFETRKTFFLGYMVNRLLLCALERKDQDDRDHFGKKRLDLAGPLLANLFRILFRKLTREIYRYMQRCIETDRDFNLNLAVKSTTITSGLKYSLATGNWGEQKKAMSSRAGVSQVLNRYTYSSTLSHLRRTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLLSGISIGSPSEPIINFLEEWGMEPLEDYDPAQHTKSTRIFVNGVWTGIHRDPSMLVSTMRDLRRSGAISPEVSIIRDIREREFKIFTDVGRVYRPLFIVEDDESKDNKGELRITKEHIRKIQQGYDDDAMNDDSEEQEQDVYGWSSLVTSGVIEYVDGEEEETIMIAMTPEDLQTRSLEQKEIDLNDTAKRIKPEMSTSSHHTFTHCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQKPLAKTQAMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEKRFGISIVEEFEKPTRATTLRLKHGTYEKLDEDGLIAPGVRVSGDDIIIGKTTPIPPDTEELGQRTKYHTKRDASTPLRSTENGIVDQVLLTTNQEGLKFVKVRMRTTKVPQIGDKFASRHGQKGTIGVTYRHEDMPFSAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVGSIRGYEGDATPFTDLTVDAVSNLLRDNGYQSRGFEVMYNGHTGKKLMAQVFFGPTYYQRLRHMVDDKIHARARGPVQVLTRQPVEGRSRDGGLRFGEMERDCMIAHGAAGFLKERLMEASDAFRVHVCGICGLMSVIANLKKNQFECRSCKNKTNIYQLHIPYAAKLLFQELMAMNIAPRLYTERSGVSMRS

Entity 3 polymer

描述 description	RNA polymerase II third largest subunit B44, part of central core
分子量 formula_weight	34216.3 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	C

MSKEPKVNIINAQDDEVELMLSDVNLSLANSLRRTMLAEVPTLAIDLVEIKMNTSVLADEFISHRLGLIPLVSEDVEEMKYSRDCTCEDYCDECSVVLELSARHEGEEGTTDVYSSSLIKVSGPGNLNVGEPVRRDDYDQGILLCKLRNHQELNIRCIAKKGIAKEHAKWSPCSAIAFEYDPHNKLKHTDFWFEVDAKKEWPDSKYATWEEPPKPGEVFDYKAKPNRFYMTVETTGSLKANQVFSRGIKTLQEKLANVLFELENSRPANTTAYGGATAYGGQTVYGRETSYGGNTNYGDYNAPY

Entity 4 polymer

描述 description	RNA polymerase II subunit B32
分子量 formula_weight	20623.0 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	D

MNVSTSTVGARRRRAKQQVDDEENATLLRLGPEFALKQYDHDGNEHDLIALSLSESRLLIREALKARSRARNGGVDIESSNGEIDDDELAKVTSGAVANGVVKKTLDYLNTFARFKDEETCTAVDQLLHNSSDCSVLHPFEIAQLSSLGCEDVDEAITLIPSLAAKKEVNLQRILDELNRLEDPYK

Entity 5 polymer

描述 description	DNA-directed RNA polymerases I, II, and III subunit RPABC1
分子量 formula_weight	24962.7 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	E

MEDNNRIISRLWRSFRTVKEMAADRGYFISQEEMDQSLEEFRSKICDSMGNPQRKLMSFLANPTPEALEKYSDLGTLWVEFCDEPSVGIKTMRNFCLRIQEKNFSTGIFIYQNNITPSANKMIPTVSPAIIETFQESDLVVNITHHELVPKHIRLSDGEKSQLLQRYKLKESQLPRIQREDPVARYLGLKRGQVVKIIRRSETSGRYASYRICL

Entity 6 polymer

描述 description	RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III
分子量 formula_weight	17803.6 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

MSEDEAFNEQTENFENFEDEHFSDDNFEDRSTQPEDYAVGVTADGRQIINGDGIQEVNGTIKAHRKRSNKELAILKEERTTTPYLTKYERARILGTRALQISMNAPVLVDIEGETDPLQIAMKELSQRKIPLVIRRYLPDGSYEDWGCDELIVDN

Entity 7 polymer

描述 description	RNA polymerase II subunit
分子量 formula_weight	18802.6 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	G

MFFLKDLSLILTLHPSYFGPQMNQYLREKLLTDVEGTCTGQFGYIVTVLDGMNIDVGKGRIIPGSGSAEFEVKYRAVVWKPFKGEVVDAIVSNVSPIGFFADVGPLNVFVSTRLIPDNLVYNPSNSPPAYMSNDELITKGSKVRLKVVGTRTDVNEIYAIGSIKEDFLGAI

Entity 8 polymer

描述 description	DNA-directed RNA polymerases I, II, and III subunit RPABC3
分子量 formula_weight	16249.2 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	H

MSSALFDDIFTVQTVDNGRYNKVSRIIGISTTNSAIKLTLDINNEMFPVSQDDSLTVTLANSLSLDGEDESANFSKSWRPPKPTDKSLADDYDYVMFGTVYKFEEGDEDKIKVYVSFGGLLMCLEGGYKSLASLKQDNLYILIRR

Entity 9 polymer

描述 description	DNA-directed RNA polymerase subunit
分子量 formula_weight	13612.3 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	I

MASFRFCLECNNMLYPKEDKENQRLLYSCRNCDYTELAEDPKVYRHELITNIGETAGIVDDIGQDPTLPRSDKECPECHSRDCVFFQSQQRRKDTNMTLFYVCLNCKKTFRDESE

Entity 10 polymer

描述 description	RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III
分子量 formula_weight	8554.1 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	J

MIIPVRCFSCGKVVGDKWDAYLRLLEEGKQEGDALDELKLKRYCCRRMVLTHVDLIEKFLRYNPLEKKDFDS

Entity 11 polymer

描述 description	RNA polymerase II subunit B12.5
分子量 formula_weight	13832.9 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	K

MNAPDRFELFILPDDVPKLKITPDSRVPNCIIIKFEREDHTLANLLREELALYPDVTFVAYKVEHPLFANFVMRLQTEEGTRPKQALERACASIINKLKTLDHKFNEEWNIKNFSLND

Entity 12 polymer

描述 description	RNA polymerase subunit ABC10-alpha
分子量 formula_weight	7862.0 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	L

MSREGFVAPSGTDLAAAASGVAPNKHYGVKYTCGACAHNFSLNKSDPVRCKECGHRVIYKARTKRMIQFDAR

Entity 13 polymer

描述 description	;5'-3' exoribonuclease ;
分子量 formula_weight	115397.6 kDa
EC 编号 ec_number	3.1.13.-
突变 mutation	E203Q, E205Q, D233N, D235N, D330N
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	R

MGVPALFRWLSRKYPKIISPVIQDEDVDIDGESRPTRYEDPNPNGELDNLYLDMNGIVHPCSHPEHKPVPETEDEMMLDVFAYTENVIMMARPRKVIYIAVDGVAPRAKMNQQRSRRFRSAQDAKDANEKKAAELKEMEKKGEIIDDAIKNKKTWDSNAITPGTPFMHRLADSLRYWAAYKLTTDPGWSGIEVIISDASVPGQGQHKIMSYVRSLRSSPKHDPNTTHCIYGLNANLIFLGLATHEPHFKILREDVFAQDKKSYSLQDQLRMTDIERQELKDKKTPFLWLHLNILREYLQIELNVPGLSFPFDLEKSIDDWVFICFFCGNNFLPHLPSLDVRDNSITTLVTIWKQILPTMKGYLTTDGYLNLPAVERLLAELAKKEDYIFRKRYEDEKRSLENQKRRKLAQEQSSARSQNAPNISTGKDKAPLTPNQNIPLYTTSGESVGIKMTDSEMVNNSALITKANEANKSIAELLKQNLQNEINKKRKISNEEQEVVKESVEEVVEEEDDVLVTSDPEDSSTEILIPKNEEIRLWEPGYRKRYYETKFHTKDPQKVKKIARNMVQKYIEGVSWVLLYYYQGCPSWNWYYPYHYAPFAADFVNLSELKIEFVEGTPFRPYEQLMSVLPAASSHNLPDVFRSLMSDANSEIIDFYPEEFPLDMNGKKVIWQAIPLLPFIDENRLLKAVQSKYDQLTEDEKFRNTNRSEILVLGRSHSHYPTLVKELYEEGKDSYEFQVDSSGVSGVAIKLQSFDRSGVLRLPVKQLEGYRHYPDISNRDFLMVEFKQLPKSHAKSMILSGLIPHLRRLTQEDKDSILYGGTNFYGRNRFSPEENADFKQYIGPHGKSQYLPRQGGYKAFIQIHSDEAKGHRHGIYHGGSHTETEFRRGGGYHQHGNRGGRGGYQGNQGYQANSGGYQNSYQGSYQGGYRGGYQGGSQGRYQAGYQSGYQGGYQGEYKNGYQGGYQGNQGNQGYNRQTYNASKSGTLPMKRRHNSGPSSGLEVLFQ

来源 Source

来源生物 organism	Komagataella phaffii
NCBI 分类编号 ncbi_taxonomy_id	460519
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 14 polymer

描述 description	Decapping nuclease
分子量 formula_weight	44596.0 kDa
EC 编号 ec_number	3.6.1.-
突变 mutation	E213A, D215A
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	S

GPGMSKEKILPLAARSKKAMLRQPKQVAYFSRDLNYKTHPDRSNLSYYYLPDGDIDNSIDLSVGSKHFLLGDSVELSKLDPILLALKEIEKESGAKTKDRIITWRGIMRKLLTLPYDSEEDFVLDVVSFDGQLFIQFNVPYLKSKDVQKQGDTEFHKKLQFSGYKFEKMATLPKPWPECTRKEIDSRAKSKCNNIEQYGAIVRTGISRIKILIGGAVACTADYYDENDPLSRYIELKTTRTINQYKDMIAFEKKLFRTWAQCFLLGIPKIIYGFRDDNCILRTVEEFSTNDIPLMVKNNPLNEQPKKENCYMSSINFYGAVVEWLNESVKDDQVWKLSYAKRNRQYLVLKEVTDENEKQQIVDSAIPAWFKEWRSELRNSEGNI

来源 Source

来源生物 organism	Komagataella phaffii
NCBI 分类编号 ncbi_taxonomy_id	460519
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 15 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	8

Entity 16 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	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	3.40 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	35181

fit	/app/data/saxs_computation/yf/8yfr/8yfr.fit
pddf	/app/data/pr_computation/yf/8yfr/8yfr.pr.out
profile	/app/data/saxs_computation/yf/8yfr/8yfr.dat

Cryo EM structure of Komagataella phaffii Rat1-Rai1 complex bound within the RNAPII cleft

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

来源 Source

Entity 14 polymer

聚合体 Polymer

来源 Source

Entity 15 non-polymer

Entity 16 non-polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)