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- PDB-9eeq: Cryo-EM model of E. coli aspartate transcarbamoylase in the R-sta... -

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基本情報

登録情報
データベース: PDB / ID: 9eeq
タイトルCryo-EM model of E. coli aspartate transcarbamoylase in the R-state complexed with CP, succinate, ATP, and Mg2+
要素
  • Aspartate carbamoyltransferase
  • Aspartate carbamoyltransferase regulatory chain
キーワードCYTOSOLIC PROTEIN / Complex / Allostery / ATCase / R-state / ATP
機能・相同性
機能・相同性情報


aspartate carbamoyltransferase complex / pyrimidine nucleotide biosynthetic process / aspartate carbamoyltransferase / aspartate carbamoyltransferase activity / amino acid metabolic process / amino acid binding / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / transferase activity / metal ion binding / cytosol
類似検索 - 分子機能
Aspartate transcarbamylase regulatory subunit / Aspartate carbamoyltransferase regulatory subunit, C-terminal / Aspartate carbamoyltransferase regulatory subunit, N-terminal / Aspartate carbamoyltransferase regulatory subunit, C-terminal domain superfamily / Aspartate carbamoyltransferase regulatory subunit, N-terminal domain superfamily / Aspartate carbamoyltransferase regulatory chain, allosteric domain / Aspartate carbamoyltransferase regulatory chain, metal binding domain / Aspartate carbamoyltransferase / Aspartate and ornithine carbamoyltransferases signature. / Aspartate/ornithine carbamoyltransferase ...Aspartate transcarbamylase regulatory subunit / Aspartate carbamoyltransferase regulatory subunit, C-terminal / Aspartate carbamoyltransferase regulatory subunit, N-terminal / Aspartate carbamoyltransferase regulatory subunit, C-terminal domain superfamily / Aspartate carbamoyltransferase regulatory subunit, N-terminal domain superfamily / Aspartate carbamoyltransferase regulatory chain, allosteric domain / Aspartate carbamoyltransferase regulatory chain, metal binding domain / Aspartate carbamoyltransferase / Aspartate and ornithine carbamoyltransferases signature. / Aspartate/ornithine carbamoyltransferase / Aspartate/ornithine carbamoyltransferase, Asp/Orn-binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding / Aspartate/ornithine carbamoyltransferase superfamily / Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain
類似検索 - ドメイン・相同性
ADENOSINE-5'-TRIPHOSPHATE / PHOSPHORIC ACID MONO(FORMAMIDE)ESTER / SUCCINIC ACID / Aspartate carbamoyltransferase / Aspartate carbamoyltransferase regulatory chain
類似検索 - 構成要素
生物種Escherichia coli (大腸菌)
手法電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.08 Å
データ登録者Patterson, M.G. / Miller, R.C. / Ando, N.
資金援助 米国, 4件
組織認可番号国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM124847 米国
National Science Foundation (NSF, United States)DMR-1719875 米国
Other governmentU24 GM129539
Simons FoundationSF349247 米国
引用
ジャーナル: Nat Commun / 年: 2026
タイトル: Cooperativity in E. coli aspartate transcarbamoylase is tuned by allosteric breathing.
著者: Robert C Miller / Michael G Patterson / Neti Bhatt / Xiaokun Pei / Nozomi Ando /
要旨: Aspartate transcarbamoylase (ATCase) from Escherichia coli catalyzes a key step in pyrimidine nucleotide biosynthesis and has long served as a model for allosteric regulation. Despite decades of ...Aspartate transcarbamoylase (ATCase) from Escherichia coli catalyzes a key step in pyrimidine nucleotide biosynthesis and has long served as a model for allosteric regulation. Despite decades of study, how nucleotide binding at distant regulatory sites controls cooperativity between active sites remained unresolved. Here we show that ATCase does not simply interconvert between two conformations, as traditionally depicted, but instead samples a continuum of conformations that tune enzyme cooperativity. Using complementary cryo-electron microscopy, small-angle X-ray scattering, and crystallography under conditions that ensure full assembly of the allosteric sites, we show that ATCase behaves like a flexible balloon whose global "breathing" motions directly regulate activity: compression enforces high cooperativity, inhibiting the enzyme, whereas expansion relieves this cooperativity and activates the enzyme. We further show that all four ribonucleoside triphosphates act in symmetric pairs to tune this motion, with the pyrimidines CTP and UTP compressing the enzyme to limit further pyrimidine production, and the purines ATP and GTP expanding it to balance pyrimidine and purine pools. Together, these findings uncover a dynamic breathing mechanism for long-range allosteric communication in ATCase.
#1: ジャーナル: Acta Crystallogr D Struct Biol / 年: 2019
タイトル: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
著者: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / ...著者: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
要旨: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
履歴
登録2024年11月19日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02026年4月15日Provider: repository / タイプ: Initial release
改定 1.02026年4月15日Data content type: EM metadata / Data content type: EM metadata / Provider: repository / タイプ: Initial release
改定 1.02026年4月15日Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / タイプ: Initial release
改定 1.02026年4月15日Data content type: FSC / Data content type: FSC / Provider: repository / タイプ: Initial release
改定 1.02026年4月15日Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / タイプ: Initial release
改定 1.02026年4月15日Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / タイプ: Initial release
改定 1.02026年4月15日Data content type: Image / Data content type: Image / Provider: repository / タイプ: Initial release
改定 1.02026年4月15日Data content type: Primary map / Data content type: Primary map / Provider: repository / タイプ: Initial release

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

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集合体

登録構造単位
A: Aspartate carbamoyltransferase
B: Aspartate carbamoyltransferase
C: Aspartate carbamoyltransferase
D: Aspartate carbamoyltransferase regulatory chain
E: Aspartate carbamoyltransferase regulatory chain
F: Aspartate carbamoyltransferase
G: Aspartate carbamoyltransferase
H: Aspartate carbamoyltransferase regulatory chain
I: Aspartate carbamoyltransferase regulatory chain
J: Aspartate carbamoyltransferase regulatory chain
K: Aspartate carbamoyltransferase
L: Aspartate carbamoyltransferase regulatory chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)317,06348
ポリマ－308,88412
非ポリマー8,17936
水00
1


  • 登録構造と同一
  • 登録者・ソフトウェアが定義した集合体
  • 根拠: 電子顕微鏡法, not applicable
タイプ名称対称操作数
identity operation1_555x,y,z1
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
d_1ens_1(chain "K" and (resid 1 through 86 or resid 88 through 134 or resid 293 through 310 or resid 401))
d_2ens_1(chain "G" and (resid 1 through 86 or resid 88 through 134 or resid 293 through 310 or resid 401))
d_3ens_1(chain "C" and (resid 1 through 86 or resid 88 through 134 or resid 293 through 310 or resid 401))
d_4ens_1(chain "A" and (resid 1 through 86 or resid 88 through 134 or resid 293 through 310 or resid 401))
d_5ens_1(chain "F" and (resid 1 through 86 or resid 88 through 134 or resid 293 through 310 or resid 401))
d_6ens_1(chain "B" and (resid 1 through 86 or resid 88 through 134 or resid 293 through 310 or resid 401))
d_1ens_2(chain "B" and (resid 137 through 291 or resid 402))
d_2ens_2(chain "G" and (resid 137 through 291 or resid 402))
d_3ens_2(chain "K" and (resid 137 through 291 or resid 402))
d_4ens_2(chain "A" and (resid 137 through 291 or resid 402))
d_5ens_2(chain "F" and (resid 137 through 291 or resid 402))
d_6ens_2(chain "C" and (resid 137 through 291 or resid 402))
d_1ens_3(chain "D" and (resid 10 through 23 or resid 25...
d_2ens_3(chain "E" and (resid 10 through 23 or resid 25...
d_3ens_3(chain "J" and (resid 10 through 23 or resid 25...
d_4ens_3(chain "I" and (resid 10 through 23 or resid 25...
d_5ens_3(chain "H" and (resid 10 through 23 or resid 25...
d_6ens_3(chain "L" and (resid 10 through 23 or resid 25...
d_1ens_4(chain "H" and (resid 102 through 118 or resid 120...
d_2ens_4(chain "E" and (resid 102 through 118 or resid 120...
d_3ens_4(chain "J" and (resid 102 through 118 or resid 120...
d_4ens_4(chain "I" and (resid 102 through 118 or resid 120...
d_5ens_4(chain "D" and (resid 102 through 118 or resid 120...
d_6ens_4(chain "L" and (resid 102 through 118 or resid 120...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1ALAALAGLUGLUKK1 - 861 - 86
d_12ens_1LEULEUHISHISKK88 - 13488 - 134
d_13ens_1ILEILELEULEUKK293 - 310293 - 310
d_14ens_1CPCPCPCPKQA401
d_21ens_1ALAALAGLUGLUGG1 - 861 - 86
d_22ens_1LEULEUHISHISGG88 - 13488 - 134
d_23ens_1ILEILELEULEUGG293 - 310293 - 310
d_24ens_1CPCPCPCPGCA401
d_31ens_1ALAALAGLUGLUCC1 - 861 - 86
d_32ens_1LEULEUHISHISCC88 - 13488 - 134
d_33ens_1ILEILELEULEUCC293 - 310293 - 310
d_34ens_1CPCPCPCPCQ401
d_41ens_1ALAALAGLUGLUAA1 - 861 - 86
d_42ens_1LEULEUHISHISAA88 - 13488 - 134
d_43ens_1ILEILELEULEUAA293 - 310293 - 310
d_44ens_1CPCPCPCPAM401
d_51ens_1ALAALAGLUGLUFF1 - 861 - 86
d_52ens_1LEULEUHISHISFF88 - 13488 - 134
d_53ens_1ILEILELEULEUFF293 - 310293 - 310
d_54ens_1CPCPCPCPFAA401
d_61ens_1ALAALAGLUGLUBB1 - 861 - 86
d_62ens_1LEULEUHISHISBB88 - 13488 - 134
d_63ens_1ILEILELEULEUBB293 - 310293 - 310
d_64ens_1CPCPCPCPBO401
d_11ens_2GLNGLNASNASNBB137 - 291137 - 291
d_12ens_2SINSINSINSINBP402
d_21ens_2GLNGLNASNASNGG137 - 291137 - 291
d_22ens_2SINSINSINSINGDA402
d_31ens_2GLNGLNASNASNKK137 - 291137 - 291
d_32ens_2SINSINSINSINKRA402
d_41ens_2GLNGLNASNASNAA137 - 291137 - 291
d_42ens_2SINSINSINSINAN402
d_51ens_2GLNGLNASNASNFF137 - 291137 - 291
d_52ens_2SINSINSINSINFBA402
d_61ens_2GLNGLNASNASNCC137 - 291137 - 291
d_62ens_2SINSINSINSINCR402
d_11ens_3GLUGLUALAALADD10 - 2310 - 23
d_12ens_3ILEILETHRTHRDD25 - 3625 - 36
d_13ens_3THRTHRPROPRODD38 - 7938 - 79
d_14ens_3ALAALALYSLYSDD81 - 9481 - 94
d_15ens_3ATPATPATPATPDT202
d_16ens_3ATPATPATPATPDU203
d_21ens_3GLUGLUALAALAEE10 - 2310 - 23
d_22ens_3ILEILETHRTHREE25 - 3625 - 36
d_23ens_3THRTHRPROPROEE38 - 7938 - 79
d_24ens_3ALAALALYSLYSEE81 - 9481 - 94
d_25ens_3ATPATPATPATPEX202
d_26ens_3ATPATPATPATPEY203
d_31ens_3GLUGLUALAALAJJ10 - 2310 - 23
d_32ens_3ILEILETHRTHRJJ25 - 3625 - 36
d_33ens_3THRTHRPROPROJJ38 - 7938 - 79
d_34ens_3ALAALALYSLYSJJ81 - 9481 - 94
d_35ens_3ATPATPATPATPJNA202
d_36ens_3ATPATPATPATPJOA203
d_41ens_3GLUGLUALAALAII10 - 2310 - 23
d_42ens_3ILEILETHRTHRII25 - 3625 - 36
d_43ens_3THRTHRPROPROII38 - 7938 - 79
d_44ens_3ALAALALYSLYSII81 - 9481 - 94
d_45ens_3ATPATPATPATPIJA202
d_46ens_3ATPATPATPATPIKA203
d_51ens_3GLUGLUALAALAHH10 - 2310 - 23
d_52ens_3ILEILETHRTHRHH25 - 3625 - 36
d_53ens_3THRTHRPROPROHH38 - 7938 - 79
d_54ens_3ALAALALYSLYSHH81 - 9481 - 94
d_55ens_3ATPATPATPATPHFA202
d_56ens_3ATPATPATPATPHGA203
d_61ens_3GLUGLUALAALALL10 - 2310 - 23
d_62ens_3ILEILETHRTHRLL25 - 3625 - 36
d_63ens_3THRTHRPROPROLL38 - 7938 - 79
d_64ens_3ALAALALYSLYSLL81 - 9481 - 94
d_65ens_3ATPATPATPATPLTA202
d_66ens_3ATPATPATPATPLUA203
d_11ens_4ARGARGALAALAHH102 - 118102 - 118
d_12ens_4PROPROVALVALHH120 - 127120 - 127
d_13ens_4ARGARGASNASNHH130 - 153130 - 153
d_21ens_4ARGARGALAALAEE102 - 118102 - 118
d_22ens_4PROPROVALVALEE120 - 127120 - 127
d_23ens_4ARGARGASNASNEE130 - 153130 - 153
d_31ens_4ARGARGALAALAJJ102 - 118102 - 118
d_32ens_4PROPROVALVALJJ120 - 127120 - 127
d_33ens_4ARGARGASNASNJJ130 - 153130 - 153
d_41ens_4ARGARGALAALAII102 - 118102 - 118
d_42ens_4PROPROVALVALII120 - 127120 - 127
d_43ens_4ARGARGASNASNII130 - 153130 - 153
d_51ens_4ARGARGALAALADD102 - 118102 - 118
d_52ens_4PROPROVALVALDD120 - 127120 - 127
d_53ens_4ARGARGASNASNDD130 - 153130 - 153
d_61ens_4ARGARGALAALALL102 - 118102 - 118
d_62ens_4PROPROVALVALLL120 - 127120 - 127
d_63ens_4ARGARGASNASNLL130 - 153130 - 153

NCSアンサンブル:
ID
ens_1
ens_2
ens_3
ens_4

NCS oper:
IDCodeMatrixベクター
1given(-0.496892182304, -0.866791037217, 0.0420886797748), (0.867812257554, -0.496295592466, 0.0243427717775), (-0.000211670132848, 0.0486208052047, 0.998817286843)358.044119052, 92.6995912017, -7.22317474682
2given(-0.501648243378, 0.865070342507, 0.00153050008821), (-0.864046407181, -0.501139014275, 0.0477859247983), (0.0421051796378, 0.0226493021308, 0.998856427601)98.4474999109, 357.158625257, -9.7225886095
3given(-0.94158814207, -0.336750565274, -0.00329051694977), (-0.336593443111, 0.941372290283, -0.0228706174177), (0.0107992948208, -0.0204271357326, -0.999733018039)349.932323212, 63.8167978358, 309.456362695
4given(0.175323137581, 0.983381137811, -0.0471522557809), (0.984235659381, -0.176205495601, -0.0152246550851), (-0.023280125239, -0.0437396972617, -0.998771682945)-18.9293728421, 30.7162312375, 318.154076532
5given(0.762385198324, -0.646854038079, -0.0186725144903), (-0.646500314859, -0.762599900812, 0.0218799947052), (-0.0283928206265, -0.00460919760548, -0.999586215909)137.089439472, 366.96005036, 313.033460544
6given(0.181086650054, 0.983175548134, -0.0239471652494), (0.982185447907, -0.182039768635, -0.0466183285302), (-0.0501933371272, -0.015078600282, -0.998625687994)-20.0696993669, 39.4539620089, 317.79327208
7given(0.762363039805, -0.646526301575, -0.0283960720972), (-0.646879287257, -0.762578745755, -0.0045655493245), (-0.0187024933248, 0.0218494369405, -0.99958632386)141.620053361, 369.956925699, 307.443065544
8given(-0.500110032036, 0.865390383365, 0.0314553689586), (-0.86504420457, -0.500922184732, 0.0278476028261), (0.0398557398258, -0.0132834190787, 0.999117145674)91.0496587201, 357.44060451, -3.88217980121
9given(-0.501547840804, -0.864313802442, 0.037568794149), (0.8646387881, -0.502253290619, -0.0118910965102), (0.0291466893259, 0.0265194828639, 0.999223292127)355.227003806, 100.218547991, -8.36970647645
10given(-0.942040121721, -0.335386576855, 0.00873230405852), (-0.3354979935, 0.941809867426, -0.0208631248166), (-0.00122695811295, -0.022583571132, -0.999744205729)347.924407787, 64.0819630994, 311.699607407
11given(-0.943910495055, -0.329753670438, -0.0171899434961), (-0.329836390318, 0.944035684181, 0.00214070446496), (0.0155220149147, 0.0076905023238, -0.999849950356)351.640528045, 58.8541652826, 306.028203327
12given(0.78697147962, -0.61612345149, 0.032676945828), (-0.616093737216, -0.787578855871, -0.0121676928064), (0.0332324724971, -0.0105564344646, -0.999391897337)123.927292204, 371.08837762, 306.367482183
13given(-0.445357039719, -0.894956259701, -0.0266533374013), (0.894944369316, -0.445855809254, 0.0169461849075), (-0.0270496395774, -0.0163061514858, 0.999501088755)364.68741324, 84.7641146002, 2.99436160912
14given(0.126487395451, 0.991553199838, 0.0286912997751), (0.991292808143, -0.127415544581, 0.0332242008696), (0.0365992802699, 0.0242390364894, -0.999036016265)-24.5880676521, 17.8698565975, 303.640831491
15given(-0.519119846041, 0.854700221758, 0.00145477624826), (-0.854530581887, -0.518981274284, -0.02087873471), (-0.0170900575555, -0.0120817163421, 0.999780957042)100.789077403, 367.208625369, 1.43115282822
16given(-0.502960131034, -0.863595488898, 0.0351274557229), (0.863505355484, -0.503829827301, -0.0226717042212), (0.0372774414414, 0.0189297828154, 0.999125645593)356.065098734, 102.355025257, -8.37254529836
17given(-0.49807271405, 0.86685165768, 0.0221760027196), (-0.866174164798, -0.498561685475, 0.0343301909796), (0.0408152882521, -0.00210934923914, 0.999164482401)92.0731630555, 356.199330059, -5.66229497327
18given(-0.944624050354, -0.328122261394, 0.0046027243749), (-0.328154537863, 0.944533366223, -0.0130889025739), (-5.26664359184E-5, -0.0138744970542, -0.999903743146)348.070675236, 61.2781182902, 310.336717451
19given(0.188843114601, 0.981563554216, -0.0295172339977), (0.980558356174, -0.190111505288, -0.048609934116), (-0.0533253054884, -0.0197637190886, -0.998381593982)-20.0389724583, 41.0511696406, 318.880467207
20given(0.753872881701, -0.656567595213, -0.0243858801617), (-0.656784162658, -0.754077694801, -0.00118062906262), (-0.0176136855135, 0.0169063041163, -0.999701923057)143.473209348, 369.62908326, 308.137721661

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要素

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タンパク質 , 2種, 12分子 ABCFGKDEHIJL

#1: タンパク質
Aspartate carbamoyltransferase / Aspartate transcarbamylase / ATCase


分子量: 34337.105 Da / 分子数: 6 / 由来タイプ: 組換発現 / 由来: (組換発現) Escherichia coli (大腸菌)
遺伝子: pyrB, A2J79_003077, ABE91_001635, ABT96_002053, ACN81_01160, ACW72_001368, ATM34_004868, AW118_07535, AWP47_22680, B6R15_003056, B6R31_000750, BANRA_02937, BE932_21750, BER14_11960, BG944_ ...遺伝子: pyrB, A2J79_003077, ABE91_001635, ABT96_002053, ACN81_01160, ACW72_001368, ATM34_004868, AW118_07535, AWP47_22680, B6R15_003056, B6R31_000750, BANRA_02937, BE932_21750, BER14_11960, BG944_000740, BGM66_001590, BGZ_01518, BGZ_05217, BJI68_10440, BK300_13470, BK383_13480, BKL28_003429, BRV02_003861, BTB68_002687, BTQ06_18960, BvCmsNSP007_04794, BVE17_001554, BXT93_08870, C0P57_000163, C1Q91_004309, C2M16_07715, C2R31_000937, C3F40_13755, C4M78_05240, C719_002693, C9114_01215, C9160_23140, C9Z68_08980, CF22_004479, CG704_05430, CIG67_22815, CLG78_001649, CQ842_08915, CQ842_12490, CR538_22700, CTR35_001468, CV628_004970, CV83915_01779, CWS33_03955, D3C88_12940, D3G36_17310, D4M65_07255, D4N09_04845, D9D43_13600, D9E49_11435, D9J61_12555, DAH27_26520, DIV22_16805, DNQ45_09630, DNX30_17140, DS732_03300, DTL43_02750, DU321_18175, E2865_05519, E5H86_07990, E6D34_03380, EAI46_26260, ECs5222, EF082_09955, EIA08_16955, EIZ93_20760, EN85_001335, EPS76_30055, EPS97_17825, EWK56_08300, ExPECSC038_04763, F7F11_04770, F7G01_01060, F7N46_16830, F9413_07035, F9B07_19120, FEH53_07480, FGAF1022_42670, FIJ20_18930, FJQ40_01260, FKO60_19415, FOI11_014380, FOI11_21300, FPI65_26085, FPS11_22335, FVB16_24685, FZU14_19575, G3V95_10555, G3W53_08345, G4A38_03455, G4A47_10535, G5603_09990, G6Z99_20225, GAI89_04005, GAJ12_10370, GKF66_08525, GNW61_17465, GNZ05_12485, GOP25_13765, GP965_09375, GP979_09965, GQE86_05410, GQM04_23140, GQM13_11160, GQM21_13835, GQN24_22415, GRC73_06815, GRW05_26905, GRW24_19535, GTP92_08545, GUC01_09445, HEP34_001710, HHH44_002259, HI055_001287, HI084_001705, HIA71_17170, HID72_003759, HIE29_003970, HJ488_000368, HJS37_003257, HKA49_000761, HLX92_11970, HLZ39_13930, HLZ50_15085, HND12_14900, HV209_29455, HVV39_15605, HVW04_12090, HVW43_13615, HVW90_11235, HVY77_22735, I6H00_15800, I6H02_17085, IFN33_000225, IG021_000549, IH772_04275, J0541_002249, J5U05_001302, J8F57_000038, KQO22_002766, NCTC10082_01748, NCTC10089_04451, NCTC10764_04395, NCTC10767_00303, NCTC10865_05523, NCTC10974_05016, NCTC11112_02870, NCTC11181_01680, NCTC11341_03161, NCTC13148_04788, NCTC7922_05337, NCTC7928_04108, NCTC8179_04755, NCTC8500_04950, NCTC8621_04481, NCTC8959_04205, NCTC8960_01943, NCTC8985_03619, NCTC9001_04952, NCTC9044_02747, NCTC9045_05133, NCTC9073_03832, NCTC9081_01672, NCTC9117_05502, NCTC9702_05190, NCTC9703_03794, OFN31_17640, OGM49_02125, P6223_000603, QDW62_23130, R8G00_26825, R8O40_003191, RZR61_03900, SAMEA3472044_01445, SAMEA3472112_04514, SAMEA3752557_01748, TUM18780_38870
発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: C3SF53, aspartate carbamoyltransferase
#2: タンパク質
Aspartate carbamoyltransferase regulatory chain


分子量: 17143.625 Da / 分子数: 6 / 由来タイプ: 組換発現 / 由来: (組換発現) Escherichia coli (大腸菌)
遺伝子: pyrI, A2J79_003078, A5U30_000934, ABE91_001630, ABT96_002052, ACN81_01165, ACU57_15645, ACW72_001369, ATM34_004869, AWP47_22675, B6R15_003055, B6R31_000751, BANRA_00251, BANRA_02936, BCB93_ ...遺伝子: pyrI, A2J79_003078, A5U30_000934, ABE91_001630, ABT96_002052, ACN81_01165, ACU57_15645, ACW72_001369, ATM34_004869, AWP47_22675, B6R15_003055, B6R31_000751, BANRA_00251, BANRA_02936, BCB93_002761, BE932_21745, BG944_000741, BGM66_001591, BGZ_01519, BGZ_05216, BJI68_10435, BK300_13465, BK383_13475, BKL28_003430, BMT50_05825, BRV02_003862, BTB68_002686, BTQ06_18965, BvCmsKKP061_03433, BvCmsNSP007_04795, BVE17_001555, BXT93_08875, C0P57_000164, C1Q91_004308, C2M16_07710, C2R31_000938, C3F40_13760, C4M78_05245, C7B02_12530, C9160_23135, CF22_004478, CG704_05435, CIG67_22820, CLG78_001650, CQ842_08920, CQ842_12485, CR538_22705, CTR35_001469, CV628_004971, CV83915_01780, CWS33_03950, D3C88_12935, D3G36_17315, D4M65_07260, D4N09_04840, D9D43_13595, D9E49_11440, D9J61_12550, DAH27_26525, DD762_15800, DIV22_16800, DL738_14650, DL968_06885, DNQ45_09635, DNX30_17145, DS732_03295, DTL43_02745, DU321_18180, E0I52_01830, E2865_05518, E4K51_15130, E5H86_07995, E6D34_03385, EAI46_26265, ECs5221, EF082_09960, EIA08_16950, EN85_001336, EPS97_17820, EWK56_08305, ExPECSC038_04762, F7G01_01055, F7N46_16835, F9413_07040, F9461_17650, F9B07_19115, FGAF1022_42660, FGAF848_40920, FIJ20_18925, FJQ40_01265, FKO60_19420, FOI11_014385, FOI11_21295, FPI65_26080, FPS11_22330, FTV93_15585, FWK02_19125, FZU14_19580, G3V95_10560, G3W53_08350, G4A38_03450, G4A47_10540, G5603_09985, GAI89_04010, GAJ12_10375, GNW61_17470, GOP25_13770, GP711_18320, GP954_15650, GP965_09380, GP979_09970, GQA06_14590, GQE86_05415, GQM04_23145, GQM13_11155, GQN24_22420, GQN34_01855, GRC73_06810, GRW05_26910, GRW24_19530, GUC01_09440, H0O72_05310, HEP30_009870, HEP34_001711, HHH44_002260, HI084_001706, HIA71_17175, HID72_003760, HIE29_003971, HJ488_000369, HJQ60_002439, HJS37_003258, HKA49_000762, HLZ39_13925, HLZ50_15090, HMV95_06310, HV109_21095, HV209_29450, HVV39_15600, HVW43_13620, HVW90_11240, HVY77_22740, I6H00_15805, I6H02_17080, IFC14_000343, IG021_000550, J0541_002250, J8F57_000039, JNP96_03410, KTF03_003069, NCTC10082_01749, NCTC10089_04452, NCTC10418_06552, NCTC10429_04598, NCTC10764_04396, NCTC10767_00304, NCTC10865_05524, NCTC10974_05017, NCTC11112_02869, NCTC11126_02378, NCTC11181_01681, NCTC11341_03160, NCTC13148_04787, NCTC7922_05338, NCTC7927_04891, NCTC8009_07825, NCTC8179_04754, NCTC8621_04480, NCTC8622_02187, NCTC8959_04206, NCTC8960_01944, NCTC8985_03620, NCTC9045_05134, NCTC9073_03833, NCTC9077_05555, NCTC9081_01671, NCTC9117_05503, NCTC9702_05191, NCTC9703_03795, NCTC9706_01714, NCTC9962_01701, OFN31_17645, OGM49_02120, P6223_000604, PWL68_003651, QDW62_23135, R8G00_26830, R8O40_003192, RZR61_03905, SAMEA3472044_01446, SAMEA3472112_04513, SAMEA3752557_01747, TUM18780_38880
発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: C3SF57

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非ポリマー , 5種, 36分子

#3: 化合物
ChemComp-CP / PHOSPHORIC ACID MONO(FORMAMIDE)ESTER


分子量: 141.020 Da / 分子数: 6 / 由来タイプ: 合成 / 式: CH4NO5P
#4: 化合物
ChemComp-SIN / SUCCINIC ACID


分子量: 118.088 Da / 分子数: 6 / 由来タイプ: 合成 / 式: C4H6O4
#5: 化合物
ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 6 / 由来タイプ: 合成 / 式: Zn
#6: 化合物
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


分子量: 507.181 Da / 分子数: 12 / 由来タイプ: 合成 / 式: C10H16N5O13P3 / コメント: ATP, エネルギー貯蔵分子*YM
#7: 化合物
ChemComp-MG / MAGNESIUM ION


分子量: 24.305 Da / 分子数: 6 / 由来タイプ: 合成 / 式: Mg

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詳細

研究の焦点であるリガンドがあるかN
Has protein modificationN

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実験情報

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実験

実験手法: 電子顕微鏡法
EM実験試料の集合状態: PARTICLE / ３次元再構成法: 単粒子再構成法

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試料調製

構成要素名称: E. coli aspartate transcarbamoylase isolated at a neutral pH and complexed with CP, succinate, ATP, and Mg2+
タイプ: COMPLEX / Entity ID: #2, #1 / 由来: RECOMBINANT
由来(天然)生物種: Escherichia coli (大腸菌)
由来(組換発現)生物種: Escherichia coli (大腸菌)
緩衝液pH: 7.5
緩衝液成分
ID濃度名称式Buffer-ID
140 mMTris(hydroxymethyl)aminomethane hydrochlorideC4H11NO31
215 mMMagnesium chlorideMgCl21
31 mMTris(2-carboxyethyl)phosphineC9H15O6P1
試料包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES
試料支持詳細: Grids were manually coated in graphene-oxide following glow-discharge as is described in the associated publication.
グリッドのタイプ: Quantifoil R1.2/1.3
急速凍結凍結剤: ETHANE

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電子顕微鏡撮影

実験機器
モデル: Titan Krios / 画像提供: FEI Company
顕微鏡モデル: TFS KRIOS
電子銃電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM
電子レンズモード: BRIGHT FIELD / 最大 デフォーカス（公称値）: 2300 nm / 最小 デフォーカス（公称値）: 800 nm
撮影電子線照射量: 52.47 e/Å2
フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k)

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解析

EMソフトウェア名称: PHENIX / バージョン: 1.21.1_5286 / カテゴリ: モデル精密化
CTF補正タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION
対称性点対称性: C1 (非対称)
3次元再構成解像度: 3.08 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 934000 / 対称性のタイプ: POINT
精密化交差検証法: NONE
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
原子変位パラメータBiso mean: 63.33 Å2
拘束条件
Refine-IDタイプDev ideal数
ELECTRON MICROSCOPYf_bond_d0.002122110
ELECTRON MICROSCOPYf_angle_d0.497430066
ELECTRON MICROSCOPYf_chiral_restr0.04063462
ELECTRON MICROSCOPYf_plane_restr0.00333912
ELECTRON MICROSCOPYf_dihedral_angle_d5.81733256
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2KKELECTRON MICROSCOPYNCS constraints1.39584122688E-12
ens_1d_3KKELECTRON MICROSCOPYNCS constraints1.05055965653E-11
ens_1d_4KKELECTRON MICROSCOPYNCS constraints3.48751321314E-13
ens_1d_5KKELECTRON MICROSCOPYNCS constraints2.90138729466E-13
ens_1d_6KKELECTRON MICROSCOPYNCS constraints5.68630707369E-13
ens_2d_2BBELECTRON MICROSCOPYNCS constraints2.50776642909E-13
ens_2d_3BBELECTRON MICROSCOPYNCS constraints3.11720943518E-13
ens_2d_4BBELECTRON MICROSCOPYNCS constraints2.82254765553E-13
ens_2d_5BBELECTRON MICROSCOPYNCS constraints8.21984366258E-13
ens_2d_6BBELECTRON MICROSCOPYNCS constraints4.75459707773E-13
ens_3d_2DDELECTRON MICROSCOPYNCS constraints5.30682626757E-13
ens_3d_3DDELECTRON MICROSCOPYNCS constraints2.12799008021E-13
ens_3d_4DDELECTRON MICROSCOPYNCS constraints5.58645709825E-13
ens_3d_5DDELECTRON MICROSCOPYNCS constraints2.19863919382E-13
ens_3d_6DDELECTRON MICROSCOPYNCS constraints1.8046797439E-13
ens_4d_2HHELECTRON MICROSCOPYNCS constraints2.2406139969E-13
ens_4d_3HHELECTRON MICROSCOPYNCS constraints6.98414424236E-13
ens_4d_4HHELECTRON MICROSCOPYNCS constraints2.53871109405E-13
ens_4d_5HHELECTRON MICROSCOPYNCS constraints1.53302785651E-13
ens_4d_6HHELECTRON MICROSCOPYNCS constraints5.54519522577E-12

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万見について

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お知らせ

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2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

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