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

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Basic information

Entry
Database: PDB / ID: 9eeu
TitleCryo-EM model of E. coli aspartate transcarbamoylase in the T-state complexed with CP, ATP, and Mg2+
Components
  • Aspartate carbamoyltransferase
  • Aspartate carbamoyltransferase regulatory chain
KeywordsCYTOSOLIC PROTEIN / Complex / Allostery / ATCase / T-state / R-state / ATP
Function / homology
Function and homology information


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
Similarity search - Function
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
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / PHOSPHORIC ACID MONO(FORMAMIDE)ESTER / Aspartate carbamoyltransferase / Aspartate carbamoyltransferase regulatory chain
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.27 Å
AuthorsPatterson, M.G. / Miller, R.C. / Ando, N.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM124847 United States
National Science Foundation (NSF, United States)DMR-1719875 United States
Other governmentU24 GM129539
Simons FoundationSF349247 United States
Citation
Journal: Nat Commun / Year: 2026
Title: Cooperativity in E. coli aspartate transcarbamoylase is tuned by allosteric breathing.
Authors: Robert C Miller / Michael G Patterson / Neti Bhatt / Xiaokun Pei / Nozomi Ando /
Abstract: 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: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: 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 ...Authors: 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 /
Abstract: 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.
History
DepositionNov 19, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: Aspartate carbamoyltransferase regulatory chain
E: Aspartate carbamoyltransferase regulatory chain
H: Aspartate carbamoyltransferase regulatory chain
I: Aspartate carbamoyltransferase regulatory chain
J: Aspartate carbamoyltransferase regulatory chain
L: Aspartate carbamoyltransferase regulatory chain
A: Aspartate carbamoyltransferase
K: Aspartate carbamoyltransferase
B: Aspartate carbamoyltransferase
C: Aspartate carbamoyltransferase
F: Aspartate carbamoyltransferase
G: Aspartate carbamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)316,35542
Polymers308,88412
Non-polymers7,47130
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1(chain "B" and (resid 1 through 134 or resid 293 through 310 or resid 401))
d_2ens_1(chain "G" and (resid 1 through 134 or resid 293 through 310 or resid 401))
d_3ens_1(chain "K" and (resid 1 through 134 or resid 293 through 310 or resid 401))
d_4ens_1(chain "A" and (resid 1 through 134 or resid 293 through 310 or resid 401))
d_5ens_1(chain "F" and (resid 1 through 134 or resid 293 through 310 or resid 401))
d_6ens_1(chain "C" and (resid 1 through 134 or resid 293 through 310 or resid 401))
d_1ens_2(chain "F" and resid 137 through 291)
d_2ens_2(chain "G" and resid 137 through 291)
d_3ens_2(chain "K" and resid 137 through 291)
d_4ens_2(chain "A" and resid 137 through 291)
d_5ens_2(chain "C" and resid 137 through 291)
d_6ens_2(chain "B" and resid 137 through 291)
d_1ens_3(chain "E" and (resid 13 through 153 or resid 201))
d_2ens_3(chain "H" and (resid 13 through 153 or resid 201))
d_3ens_3(chain "J" and (resid 13 through 153 or resid 201))
d_4ens_3(chain "I" and (resid 13 through 153 or resid 201))
d_5ens_3(chain "D" and (resid 13 through 153 or resid 201))
d_6ens_3(chain "L" and (resid 13 through 153 or resid 201))
d_1ens_4(chain "E" and (resid 6 through 12 or resid 202 through 204))
d_2ens_4(chain "H" and (resid 6 through 12 or resid 202 through 204))
d_3ens_4(chain "J" and (resid 6 through 12 or resid 202 through 204))
d_1ens_5(chain "D" and (resid 6 through 12 or resid 202 through 204))
d_2ens_5(chain "I" and (resid 6 through 12 or resid 202 through 204))
d_3ens_5(chain "L" and (resid 6 through 12 or resid 202 through 204))

NCS domain segments:
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_1ALAALAHISHISBI1 - 1341 - 134
d_12ens_1ILEILELEULEUBI293 - 310293 - 310
d_13ens_1CPCPCPCPBMA401
d_21ens_1ALAALAHISHISGL1 - 1341 - 134
d_22ens_1ILEILELEULEUGL293 - 310293 - 310
d_23ens_1CPCPCPCPGPA401
d_31ens_1ALAALAHISHISKH1 - 1341 - 134
d_32ens_1ILEILELEULEUKH293 - 310293 - 310
d_33ens_1CPCPCPCPKLA401
d_41ens_1ALAALAHISHISAG1 - 1341 - 134
d_42ens_1ILEILELEULEUAG293 - 310293 - 310
d_43ens_1CPCPCPCPAKA401
d_51ens_1ALAALAHISHISFK1 - 1341 - 134
d_52ens_1ILEILELEULEUFK293 - 310293 - 310
d_53ens_1CPCPCPCPFOA401
d_61ens_1ALAALAHISHISCJ1 - 1341 - 134
d_62ens_1ILEILELEULEUCJ293 - 310293 - 310
d_63ens_1CPCPCPCPCNA401
d_11ens_2GLNGLNASNASNFK137 - 291137 - 291
d_21ens_2GLNGLNASNASNGL137 - 291137 - 291
d_31ens_2GLNGLNASNASNKH137 - 291137 - 291
d_41ens_2GLNGLNASNASNAG137 - 291137 - 291
d_51ens_2GLNGLNASNASNCJ137 - 291137 - 291
d_61ens_2GLNGLNASNASNBI137 - 291137 - 291
d_11ens_3LYSLYSASNASNEB13 - 15313 - 153
d_21ens_3LYSLYSASNASNHC13 - 15313 - 153
d_31ens_3LYSLYSASNASNJE13 - 15313 - 153
d_41ens_3LYSLYSASNASNID13 - 15313 - 153
d_51ens_3LYSLYSASNASNDA13 - 15313 - 153
d_61ens_3LYSLYSASNASNLF13 - 15313 - 153
d_11ens_4LYSLYSILEILEEB6 - 126 - 12
d_12ens_4ATPATPATPATPER202
d_13ens_4ATPATPATPATPES203
d_21ens_4LYSLYSILEILEHC6 - 126 - 12
d_22ens_4ATPATPATPATPHV202
d_23ens_4ATPATPATPATPHW203
d_31ens_4LYSLYSILEILEJE6 - 126 - 12
d_32ens_4ATPATPATPATPJDA202
d_33ens_4ATPATPATPATPJEA203
d_11ens_5LYSLYSILEILEDA6 - 126 - 12
d_12ens_5ATPATPATPATPDN202
d_13ens_5ATPATPATPATPDO203
d_21ens_5LYSLYSILEILEID6 - 126 - 12
d_22ens_5ATPATPATPATPIZ202
d_23ens_5ATPATPATPATPIAA203
d_31ens_5LYSLYSILEILELF6 - 126 - 12
d_32ens_5ATPATPATPATPLHA202
d_33ens_5ATPATPATPATPLIA203

NCS ensembles :
ID
ens_1
ens_2
ens_3
ens_4
ens_5

NCS oper:
IDCodeMatrixVector
1given(0.803713018316, -0.595016524451, 0.000848422036713), (-0.595017096748, -0.803711685455, 0.00147690235867), (-0.000196894603304, -0.00169183126954, -0.999998549469)117.494764922, 356.385966261, 297.090974035
2given(-0.917262802964, -0.398281876229, 0.000705242225073), (-0.398282499593, 0.917261489637, -0.00155246467334), (-2.85729910489E-5, -0.00170490373399, -0.999998546242)344.153338905, 71.7950630427, 297.067533974
3given(-0.500493970436, 0.865735517519, -0.00279271605056), (-0.865739853071, -0.500489254068, 0.00223905502735), (0.00054070508989, 0.00353839912394, 0.999993593664)94.8606072426, 351.439772319, -0.656666060751
4given(-0.50055605677, -0.865703901887, 0.000623127084588), (0.865704087254, -0.500556120377, 6.05365083828E-5), (0.000259503384449, 0.000569745579933, 0.999999804024)351.728146078, 94.3998637261, -0.144337987804
5given(0.113639425176, 0.993521135384, -0.00135447047686), (0.993522058478, -0.113639345706, 0.000135739086239), (-1.90614876931E-5, -0.00136112160806, -0.999999073492)-15.6947852488, 17.8316166267, 297.011583613
6given(0.112800018132, 0.993617446705, 0.000724922992646), (0.99361726565, -0.112800628414, 0.000864657100855), (0.000940910149948, 0.000622762665106, -0.999999363427)-15.9799640998, 17.5509195202, 296.556858082
7given(0.803925403972, -0.594730109964, 0.000202857594514), (-0.594729568748, -0.803925053496, -0.0011173264788), (0.000827590002126, 0.000777601731138, -0.999999355215)117.537297275, 356.861679893, 296.54987423
8given(-0.498926526477, -0.866640968174, -0.00239863687912), (0.866640378095, -0.498930678196, 0.00162277837815), (-0.00260311974962, -0.00126910839238, 0.999995806557)352.157654986, 93.7361981624, 0.548195630024
9given(-0.916983958902, -0.398923349759, -0.000761664865561), (-0.398923670985, 0.916984078146, 0.000324276008591), (0.000569073283009, 0.000601202042365, -0.999999657356)344.491087723, 71.5843832746, 296.611780725
10given(-0.500539887054, 0.86571342777, 0.000287136266204), (-0.865713223029, -0.500539966863, 0.00059753268322), (0.000661015244566, 5.05112793054E-5, 0.999999780254)94.3294291227, 351.738908712, -0.0845555440802
11given(-0.499700478513, 0.866198260037, -7.79889980817E-5), (-0.866198190689, -0.499700471385, -0.000365163589061), (-0.000355275204578, -0.000114918491157, 0.999999930287)94.1953819679, 351.804708284, 0.0773050483041
12given(-0.499965605762, -0.866045131556, -0.000472402711127), (0.866045081797, -0.49996577859, 0.000369504289822), (-0.000556192580566, -0.000224382608507, 0.999999820151)351.855720927, 94.1898723101, 0.127879017788
13given(-0.917903029659, -0.396801761911, -0.00154592562511), (-0.396802774716, 0.917903805528, 0.000402212516333), (0.00125941237921, 0.000982619664856, -0.999998724169)344.350537749, 71.1344298786, 296.407267491
14given(0.115398649913, 0.993318581699, 0.00116053818853), (0.993318140104, -0.115400195222, 0.00136655859677), (0.00149135438068, 0.00099508461786, -0.999998392833)-16.3354924422, 17.9754442016, 296.370324488
15given(0.802561560141, -0.596568997673, 0.000610900049789), (-0.59656718567, -0.802561013956, -0.00184712201653), (0.00159222029337, 0.00111798620393, -0.999998107469)117.982046038, 356.958224118, 296.331405492
16given(-0.499677417935, 0.866211560842, -9.93392166806E-5), (-0.866211517123, -0.499677424881, -0.000280478309606), (-0.000292591118327, -5.409990394E-5, 0.999999955732)94.192218525, 351.788103447, 0.0553596106191
17given(-0.499996850453, -0.866027133033, -0.00039292072976), (0.866027071939, -0.499996979497, 0.000362164121383), (-0.000510103133791, -0.00015919906906, 0.999999857225)351.843892217, 94.2007090522, 0.107348532537
18given(-0.50010744476, -0.865963344705, -0.000171238830945), (0.865963358453, -0.500107450098, -1.31526146457E-5), (-7.42481329314E-5, -0.000154864273645, 0.999999985252)351.809939308, 94.2919017736, 0.0381530918076
19given(-0.499879078948, 0.866095206305, -6.7520141137E-6), (-0.866095155567, -0.499879046965, 0.000346279650848), (0.00029653595526, 0.000178945839639, 0.999999940022)94.2232156717, 351.723422473, -0.0860157397433

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Components

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Protein , 2 types, 12 molecules DEHIJLAKBCFG

#1: Protein
Aspartate carbamoyltransferase regulatory chain


Mass: 17143.625 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: 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_ ...Gene: 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
Production host: Escherichia coli (E. coli) / References: UniProt: C3SF57
#2: Protein
Aspartate carbamoyltransferase / Aspartate transcarbamylase / ATCase


Mass: 34337.105 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: 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_ ...Gene: 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
Production host: Escherichia coli (E. coli) / References: UniProt: C3SF53, aspartate carbamoyltransferase

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Non-polymers , 4 types, 30 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-CP / PHOSPHORIC ACID MONO(FORMAMIDE)ESTER


Mass: 141.020 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CH4NO5P

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Details

Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: E. coli aspartate transcarbamoylase complexed with CP, ATP, and Mg2+ at a neutral pH
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
140 mMTris(hydroxymethyl)aminomethane hydrochlorideC4H11NO31
215 mMMagnesium chlorideMgCl21
31 mMTris(2-carboxyethyl)phosphineC9H15O6P1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: E. coli aspartate transcarbamoylase complexed with CP, ATP, and Mg2+ at a neutral pH
Specimen supportDetails: Grids were manually coated in graphene-oxide as is described in the associated publication.
Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2300 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 63.45 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
2PHENIX1.21.1_5286model refinement
3Leginonimage acquisition
10cryoSPARC4initial Euler assignment
11RELION4final Euler assignment
13RELION43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 207000 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 67.74 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.001722242
ELECTRON MICROSCOPYf_angle_d0.425530258
ELECTRON MICROSCOPYf_chiral_restr0.04053498
ELECTRON MICROSCOPYf_plane_restr0.00273930
ELECTRON MICROSCOPYf_dihedral_angle_d6.25323264
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2IBELECTRON MICROSCOPYNCS constraints4.29794068565E-11
ens_1d_3IBELECTRON MICROSCOPYNCS constraints9.05083487125E-12
ens_1d_4IBELECTRON MICROSCOPYNCS constraints4.65892066377E-13
ens_1d_5IBELECTRON MICROSCOPYNCS constraints5.27913729473E-11
ens_1d_6IBELECTRON MICROSCOPYNCS constraints2.30025045153E-13
ens_2d_2KFELECTRON MICROSCOPYNCS constraints6.04927884066E-12
ens_2d_3KFELECTRON MICROSCOPYNCS constraints2.92731224833E-11
ens_2d_4KFELECTRON MICROSCOPYNCS constraints1.83357242467E-11
ens_2d_5KFELECTRON MICROSCOPYNCS constraints1.84505711391E-13
ens_2d_6KFELECTRON MICROSCOPYNCS constraints3.97895765723E-13
ens_3d_2BEELECTRON MICROSCOPYNCS constraints4.51967108889E-13
ens_3d_3BEELECTRON MICROSCOPYNCS constraints6.14977775019E-13
ens_3d_4BEELECTRON MICROSCOPYNCS constraints2.95359650234E-13
ens_3d_5BEELECTRON MICROSCOPYNCS constraints6.88387091259E-12
ens_3d_6BEELECTRON MICROSCOPYNCS constraints2.73334214241E-13
ens_4d_2BEELECTRON MICROSCOPYNCS constraints1.9822942639E-13
ens_4d_3BEELECTRON MICROSCOPYNCS constraints7.96970106138E-13
ens_5d_2ADELECTRON MICROSCOPYNCS constraints8.05868173074E-14
ens_5d_3ADELECTRON MICROSCOPYNCS constraints5.94889509981E-11

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