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

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Basic information

Entry
Database: PDB / ID: 9eer
TitleCryo-EM model of E. coli aspartate transcarbamoylase in the R-state complexed with CP, succinate, ATP, GTP, and Mg2+
Components
  • Aspartate carbamoyltransferase
  • Aspartate carbamoyltransferase regulatory chain
KeywordsCYTOSOLIC PROTEIN / Complex / Allostery / ATCase / T-state / R-state / ATP / GTP
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 / GUANOSINE-5'-TRIPHOSPHATE / SUCCINIC ACID / Aspartate carbamoyltransferase / Aspartate carbamoyltransferase regulatory chain
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.26 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
Revision 1.1May 27, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation_author.identifier_ORCID / _em_admin.last_update
Revision 1.1May 27, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin / Data content type: EM metadata / EM metadata / EM metadata
Item: _citation.journal_volume / _citation_author.identifier_ORCID / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)317,15948
Polymers308,88412
Non-polymers8,27536
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 "C" 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 "B" and (resid 1 through 134 or resid 293 through 310 or resid 401))
d_1ens_2(chain "F" 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 "C" and (resid 137 through 291 or resid 402))
d_6ens_2(chain "B" and (resid 137 through 291 or resid 402))
d_1ens_3(chain "D" and (resid 101 through 153 or resid 201))
d_2ens_3(chain "H" and (resid 101 through 153 or resid 201))
d_3ens_3(chain "E" and (resid 101 through 153 or resid 201))
d_4ens_3(chain "I" and (resid 101 through 153 or resid 201))
d_5ens_3(chain "L" and (resid 101 through 153 or resid 201))
d_6ens_3(chain "J" and (resid 101 through 153 or resid 201))
d_1ens_4(chain "J" and resid 13 through 95)
d_2ens_4(chain "H" and resid 13 through 95)
d_3ens_4(chain "E" and resid 13 through 95)
d_4ens_4(chain "I" and resid 13 through 95)
d_5ens_4(chain "L" and resid 13 through 95)
d_6ens_4(chain "D" and resid 13 through 95)

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_1ALAALAHISHISCC1 - 1341 - 134
d_12ens_1ILEILELEULEUCC293 - 310293 - 310
d_13ens_1CPCPCPCPCQ401
d_21ens_1ALAALAHISHISGG1 - 1341 - 134
d_22ens_1ILEILELEULEUGG293 - 310293 - 310
d_23ens_1CPCPCPCPGCA401
d_31ens_1ALAALAHISHISKK1 - 1341 - 134
d_32ens_1ILEILELEULEUKK293 - 310293 - 310
d_33ens_1CPCPCPCPKQA401
d_41ens_1ALAALAHISHISAA1 - 1341 - 134
d_42ens_1ILEILELEULEUAA293 - 310293 - 310
d_43ens_1CPCPCPCPAM401
d_51ens_1ALAALAHISHISFF1 - 1341 - 134
d_52ens_1ILEILELEULEUFF293 - 310293 - 310
d_53ens_1CPCPCPCPFAA401
d_61ens_1ALAALAHISHISBB1 - 1341 - 134
d_62ens_1ILEILELEULEUBB293 - 310293 - 310
d_63ens_1CPCPCPCPBO401
d_11ens_2GLNGLNASNASNFF137 - 291137 - 291
d_12ens_2SINSINSINSINFBA402
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_2GLNGLNASNASNCC137 - 291137 - 291
d_52ens_2SINSINSINSINCR402
d_61ens_2GLNGLNASNASNBB137 - 291137 - 291
d_62ens_2SINSINSINSINBP402
d_11ens_3GLUGLUASNASNDD101 - 153101 - 153
d_21ens_3GLUGLUASNASNHH101 - 153101 - 153
d_31ens_3GLUGLUASNASNEE101 - 153101 - 153
d_41ens_3GLUGLUASNASNII101 - 153101 - 153
d_51ens_3GLUGLUASNASNLL101 - 153101 - 153
d_61ens_3GLUGLUASNASNJJ101 - 153101 - 153
d_11ens_4LYSLYSSERSERJJ13 - 9513 - 95
d_21ens_4LYSLYSSERSERHH13 - 9513 - 95
d_31ens_4LYSLYSSERSEREE13 - 9513 - 95
d_41ens_4LYSLYSSERSERII13 - 9513 - 95
d_51ens_4LYSLYSSERSERLL13 - 9513 - 95
d_61ens_4LYSLYSSERSERDD13 - 9513 - 95

NCS ensembles :
ID
ens_1
ens_2
ens_3
ens_4

NCS oper:
IDCodeMatrixVector
1given(0.942690957266, 0.329856575511, 0.0502831848771), (0.115413887595, -0.463745009181, 0.878419148818), (0.313070908325, -0.822274410432, -0.475238256361)-50.2028406423, 74.0043061579, 307.926194979
2given(0.942249808169, 0.119975417498, 0.312683863034), (0.331490707843, -0.467183974137, -0.819666422957), (0.0477410684779, 0.875982324882, -0.47997474608)-57.9066177285, 303.65579815, 85.1750165366
3given(-0.921157823022, -0.333766716864, -0.200170037215), (-0.334429071089, 0.415761606149, 0.84575379589), (-0.199061451554, 0.846015405041, -0.494603349097)376.074468056, 13.5301182657, 128.588818952
4given(-0.988060377754, -0.131785685552, 0.0798074119115), (-0.136626164158, 0.510088153921, -0.849201605331), (0.0712038003194, -0.849966239514, -0.522003266759)311.704322607, 230.129910169, 355.273009683
5given(-0.971307118111, 0.0174784421785, -0.237185552608), (-0.00354163025515, -0.99824824324, -0.0590584602169), (-0.237802311095, -0.0565238792642, 0.969667526481)335.104262569, 322.035924453, 48.7207672118
6given(-0.970208115761, -0.00726898964055, -0.242163940132), (0.0213337200145, -0.998230304331, -0.0555079445317), (-0.241331896982, -0.0590205159703, 0.96864621725)339.325490731, 317.424786827, 52.0702489768
7given(-0.920140968376, -0.334748691653, -0.203184427927), (-0.337493252138, 0.414778954016, 0.845018771428), (-0.19859230367, 0.846109764003, -0.494630533006)377.429948549, 11.8668498806, 127.99370344
8given(0.935644117822, 0.131421106194, 0.327564615963), (0.350030593956, -0.464535660786, -0.813440350089), (0.0452622146948, 0.875748315845, -0.480641466393)-61.516685594, 301.956192728, 82.8673013701
9given(-0.988303958916, -0.138184962449, 0.0644996197189), (-0.126617393003, 0.507847922296, -0.852090678044), (0.0849901204853, -0.850291364164, -0.51940473183)315.816545073, 225.60203432, 354.559428428
10given(0.936812003349, 0.346290462483, 0.0496607085664), (0.123039861806, -0.459035244924, 0.879856713519), (0.327482003763, -0.818150083733, -0.472637258053)-52.5136603463, 75.7547842519, 304.055204655
11given(-0.927144810089, -0.323629559163, -0.18885552563), (-0.318112091489, 0.413490355366, 0.853129781022), (-0.198008076536, 0.851052075055, -0.486315912933)373.976167062, 10.6751312904, 126.44987107
12given(-0.971726967163, 0.0149043343426, -0.235636504187), (0.00148234594954, -0.997600832272, -0.0692125862872), (-0.236102740217, -0.06760503138, 0.969373537804)335.384384245, 322.69052612, 50.0226295869
13given(0.944760368041, 0.117515430046, 0.305970538907), (0.324672699656, -0.463406147253, -0.824525548898), (0.0448941541451, 0.878319341919, -0.475961814156)-56.7919670359, 304.589365829, 84.5206097338
14given(0.945867806615, 0.321155808658, 0.0468298940242), (0.12310089613, -0.488517101765, 0.863827072194), (0.300300286016, -0.811301416151, -0.501607167383)-49.0927325114, 78.5266646008, 311.965441823
15given(-0.987166608524, -0.132067151194, 0.0897794775564), (-0.146372887085, 0.523501358105, -0.839357674647), (0.0638518984928, -0.841727150351, -0.536114110448)310.28412884, 228.019117264, 357.351552868
16given(0.939409466306, 0.161578052039, 0.302328278058), (0.342768285075, -0.431319308723, -0.834549912629), (-0.00444492531221, 0.887612633428, -0.460569273419)-62.0953444626, 301.701056126, 85.1921369967
17given(0.936496908326, 0.349937278051, -0.022747354264), (0.185355354808, -0.438892747927, 0.879213596494), (0.297685963962, -0.827597158796, -0.475884449854)-37.4926493338, 61.4916809915, 310.92642007
18given(-0.912988567387, -0.345936572913, -0.216286299476), (-0.351401060218, 0.397419085031, 0.847688247961), (-0.207290064156, 0.849932914043, -0.484401559585)380.915056273, 16.4796299932, 126.729556106
19given(-0.980152161731, -0.0082806964603, -0.198073647717), (0.0147258616052, -0.999408155568, -0.0310883834393), (-0.197698985465, -0.0333881513567, 0.979694004521)331.917087959, 314.19254461, 38.5014908307
20given(-0.975799106285, -0.188011649329, 0.111658962429), (-0.190302958684, 0.478641807422, -0.857138730955), (0.107707418919, -0.857644238542, -0.502837421048)311.843020565, 242.94196972, 348.159349446

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Components

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Protein , 2 types, 12 molecules ABCFGKDEHIJL

#1: 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
#2: 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

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Non-polymers , 6 types, 36 molecules

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


Mass: 141.020 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CH4NO5P
#4: Chemical
ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H6O4
#5: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 507.181 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#7: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#8: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg

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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 isolated at a neutral pH complexed with CP, succinate, ATP, GTP and Mg2+
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
11 mMTris(2-carboxyethyl)phosphineC9H15O6P1
215 mMMagnesium ChlorideMgCl21
340 mMtris(hydroxymethyl)aminomethaneC4H11NO31
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Grids were manually coated in graphene-oxide following glow-discharge 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: 52.47 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
5cryoSPARC4CTF correction
10cryoSPARC4initial Euler assignment
11RELION4final Euler assignment
13RELION43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 865000 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 74.84 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002122410
ELECTRON MICROSCOPYf_angle_d0.470230474
ELECTRON MICROSCOPYf_chiral_restr0.04093510
ELECTRON MICROSCOPYf_plane_restr0.00263972
ELECTRON MICROSCOPYf_dihedral_angle_d4.88293282
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2CCELECTRON MICROSCOPYNCS constraints2.76895368569E-13
ens_1d_3CCELECTRON MICROSCOPYNCS constraints1.00232111445E-10
ens_1d_4CCELECTRON MICROSCOPYNCS constraints2.26468791543E-13
ens_1d_5CCELECTRON MICROSCOPYNCS constraints1.34621982166E-12
ens_1d_6CCELECTRON MICROSCOPYNCS constraints1.62533233597E-11
ens_2d_2FFELECTRON MICROSCOPYNCS constraints5.91221721932E-13
ens_2d_3FFELECTRON MICROSCOPYNCS constraints5.05764355525E-13
ens_2d_4FFELECTRON MICROSCOPYNCS constraints1.84102040227E-11
ens_2d_5FFELECTRON MICROSCOPYNCS constraints9.1601456908E-11
ens_2d_6FFELECTRON MICROSCOPYNCS constraints5.06803652991E-13
ens_3d_2DDELECTRON MICROSCOPYNCS constraints1.87352533782E-13
ens_3d_3DDELECTRON MICROSCOPYNCS constraints1.35627668187E-13
ens_3d_4DDELECTRON MICROSCOPYNCS constraints1.54498898588E-13
ens_3d_5DDELECTRON MICROSCOPYNCS constraints8.04479635616E-12
ens_3d_6DDELECTRON MICROSCOPYNCS constraints2.13215447027E-13
ens_4d_2JJELECTRON MICROSCOPYNCS constraints3.17101387019E-13
ens_4d_3JJELECTRON MICROSCOPYNCS constraints1.3427956216E-12
ens_4d_4JJELECTRON MICROSCOPYNCS constraints1.55373978337E-10
ens_4d_5JJELECTRON MICROSCOPYNCS constraints1.89315681971E-13
ens_4d_6JJELECTRON MICROSCOPYNCS constraints3.96275023458E-13

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