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

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Basic information

Entry
Database: PDB / ID: 9eem
TitleCryo-EM model of E. coli aspartate transcarbamoylase in the R-state complexed with CP, succinate, CTP, UTP, and Mg2+
Components
  • Aspartate carbamoyltransferase
  • Aspartate carbamoyltransferase regulatory chain
KeywordsCYTOSOLIC PROTEIN / Complex / Allostery / ATCase / R-State / CTP / UTP / CP / Succinate
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
PHOSPHORIC ACID MONO(FORMAMIDE)ESTER / CYTIDINE-5'-TRIPHOSPHATE / SUCCINIC ACID / URIDINE 5'-TRIPHOSPHATE / Aspartate carbamoyltransferase / Aspartate carbamoyltransferase regulatory chain
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.05 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
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)316,78148
Polymers308,88412
Non-polymers7,89736
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_1chain "C"
d_2ens_1chain "G"
d_3ens_1chain "K"
d_4ens_1chain "A"
d_5ens_1chain "F"
d_6ens_1chain "B"
d_1ens_2(chain "J" and (resid 104 through 105 or resid 108 through 143 or resid 201))
d_2ens_2(chain "H" and (resid 104 through 105 or resid 108 through 143 or resid 201))
d_3ens_2(chain "E" and (resid 104 through 105 or resid 108 through 143 or resid 201))
d_4ens_2(chain "D" and (resid 104 through 105 or resid 108 through 143 or resid 201))
d_5ens_2(chain "L" and (resid 104 through 105 or resid 108 through 143 or resid 201))
d_6ens_2(chain "I" and (resid 104 through 105 or resid 108 through 143 or resid 201))
d_1ens_3(chain "E" and (resid 7 through 71 or resid 73...
d_2ens_3(chain "L" and (resid 7 through 71 or resid 73...
d_3ens_3(chain "D" and (resid 7 through 71 or resid 73...
d_1ens_4(chain "H" and (resid 7 through 71 or resid 73...
d_2ens_4(chain "J" and (resid 7 through 71 or resid 73...
d_3ens_4(chain "I" and (resid 7 through 71 or resid 73...
d_1ens_5(chain "E" and (resid 146 through 150 or resid 152 through 153))
d_2ens_5(chain "L" and (resid 146 through 150 or resid 152 through 153))
d_3ens_5(chain "D" and (resid 146 through 150 or resid 152 through 153))
d_1ens_6(chain "J" and (resid 146 through 150 or resid 152 through 153))
d_2ens_6(chain "I" and (resid 146 through 150 or resid 152 through 153))
d_3ens_6(chain "H" and (resid 146 through 150 or resid 152 through 153))

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_1ALAALALEULEUCC1 - 3101 - 310
d_12ens_1CPCPCPCPCQ401
d_13ens_1SINSINSINSINCR402
d_21ens_1ALAALALEULEUGG1 - 3101 - 310
d_22ens_1CPCPCPCPGCA401
d_23ens_1SINSINSINSINGDA402
d_31ens_1ALAALALEULEUKK1 - 3101 - 310
d_32ens_1CPCPCPCPKQA401
d_33ens_1SINSINSINSINKRA402
d_41ens_1ALAALALEULEUAA1 - 3101 - 310
d_42ens_1CPCPCPCPAM401
d_43ens_1SINSINSINSINAN402
d_51ens_1ALAALALEULEUFF1 - 3101 - 310
d_52ens_1CPCPCPCPFAA401
d_53ens_1SINSINSINSINFBA402
d_61ens_1ALAALALEULEUBB1 - 3101 - 310
d_62ens_1CPCPCPCPBO401
d_63ens_1SINSINSINSINBP402
d_11ens_2ASPASPASNASNJJ104 - 105104 - 105
d_12ens_2VALVALLYSLYSJJ108 - 143108 - 143
d_21ens_2ASPASPASNASNHH104 - 105104 - 105
d_22ens_2VALVALLYSLYSHH108 - 143108 - 143
d_31ens_2ASPASPASNASNEE104 - 105104 - 105
d_32ens_2VALVALLYSLYSEE108 - 143108 - 143
d_41ens_2ASPASPASNASNDD104 - 105104 - 105
d_42ens_2VALVALLYSLYSDD108 - 143108 - 143
d_51ens_2ASPASPASNASNLL104 - 105104 - 105
d_52ens_2VALVALLYSLYSLL108 - 143108 - 143
d_61ens_2ASPASPASNASNII104 - 105104 - 105
d_62ens_2VALVALLYSLYSII108 - 143108 - 143
d_11ens_3LEULEUVALVALEE7 - 717 - 71
d_12ens_3GLNGLNALAALAEE73 - 7573 - 75
d_13ens_3TYRTYRLYSLYSEE77 - 9477 - 94
d_14ens_3CTPCTPCTPCTPEX202
d_15ens_3UTPUTPUTPUTPEY203
d_21ens_3LEULEUVALVALLL7 - 717 - 71
d_22ens_3GLNGLNALAALALL73 - 7573 - 75
d_23ens_3TYRTYRLYSLYSLL77 - 9477 - 94
d_24ens_3CTPCTPCTPCTPLTA202
d_25ens_3UTPUTPUTPUTPLUA203
d_31ens_3LEULEUVALVALDD7 - 717 - 71
d_32ens_3GLNGLNALAALADD73 - 7573 - 75
d_33ens_3TYRTYRLYSLYSDD77 - 9477 - 94
d_34ens_3CTPCTPCTPCTPDT202
d_35ens_3UTPUTPUTPUTPDU203
d_11ens_4LEULEUVALVALHH7 - 717 - 71
d_12ens_4GLNGLNALAALAHH73 - 7573 - 75
d_13ens_4TYRTYRLYSLYSHH77 - 9477 - 94
d_14ens_4CTPCTPCTPCTPHFA202
d_15ens_4UTPUTPUTPUTPHGA203
d_21ens_4LEULEUVALVALJJ7 - 717 - 71
d_22ens_4GLNGLNALAALAJJ73 - 7573 - 75
d_23ens_4TYRTYRLYSLYSJJ77 - 9477 - 94
d_24ens_4CTPCTPCTPCTPJNA202
d_25ens_4UTPUTPUTPUTPJOA203
d_31ens_4LEULEUVALVALII7 - 717 - 71
d_32ens_4GLNGLNALAALAII73 - 7573 - 75
d_33ens_4TYRTYRLYSLYSII77 - 9477 - 94
d_34ens_4CTPCTPCTPCTPIJA202
d_35ens_4UTPUTPUTPUTPIKA203
d_11ens_5SERSERVALVALEE146 - 150146 - 150
d_12ens_5ALAALAASNASNEE152 - 153152 - 153
d_21ens_5SERSERVALVALLL146 - 150146 - 150
d_22ens_5ALAALAASNASNLL152 - 153152 - 153
d_31ens_5SERSERVALVALDD146 - 150146 - 150
d_32ens_5ALAALAASNASNDD152 - 153152 - 153
d_11ens_6SERSERVALVALJJ146 - 150146 - 150
d_12ens_6ALAALAASNASNJJ152 - 153152 - 153
d_21ens_6SERSERVALVALII146 - 150146 - 150
d_22ens_6ALAALAASNASNII152 - 153152 - 153
d_31ens_6SERSERVALVALHH146 - 150146 - 150
d_32ens_6ALAALAASNASNHH152 - 153152 - 153

NCS ensembles :
ID
ens_1
ens_2
ens_3
ens_4
ens_5
ens_6

NCS oper:
IDCodeMatrixVector
1given(-0.488374076532, 0.859542156453, -0.150592306086), (-0.860904000525, -0.502781246935, -0.077815934163), (-0.14260106329, 0.0916422337715, 0.98552860828)147.758908966, 470.632745006, 12.3996352836
2given(-0.48318248685, -0.86336805492, -0.145362602291), (0.862166019203, -0.498096175668, 0.0925740520693), (-0.152330035557, -0.0805965354614, 0.985037947867)478.896080803, 107.046975961, 47.5954580381
3given(0.889674378288, -0.421580864718, 0.175354142016), (-0.417747554615, -0.906574560096, -0.0600795106478), (0.18429997621, -0.0198025627354, -0.982670533433)70.8393090551, 457.691078285, 347.348035257
4given(-0.819881772279, -0.572486188104, 0.00731053452474), (-0.57112705696, 0.816907694603, -0.0804717547193), (0.0400969362044, -0.0701525689456, -0.996730080201)459.676273598, 157.643950322, 387.368345509
5given(-0.0913758651564, 0.993344746559, 0.0701189400266), (0.993297859738, 0.0859137173835, 0.0773187881807), (0.0707800332529, 0.0767140642183, -0.994537650994)5.207950881, -30.9614280099, 352.622870828
6given(-0.505860136364, -0.856390445808, -0.103445283928), (0.849579620218, -0.515389540127, 0.112196661437), (-0.149398766218, -0.0311291865783, 0.988286892757)473.823246843, 103.095827298, 37.0258506857
7given(-0.479090431635, 0.866181032606, -0.142136473398), (-0.872204128307, -0.487971503735, -0.0338196704037), (-0.0986525056922, 0.107769338389, 0.98926915085)147.954542667, 458.537800367, 0.63740353983
8given(-0.829186866618, -0.556523808131, 0.052253145475), (-0.558891854885, 0.827016308832, -0.0606953002282), (-0.00943582387691, -0.0795316032127, -0.996787685176)447.757382394, 155.386065582, 398.240735267
9given(-0.0882016067095, 0.994063164814, 0.0637095042702), (0.993804377798, 0.0834757030271, 0.0733802812329), (0.0676264389388, 0.0697870429566, -0.995267016128)6.97448489647, -28.3636658196, 354.703921569
10given(0.882259673384, -0.429322708531, 0.1931317702), (-0.431822890483, -0.901419654722, -0.0311704561339), (0.187474958263, -0.0558982828041, -0.980677583105)65.7982353728, 454.925114637, 353.350853473
11given(0.862304214754, -0.500855081458, 0.0746701318796), (-0.501306346581, -0.86515774876, -0.0139289855634), (0.0715778463956, -0.0254215880527, -0.997111004235)111.16604287, 454.584594607, 369.574552574
12given(-0.0542930471049, 0.994928136305, 0.0846774386992), (0.996007513756, 0.0479430008885, 0.0753027304119), (0.0708611147086, 0.0884277798794, -0.993558871013)-3.84433166015, -21.1932439938, 349.571907475
13given(-0.548018511253, 0.834984451202, -0.0497662292664), (-0.828968633586, -0.550092402811, -0.101041342529), (-0.111743974576, -0.014117883034, 0.993636739218)148.800249759, 474.748276946, 22.9134021683
14given(-0.0592356647727, 0.994250626527, 0.089201051953), (0.994073632391, 0.0505927009547, 0.0962184597369), (0.0911523417306, 0.0943719781539, -0.991355224093)-5.80421268401, -27.7926674441, 343.712724223
15given(0.909657894629, -0.289275537339, 0.29806405056), (-0.275737358437, -0.957242360049, -0.0874984187872), (0.310630687315, -0.00259376652887, -0.950527142418)7.83323731417, 448.563175333, 310.087548243
16given(-0.190861924803, 0.976919369973, 0.0959180391385), (0.961264286419, 0.166215487275, 0.219871288359), (0.198853456885, 0.134167642752, -0.9708019089)24.2560128879, -70.8512534646, 309.85880966
17given(0.899278446481, -0.407008916152, 0.160131252002), (-0.408464872338, -0.91242504673, -0.0252385056041), (0.156380061902, -0.0427115472953, -0.98677302353)65.9883730973, 451.909320805, 357.095962974
18given(-0.531620334018, -0.845205632009, -0.0548384908461), (0.82929465279, -0.532588845511, 0.169172989839), (-0.172192332325, 0.0444585341396, 0.984059571078)466.208756878, 97.9281369723, 28.3627110003

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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-CTP / CYTIDINE-5'-TRIPHOSPHATE


Mass: 483.156 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C9H16N3O14P3
#7: Chemical
ChemComp-UTP / URIDINE 5'-TRIPHOSPHATE


Mass: 484.141 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C9H15N2O15P3 / Comment: UTP*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 in the R-state complexed with CP, succinate, CTP, UTP, 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
140 mMTris HydrochlorideTris-HCl1
215 mMMagnesium chlorideMgCl21
31 mMtris(2-carboxyethyl)phosphineTCEP1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: E. coli aspartate transcarbamoylase was isolated in a neutral buffer and complexed with substrate analogs (CP/Succinate) and nucleotides effectors (CTP/UTP) in the presence of a physilogical ...Details: E. coli aspartate transcarbamoylase was isolated in a neutral buffer and complexed with substrate analogs (CP/Succinate) and nucleotides effectors (CTP/UTP) in the presence of a physilogical concentration of Mg2+
Specimen supportDetails: Grid was manually coated in graphene-oxide following glow-dischage 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: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 51.75 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
5cryoSPARC4CTF correction
10cryoSPARC4initial Euler assignment
11RELION4final Euler assignment
13RELION43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 830000 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 69.86 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002322218
ELECTRON MICROSCOPYf_angle_d0.469530204
ELECTRON MICROSCOPYf_chiral_restr0.04153492
ELECTRON MICROSCOPYf_plane_restr0.00383912
ELECTRON MICROSCOPYf_dihedral_angle_d6.20853218
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2CCELECTRON MICROSCOPYNCS constraints5.79324716149E-13
ens_1d_3CCELECTRON MICROSCOPYNCS constraints2.68621415007E-13
ens_1d_4CCELECTRON MICROSCOPYNCS constraints9.11609823541E-11
ens_1d_5CCELECTRON MICROSCOPYNCS constraints5.82674199719E-13
ens_1d_6CCELECTRON MICROSCOPYNCS constraints7.95006184171E-13
ens_2d_2JJELECTRON MICROSCOPYNCS constraints2.2610655064E-13
ens_2d_3JJELECTRON MICROSCOPYNCS constraints1.00308251111E-10
ens_2d_4JJELECTRON MICROSCOPYNCS constraints1.67316522282E-11
ens_2d_5JJELECTRON MICROSCOPYNCS constraints2.66455130934E-12
ens_2d_6JJELECTRON MICROSCOPYNCS constraints2.45766772793E-13
ens_3d_2EEELECTRON MICROSCOPYNCS constraints2.9268760792E-12
ens_3d_3EEELECTRON MICROSCOPYNCS constraints8.6708871063E-12
ens_4d_2HHELECTRON MICROSCOPYNCS constraints1.31088122901E-12
ens_4d_3HHELECTRON MICROSCOPYNCS constraints1.05871289039E-11
ens_5d_2EEELECTRON MICROSCOPYNCS constraints1.28346593181E-11
ens_5d_3EEELECTRON MICROSCOPYNCS constraints2.61313028776E-12
ens_6d_2JJELECTRON MICROSCOPYNCS constraints2.15904967533E-11
ens_6d_3JJELECTRON MICROSCOPYNCS constraints9.70252645101E-14

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