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

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Basic information

Entry
Database: PDB / ID: 9eep
TitleCryo-EM model of E. coli aspartate transcarbamoylase in the R-state complexed with CP and succinate
Components
  • Aspartate carbamoyltransferase
  • Aspartate carbamoyltransferase regulatory chain
KeywordsCYTOSOLIC PROTEIN / Complex / Allostery / ATCase / T-state / R-state / 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 / SUCCINIC ACID / Aspartate carbamoyltransferase / Aspartate carbamoyltransferase regulatory chain
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.08 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)310,83130
Polymers308,88412
Non-polymers1,94718
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 85 or resid 88...
d_2ens_1(chain "G" and (resid 1 through 85 or resid 88...
d_3ens_1(chain "K" and (resid 1 through 85 or resid 88...
d_4ens_1(chain "A" and (resid 1 through 85 or resid 88...
d_5ens_1(chain "F" and (resid 1 through 85 or resid 88...
d_6ens_1(chain "B" and (resid 1 through 85 or resid 88...
d_1ens_2(chain "C" and (resid 141 through 194 or resid 208 through 291 or resid 402))
d_2ens_2(chain "G" and (resid 141 through 194 or resid 208 through 291 or resid 402))
d_3ens_2(chain "K" and (resid 141 through 194 or resid 208 through 291 or resid 402))
d_4ens_2(chain "A" and (resid 141 through 194 or resid 208 through 291 or resid 402))
d_5ens_2(chain "F" and (resid 141 through 194 or resid 208 through 291 or resid 402))
d_6ens_2(chain "B" and (resid 141 through 194 or resid 208 through 291 or resid 402))
d_1ens_3(chain "J" and (resid 12 through 23 or resid 25...
d_2ens_3(chain "E" and (resid 12 through 23 or resid 25...
d_3ens_3(chain "D" and (resid 12 through 23 or resid 25...
d_4ens_3(chain "I" and (resid 12 through 23 or resid 25...
d_5ens_3(chain "H" and (resid 12 through 23 or resid 25...
d_6ens_3(chain "L" and (resid 12 through 23 or resid 25...
d_1ens_4(chain "D" and (resid 103 through 112 or resid 114...
d_2ens_4(chain "E" and (resid 103 through 112 or resid 114...
d_3ens_4(chain "J" and (resid 103 through 112 or resid 114...
d_4ens_4(chain "I" and (resid 103 through 112 or resid 114...
d_5ens_4(chain "H" and (resid 103 through 112 or resid 114...
d_6ens_4(chain "L" and (resid 103 through 112 or resid 114...

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_1ALAALAGLYGLYCC1 - 851 - 85
d_12ens_1LEULEUPROPROCC88 - 10788 - 107
d_13ens_1GLUGLUTHRTHRCC109 - 116109 - 116
d_14ens_1PHEPHEHISHISCC118 - 134118 - 134
d_15ens_1ILEILELEULEUCC293 - 310293 - 310
d_16ens_1CPCPCPCPCQ401
d_21ens_1ALAALAGLYGLYGG1 - 851 - 85
d_22ens_1LEULEUPROPROGG88 - 10788 - 107
d_23ens_1GLUGLUTHRTHRGG109 - 116109 - 116
d_24ens_1PHEPHEHISHISGG118 - 134118 - 134
d_25ens_1ILEILELEULEUGG293 - 310293 - 310
d_26ens_1CPCPCPCPGW401
d_31ens_1ALAALAGLYGLYKK1 - 851 - 85
d_32ens_1LEULEUPROPROKK88 - 10788 - 107
d_33ens_1GLUGLUTHRTHRKK109 - 116109 - 116
d_34ens_1PHEPHEHISHISKK118 - 134118 - 134
d_35ens_1ILEILELEULEUKK293 - 310293 - 310
d_36ens_1CPCPCPCPKBA401
d_41ens_1ALAALAGLYGLYAA1 - 851 - 85
d_42ens_1LEULEUPROPROAA88 - 10788 - 107
d_43ens_1GLUGLUTHRTHRAA109 - 116109 - 116
d_44ens_1PHEPHEHISHISAA118 - 134118 - 134
d_45ens_1ILEILELEULEUAA293 - 310293 - 310
d_46ens_1CPCPCPCPAM401
d_51ens_1ALAALAGLYGLYFF1 - 851 - 85
d_52ens_1LEULEUPROPROFF88 - 10788 - 107
d_53ens_1GLUGLUTHRTHRFF109 - 116109 - 116
d_54ens_1PHEPHEHISHISFF118 - 134118 - 134
d_55ens_1ILEILELEULEUFF293 - 310293 - 310
d_56ens_1CPCPCPCPFU401
d_61ens_1ALAALAGLYGLYBB1 - 851 - 85
d_62ens_1LEULEUPROPROBB88 - 10788 - 107
d_63ens_1GLUGLUTHRTHRBB109 - 116109 - 116
d_64ens_1PHEPHEHISHISBB118 - 134118 - 134
d_65ens_1ILEILELEULEUBB293 - 310293 - 310
d_66ens_1CPCPCPCPBO401
d_11ens_2ASPASPMETMETCC141 - 194141 - 194
d_12ens_2ALAALAASNASNCC208 - 291208 - 291
d_13ens_2SINSINSINSINCR402
d_21ens_2ASPASPMETMETGG141 - 194141 - 194
d_22ens_2ALAALAASNASNGG208 - 291208 - 291
d_23ens_2SINSINSINSINGX402
d_31ens_2ASPASPMETMETKK141 - 194141 - 194
d_32ens_2ALAALAASNASNKK208 - 291208 - 291
d_33ens_2SINSINSINSINKCA402
d_41ens_2ASPASPMETMETAA141 - 194141 - 194
d_42ens_2ALAALAASNASNAA208 - 291208 - 291
d_43ens_2SINSINSINSINAN402
d_51ens_2ASPASPMETMETFF141 - 194141 - 194
d_52ens_2ALAALAASNASNFF208 - 291208 - 291
d_53ens_2SINSINSINSINFV402
d_61ens_2ASPASPMETMETBB141 - 194141 - 194
d_62ens_2ALAALAASNASNBB208 - 291208 - 291
d_63ens_2SINSINSINSINBP402
d_11ens_3ILEILEALAALAJJ12 - 2312 - 23
d_12ens_3ILEILEGLYGLYJJ25 - 2625 - 26
d_13ens_3LEULEULEULEUJJ2929
d_14ens_3SERSERSERSERJJ3131
d_15ens_3PHEPHETHRTHRJJ33 - 3833 - 38
d_16ens_3GLNGLNLEULEUJJ40 - 4640 - 46
d_17ens_3LEULEUGLUGLUJJ48 - 5248 - 52
d_18ens_3GLYGLYGLYGLYJJ5454
d_19ens_3LYSLYSGLNGLNJJ56 - 7356 - 73
d_110ens_3ALAALALEULEUJJ75 - 7675 - 76
d_111ens_3ALAALAARGARGJJ78 - 9678 - 96
d_21ens_3ILEILEALAALAEE12 - 2312 - 23
d_22ens_3ILEILEGLYGLYEE25 - 2625 - 26
d_23ens_3LEULEULEULEUEE2929
d_24ens_3SERSERSERSEREE3131
d_25ens_3PHEPHETHRTHREE33 - 3833 - 38
d_26ens_3GLNGLNLEULEUEE40 - 4640 - 46
d_27ens_3LEULEUGLUGLUEE48 - 5248 - 52
d_28ens_3GLYGLYGLYGLYEE5454
d_29ens_3LYSLYSGLNGLNEE56 - 7356 - 73
d_210ens_3ALAALALEULEUEE75 - 7675 - 76
d_211ens_3ALAALAARGARGEE78 - 9678 - 96
d_31ens_3ILEILEALAALADD12 - 2312 - 23
d_32ens_3ILEILEGLYGLYDD25 - 2625 - 26
d_33ens_3LEULEULEULEUDD2929
d_34ens_3SERSERSERSERDD3131
d_35ens_3PHEPHETHRTHRDD33 - 3833 - 38
d_36ens_3GLNGLNLEULEUDD40 - 4640 - 46
d_37ens_3LEULEUGLUGLUDD48 - 5248 - 52
d_38ens_3GLYGLYGLYGLYDD5454
d_39ens_3LYSLYSGLNGLNDD56 - 7356 - 73
d_310ens_3ALAALALEULEUDD75 - 7675 - 76
d_311ens_3ALAALAARGARGDD78 - 9678 - 96
d_41ens_3ILEILEALAALAII12 - 2312 - 23
d_42ens_3ILEILEGLYGLYII25 - 2625 - 26
d_43ens_3LEULEULEULEUII2929
d_44ens_3SERSERSERSERII3131
d_45ens_3PHEPHETHRTHRII33 - 3833 - 38
d_46ens_3GLNGLNLEULEUII40 - 4640 - 46
d_47ens_3LEULEUGLUGLUII48 - 5248 - 52
d_48ens_3GLYGLYGLYGLYII5454
d_49ens_3LYSLYSGLNGLNII56 - 7356 - 73
d_410ens_3ALAALALEULEUII75 - 7675 - 76
d_411ens_3ALAALAARGARGII78 - 9678 - 96
d_51ens_3ILEILEALAALAHH12 - 2312 - 23
d_52ens_3ILEILEGLYGLYHH25 - 2625 - 26
d_53ens_3LEULEULEULEUHH2929
d_54ens_3SERSERSERSERHH3131
d_55ens_3PHEPHETHRTHRHH33 - 3833 - 38
d_56ens_3GLNGLNLEULEUHH40 - 4640 - 46
d_57ens_3LEULEUGLUGLUHH48 - 5248 - 52
d_58ens_3GLYGLYGLYGLYHH5454
d_59ens_3LYSLYSGLNGLNHH56 - 7356 - 73
d_510ens_3ALAALALEULEUHH75 - 7675 - 76
d_511ens_3ALAALAARGARGHH78 - 9678 - 96
d_61ens_3ILEILEALAALALL12 - 2312 - 23
d_62ens_3ILEILEGLYGLYLL25 - 2625 - 26
d_63ens_3LEULEULEULEULL2929
d_64ens_3SERSERSERSERLL3131
d_65ens_3PHEPHETHRTHRLL33 - 3833 - 38
d_66ens_3GLNGLNLEULEULL40 - 4640 - 46
d_67ens_3LEULEUGLUGLULL48 - 5248 - 52
d_68ens_3GLYGLYGLYGLYLL5454
d_69ens_3LYSLYSGLNGLNLL56 - 7356 - 73
d_610ens_3ALAALALEULEULL75 - 7675 - 76
d_611ens_3ALAALAARGARGLL78 - 9678 - 96
d_11ens_4ILEILESERSERDD103 - 112103 - 112
d_12ens_4CYSCYSALAALADD114 - 118114 - 118
d_13ens_4PROPROVALVALDD120 - 127120 - 127
d_14ens_4ARGARGLYSLYSDD130 - 143130 - 143
d_21ens_4ILEILESERSEREE103 - 112103 - 112
d_22ens_4CYSCYSALAALAEE114 - 118114 - 118
d_23ens_4PROPROVALVALEE120 - 127120 - 127
d_24ens_4ARGARGLYSLYSEE130 - 143130 - 143
d_31ens_4ILEILESERSERJJ103 - 112103 - 112
d_32ens_4CYSCYSALAALAJJ114 - 118114 - 118
d_33ens_4PROPROVALVALJJ120 - 127120 - 127
d_34ens_4ARGARGLYSLYSJJ130 - 143130 - 143
d_41ens_4ILEILESERSERII103 - 112103 - 112
d_42ens_4CYSCYSALAALAII114 - 118114 - 118
d_43ens_4PROPROVALVALII120 - 127120 - 127
d_44ens_4ARGARGLYSLYSII130 - 143130 - 143
d_51ens_4ILEILESERSERHH103 - 112103 - 112
d_52ens_4CYSCYSALAALAHH114 - 118114 - 118
d_53ens_4PROPROVALVALHH120 - 127120 - 127
d_54ens_4ARGARGLYSLYSHH130 - 143130 - 143
d_61ens_4ILEILESERSERLL103 - 112103 - 112
d_62ens_4CYSCYSALAALALL114 - 118114 - 118
d_63ens_4PROPROVALVALLL120 - 127120 - 127
d_64ens_4ARGARGLYSLYSLL130 - 143130 - 143

NCS ensembles :
ID
ens_1
ens_2
ens_3
ens_4

NCS oper:
IDCodeMatrixVector
1given(-0.491236806295, -0.853829179424, -0.172226979608), (0.870957862417, -0.483974784921, -0.0848575833644), (-0.0108996346413, -0.191687610252, 0.981395464653)387.113540049, 107.595890225, 34.0591773211
2given(-0.497387512932, 0.867472483752, -0.00985656698537), (-0.850704234308, -0.489936770333, -0.190431790427), (-0.170023432823, -0.0863333713538, 0.981650946764)98.3813431777, 389.280707437, 42.3578207889
3given(-0.554434859249, 0.82694729029, 0.0935957580825), (0.825572584411, 0.532318470016, 0.187261726866), (0.105032826865, 0.181094521068, -0.977840927616)99.3697554023, -86.11735097, 258.830884548
4given(-0.451389206967, -0.890393858646, -0.0587074128168), (-0.891474963031, 0.447106373872, 0.0732685521338), (-0.0389894103878, 0.0854088223139, -0.995582823751)371.168519157, 208.577473264, 298.419426837
5given(0.992353321587, 0.0492324317538, 0.113185921381), (0.0503385891783, -0.998708138298, -0.00693404183773), (0.112698321083, 0.0125786390469, -0.993549629493)-21.6562385699, 298.503810782, 286.063941692
6given(-0.492790293572, -0.852719806302, -0.173282020136), (0.870016492471, -0.486310575031, -0.0810760596101), (-0.0151337170087, -0.190711710584, 0.981529425975)387.351915821, 107.333435379, 34.445312182
7given(-0.495107802583, 0.86872377923, -0.0136842691227), (-0.850973947246, -0.48804829655, -0.194041751548), (-0.175247267968, -0.0844266287077, 0.980897823137)98.6633043712, 389.744127982, 42.9465594926
8given(-0.554234864742, 0.827391149168, 0.0908163035013), (0.825536322327, 0.532466928309, 0.186999333627), (0.106364915378, 0.17861370758, -0.978153182401)99.8184207392, -86.0943318316, 259.045961354
9given(-0.451763312576, -0.890113011908, -0.0600727512563), (-0.891412032969, 0.447655691931, 0.070632633821), (-0.0359791173996, 0.0854588059543, -0.995691867796)371.436345052, 208.993508213, 298.045978207
10given(0.991855566018, 0.0475278864587, 0.118167830509), (0.048485874779, -0.998810103188, -0.00524382644581), (0.117777994997, 0.0109305890805, -0.992979791394)-22.3207447226, 298.430498931, 285.50104566
11given(-0.504002241935, -0.844422481513, -0.18147289836), (0.857776295972, -0.513941523259, 0.00916169957145), (-0.1010028029, -0.151045633451, 0.983353268374)390.685270092, 96.3712720523, 46.5941905719
12given(-0.481294141223, -0.876497309038, -0.0104123423573), (-0.876395178267, 0.481399908868, -0.0136242156386), (0.0169540890069, 0.0025680714708, -0.999852971129)365.822373054, 216.614259153, 299.624913074
13given(-0.537868878222, 0.838850360182, 0.083828056539), (0.841131282355, 0.527331268383, 0.120082884832), (0.0565264158125, 0.135099247252, -0.98921835694)96.692762198, -76.9649083394, 277.760693794
14given(-0.475156668415, 0.875669677334, -0.0861902352831), (-0.864446691059, -0.482844357802, -0.139975870977), (-0.164189094577, 0.00799639518006, 0.986396471448)106.823848435, 381.977241142, 26.4108928352
15given(0.977359588558, 0.0392108268617, 0.207920046437), (0.0373640510617, -0.999219693828, 0.0128035602362), (0.208259843325, -0.00474494713273, -0.978062024176)-34.2529170271, 298.805612024, 266.193251974
16given(0.991047717897, 0.0572266096126, 0.120621457474), (0.0566183377646, -0.998359993373, 0.00846684480709), (0.120908166307, -0.00156166080292, -0.992662468584)-23.6437188348, 294.817727563, 286.624007546
17given(-0.448967344988, -0.8908510649, -0.0693736499055), (-0.893274501142, 0.44555372929, 0.0595192399564), (-0.0221130898674, 0.0886919076507, -0.995813615479)372.613441855, 211.550505024, 295.717991931
18given(-0.502428588372, 0.864112793349, -0.0295735347606), (-0.843282875808, -0.497295257037, -0.20389070282), (-0.190891343322, -0.0775016625591, 0.978546875395)102.92186536, 391.222314329, 44.5888000599
19given(-0.558811451125, 0.823731440207, 0.0958972184494), (0.822825634349, 0.536317243139, 0.18794092202), (0.103381514546, 0.183930228963, -0.977487561723)99.7766148472, -86.0924929191, 258.554401929
20given(-0.48507628782, -0.858641217466, -0.165638928588), (0.874349179897, -0.479400535894, -0.075423058792), (-0.0146460441038, -0.181412198745, 0.983298076648)385.698485572, 105.062324323, 32.8919262397

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Components

#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
#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
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 asparate transcarbamoylase isolated in a neutral buffer and complexed with CP and succinate
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
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: 50.47 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
3SerialEMimage acquisition
5cryoSPARC4CTF correction
10cryoSPARC4initial Euler assignment
11RELION4final Euler assignment
13RELION43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.08 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 682000 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 71.09 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.001621630
ELECTRON MICROSCOPYf_angle_d0.440729328
ELECTRON MICROSCOPYf_chiral_restr0.04083402
ELECTRON MICROSCOPYf_plane_restr0.00283822
ELECTRON MICROSCOPYf_dihedral_angle_d6.17993004
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2CCELECTRON MICROSCOPYNCS constraints1.39198989985E-11
ens_1d_3CCELECTRON MICROSCOPYNCS constraints3.31318338206E-13
ens_1d_4CCELECTRON MICROSCOPYNCS constraints7.33777678678E-13
ens_1d_5CCELECTRON MICROSCOPYNCS constraints2.92419052207E-12
ens_1d_6CCELECTRON MICROSCOPYNCS constraints3.52950745386E-13
ens_2d_2CCELECTRON MICROSCOPYNCS constraints2.70445372677E-13
ens_2d_3CCELECTRON MICROSCOPYNCS constraints3.51572215943E-11
ens_2d_4CCELECTRON MICROSCOPYNCS constraints1.69923759054E-13
ens_2d_5CCELECTRON MICROSCOPYNCS constraints1.84212604506E-11
ens_2d_6CCELECTRON MICROSCOPYNCS constraints1.05500569781E-11
ens_3d_2JJELECTRON MICROSCOPYNCS constraints2.88157391785E-13
ens_3d_3JJELECTRON MICROSCOPYNCS constraints1.67859296555E-13
ens_3d_4JJELECTRON MICROSCOPYNCS constraints1.73901382434E-11
ens_3d_5JJELECTRON MICROSCOPYNCS constraints4.91937108835E-12
ens_3d_6JJELECTRON MICROSCOPYNCS constraints2.5977265411E-13
ens_4d_2DDELECTRON MICROSCOPYNCS constraints1.22609647938E-13
ens_4d_3DDELECTRON MICROSCOPYNCS constraints1.62179337922E-13
ens_4d_4DDELECTRON MICROSCOPYNCS constraints4.50809716721E-12
ens_4d_5DDELECTRON MICROSCOPYNCS constraints7.70499803543E-14
ens_4d_6DDELECTRON MICROSCOPYNCS constraints3.39007720118E-12

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