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

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Basic information

Entry
Database: PDB / ID: 9eeo
TitleCryo-EM model of E. coli aspartate transcarbamoylase in the R-state complexed with CP, succinate, CTP, and Mg2+
Components
  • Aspartate carbamoyltransferase
  • Aspartate carbamoyltransferase regulatory chain
KeywordsCYTOSOLIC PROTEIN / Complex / Allostery / ATCase / R-State / CP / Succinate / CTP
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 / Aspartate carbamoyltransferase / Aspartate carbamoyltransferase regulatory chain
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.53 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)316,77548
Polymers308,88412
Non-polymers7,89136
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 "G" and (resid 137 through 291 or resid 402))
d_2ens_2(chain "C" and (resid 137 through 291 or resid 402))
d_3ens_2(chain "K" and (resid 137 through 291 or resid 402))
d_4ens_2(chain "A" and (resid 137 through 291 or resid 402))
d_5ens_2(chain "F" and (resid 137 through 291 or resid 402))
d_6ens_2(chain "B" and (resid 137 through 291 or resid 402))
d_1ens_3(chain "D" and (resid 103 through 126 or resid 128...
d_2ens_3(chain "E" and (resid 103 through 126 or resid 128...
d_3ens_3(chain "H" and (resid 103 through 126 or resid 128...
d_4ens_3(chain "I" and (resid 103 through 126 or resid 128...
d_5ens_3(chain "L" and (resid 103 through 126 or resid 128...
d_6ens_3(chain "J" and (resid 103 through 126 or resid 128...
d_1ens_4(chain "I" and resid 46 through 55)
d_2ens_4(chain "E" and resid 46 through 55)
d_3ens_4(chain "H" and resid 46 through 55)
d_4ens_4(chain "D" and resid 46 through 55)
d_5ens_4(chain "L" and resid 46 through 55)
d_6ens_4(chain "J" and resid 46 through 55)
d_1ens_5(chain "D" and (resid 12 through 43 or resid 45...
d_2ens_5(chain "E" and (resid 12 through 43 or resid 45...
d_1ens_6(chain "I" and (resid 12 through 43 or resid 45...
d_2ens_6(chain "H" and (resid 12 through 43 or resid 45...
d_1ens_7(chain "L" and (resid 12 through 43 or resid 45...
d_2ens_7(chain "J" and (resid 12 through 43 or resid 45...
d_1ens_8(chain "D" and (resid 145 through 150 or resid 152 through 153))
d_2ens_8(chain "E" and (resid 145 through 150 or resid 152 through 153))
d_1ens_9(chain "H" and (resid 145 through 150 or resid 152 through 153))
d_2ens_9(chain "I" and (resid 145 through 150 or resid 152 through 153))
d_1ens_10(chain "L" and (resid 145 through 150 or resid 152 through 153))
d_2ens_10(chain "J" and (resid 145 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_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_2GLNGLNASNASNGG137 - 291137 - 291
d_12ens_2SINSINSINSINGDA402
d_21ens_2GLNGLNASNASNCC137 - 291137 - 291
d_22ens_2SINSINSINSINCR402
d_31ens_2GLNGLNASNASNKK137 - 291137 - 291
d_32ens_2SINSINSINSINKRA402
d_41ens_2GLNGLNASNASNAA137 - 291137 - 291
d_42ens_2SINSINSINSINAN402
d_51ens_2GLNGLNASNASNFF137 - 291137 - 291
d_52ens_2SINSINSINSINFBA402
d_61ens_2GLNGLNASNASNBB137 - 291137 - 291
d_62ens_2SINSINSINSINBP402
d_11ens_3ILEILEALAALADD103 - 126103 - 126
d_12ens_3ARGARGALAALADD128 - 135128 - 135
d_13ens_3LYSLYSLYSLYSDD137 - 143137 - 143
d_21ens_3ILEILEALAALAEE103 - 126103 - 126
d_22ens_3ARGARGALAALAEE128 - 135128 - 135
d_23ens_3LYSLYSLYSLYSEE137 - 143137 - 143
d_31ens_3ILEILEALAALAHH103 - 126103 - 126
d_32ens_3ARGARGALAALAHH128 - 135128 - 135
d_33ens_3LYSLYSLYSLYSHH137 - 143137 - 143
d_41ens_3ILEILEALAALAII103 - 126103 - 126
d_42ens_3ARGARGALAALAII128 - 135128 - 135
d_43ens_3LYSLYSLYSLYSII137 - 143137 - 143
d_51ens_3ILEILEALAALALL103 - 126103 - 126
d_52ens_3ARGARGALAALALL128 - 135128 - 135
d_53ens_3LYSLYSLYSLYSLL137 - 143137 - 143
d_61ens_3ILEILEALAALAJJ103 - 126103 - 126
d_62ens_3ARGARGALAALAJJ128 - 135128 - 135
d_63ens_3LYSLYSLYSLYSJJ137 - 143137 - 143
d_11ens_4LEULEUARGARGII46 - 5546 - 55
d_21ens_4LEULEUARGARGEE46 - 5546 - 55
d_31ens_4LEULEUARGARGHH46 - 5546 - 55
d_41ens_4LEULEUARGARGDD46 - 5546 - 55
d_51ens_4LEULEUARGARGLL46 - 5546 - 55
d_61ens_4LEULEUARGARGJJ46 - 5546 - 55
d_11ens_5ILEILETHRTHRDD12 - 4312 - 43
d_12ens_5GLYGLYGLYGLYDD4545
d_13ens_5LYSLYSVALVALDD56 - 7156 - 71
d_14ens_5GLNGLNALAALADD73 - 7573 - 75
d_15ens_5TYRTYRSERSERDD77 - 9577 - 95
d_16ens_5CTPCTPCTPCTPDT202
d_17ens_5CTPCTPCTPCTPDU203
d_21ens_5ILEILETHRTHREE12 - 4312 - 43
d_22ens_5GLYGLYGLYGLYEE4545
d_23ens_5LYSLYSVALVALEE56 - 7156 - 71
d_24ens_5GLNGLNALAALAEE73 - 7573 - 75
d_25ens_5TYRTYRSERSEREE77 - 9577 - 95
d_26ens_5CTPCTPCTPCTPEX202
d_27ens_5CTPCTPCTPCTPEY203
d_11ens_6ILEILETHRTHRII12 - 4312 - 43
d_12ens_6GLYGLYGLYGLYII4545
d_13ens_6LYSLYSVALVALII56 - 7156 - 71
d_14ens_6GLNGLNALAALAII73 - 7573 - 75
d_15ens_6TYRTYRSERSERII77 - 9577 - 95
d_16ens_6CTPCTPCTPCTPIJA202
d_17ens_6CTPCTPCTPCTPIKA203
d_21ens_6ILEILETHRTHRHH12 - 4312 - 43
d_22ens_6GLYGLYGLYGLYHH4545
d_23ens_6LYSLYSVALVALHH56 - 7156 - 71
d_24ens_6GLNGLNALAALAHH73 - 7573 - 75
d_25ens_6TYRTYRSERSERHH77 - 9577 - 95
d_26ens_6CTPCTPCTPCTPHFA202
d_27ens_6CTPCTPCTPCTPHGA203
d_11ens_7ILEILETHRTHRLL12 - 4312 - 43
d_12ens_7GLYGLYGLYGLYLL4545
d_13ens_7LYSLYSVALVALLL56 - 7156 - 71
d_14ens_7GLNGLNALAALALL73 - 7573 - 75
d_15ens_7TYRTYRSERSERLL77 - 9577 - 95
d_16ens_7CTPCTPCTPCTPLTA202
d_17ens_7CTPCTPCTPCTPLUA203
d_21ens_7ILEILETHRTHRJJ12 - 4312 - 43
d_22ens_7GLYGLYGLYGLYJJ4545
d_23ens_7LYSLYSVALVALJJ56 - 7156 - 71
d_24ens_7GLNGLNALAALAJJ73 - 7573 - 75
d_25ens_7TYRTYRSERSERJJ77 - 9577 - 95
d_26ens_7CTPCTPCTPCTPJNA202
d_27ens_7CTPCTPCTPCTPJOA203
d_11ens_8PHEPHEVALVALDD145 - 150145 - 150
d_12ens_8ALAALAASNASNDD152 - 153152 - 153
d_21ens_8PHEPHEVALVALEE145 - 150145 - 150
d_22ens_8ALAALAASNASNEE152 - 153152 - 153
d_11ens_9PHEPHEVALVALHH145 - 150145 - 150
d_12ens_9ALAALAASNASNHH152 - 153152 - 153
d_21ens_9PHEPHEVALVALII145 - 150145 - 150
d_22ens_9ALAALAASNASNII152 - 153152 - 153
d_11ens_10PHEPHEVALVALLL145 - 150145 - 150
d_12ens_10ALAALAASNASNLL152 - 153152 - 153
d_21ens_10PHEPHEVALVALJJ145 - 150145 - 150
d_22ens_10ALAALAASNASNJJ152 - 153152 - 153

NCS ensembles :
ID
ens_1
ens_2
ens_3
ens_4
ens_5
ens_6
ens_7
ens_8
ens_9
ens_10

NCS oper:
IDCodeMatrixVector
1given(-0.49776183135, 0.86717017836, 0.015781033365), (-0.867027585642, -0.497982591347, 0.0166284229863), (0.0222783524161, -0.00540559697928, 0.999737192734)120.546301591, 449.795091293, -3.18237693874
2given(-0.501982943936, -0.864666991417, 0.0190818749478), (0.864805840449, -0.502103206232, -0.00179683554356), (0.0111347349757, 0.0156001361056, 0.999816309844)450.919874877, 120.073625101, -4.98251463896
3given(0.547061296857, -0.837030171763, -0.0102190527867), (-0.837019184925, -0.547134210735, 0.00656045051723), (-0.0110824884042, 0.00496457466628, -0.999926263006)247.245014541, 457.904070318, 390.535789442
4given(-0.998674350475, -0.0513128828509, 0.00406568042385), (-0.0513498163671, 0.998634869525, -0.00957046116531), (-0.003569042287, -0.00976654603118, -0.999945936796)392.854499511, 14.7421856078, 391.920796689
5given(0.455583510317, 0.890069764276, -0.0148148523331), (0.890024203894, -0.455758138755, -0.0118926633506), (-0.0173372895903, -0.00776747583731, -0.999819526069)-63.5706042394, 111.009908238, 394.198944806
6given(-0.49967596004, -0.86586655344, 0.0244754283416), (0.866119267191, -0.499837095532, -0.000541230454099), (0.0127023603621, 0.0209282002126, 0.999700285324)449.812765706, 119.166150925, -6.31535249758
7given(-0.496655367928, 0.867878548551, 0.0109667895716), (-0.867624246338, -0.496775565033, 0.021028674545), (0.0236983686281, 0.000928951556331, 0.999718722628)121.017367312, 448.938590797, -4.51340066456
8given(-0.998518193776, -0.0542165058283, 0.00468905035946), (-0.0542690462706, 0.998455244769, -0.0119161575383), (-0.00403575449976, -0.0121529703928, -0.999918005637)393.356168579, 15.5614292726, 392.387642501
9given(0.456585159907, 0.889459764921, -0.0197817678501), (0.889466133876, -0.456849872753, -0.011755443527), (-0.0194932921612, -0.0122278515083, -0.999735210547)-62.7617075682, 111.328227629, 395.366087652
10given(0.545953785298, -0.837789013522, -0.00663574723929), (-0.837732249457, -0.545994060855, 0.00975518995001), (-0.0117958695469, 0.000233096582088, -0.999930399142)247.011408011, 457.355520052, 391.642575487
11given(0.472249749677, 0.881021958744, -0.0279371104493), (0.881315394845, -0.47251599754, -0.00343611372807), (-0.0162280232595, -0.0229987016785, -0.999603776995)-63.3300940405, 114.602047835, 396.655259232
12given(0.536039583497, -0.843848313443, -0.0241161527776), (-0.843624107089, -0.536508268095, 0.0213832692626), (-0.0309827510629, 0.00888268910406, -0.999480448519)253.316907836, 454.796032921, 393.970750527
13given(-0.517092472605, -0.854782231401, 0.0443025017008), (0.855061273637, -0.518206293566, -0.0182333659695), (0.0385433924514, 0.0284530172365, 0.998851757123)447.87043631, 128.122376592, -12.9832193601
14given(-0.500498423441, 0.865727686612, 0.00411105419281), (-0.865362734445, -0.500415852854, 0.0270427817769), (0.0254689215973, 0.00997731654708, 0.99962582359)123.342763997, 448.11539196, -6.52193605906
15given(-0.998214207164, -0.0517030787712, 0.0299196968713), (-0.0522996181689, 0.998440823727, -0.0195108035511), (-0.0288642781769, -0.02104075002, -0.999361866535)388.482877095, 16.657682907, 399.301246957
16given(-0.958052778519, -0.286590471785, -0.000880371196963), (-0.286561129079, 0.957990606179, -0.0116926375796), (0.00419438585699, -0.0109498837571, -0.999931251223)442.612636007, 67.2894261157, 392.059055299
17given(0.434796641542, 0.898754647805, -0.0564974650038), (0.89968043652, -0.436253766246, -0.0160550172573), (-0.0390767532718, -0.0438489963936, -0.998273646286)-53.3994606208, 105.320233538, 407.173876985
18given(-0.669743000056, 0.742571877117, 0.00559653389674), (-0.741731635046, -0.669310052057, 0.0431072591088), (0.0357560547075, 0.0247196588019, 0.999054774785)182.941060358, 463.13094051, -13.5217555675
19given(-0.424380258841, -0.903197741003, 0.064305804973), (0.903214563322, -0.427272740486, -0.0405149088643), (0.0640690916832, 0.040888212047, 0.997107469437)436.270788412, 104.068223914, -21.2661664633
20given(0.595966964758, -0.802961017682, -0.00877388169709), (-0.802242183301, -0.59583972238, 0.0371820462956), (-0.0350835609676, -0.0151204932656, -0.99926999076)230.966102023, 456.335052804, 400.211653397
21given(0.425278393847, 0.904260498725, -0.0380951200466), (0.905036059479, -0.4252113156, 0.0102502745966), (-0.00692955769412, -0.0388366776493, -0.999221543853)-54.4758318659, 98.1465439087, 397.193699215
22given(0.423078748221, 0.905605951884, -0.0297024025207), (0.905493321619, -0.423763907543, -0.0224943363136), (-0.0329578110049, -0.0173784514689, -0.999305644995)-58.228265459, 102.398791298, 399.626325066
23given(0.469876818778, 0.882511850027, -0.01971318689), (0.881643183686, -0.470289053048, -0.0391599699036), (-0.0438300334817, 0.00102036523141, -0.999038481251)-63.4470131072, 120.017805199, 396.259210839
24given(0.508139824945, 0.85314513781, -0.118056309174), (0.848477737245, -0.519405821633, -0.101504294755), (-0.147917029803, -0.0485897755072, -0.987805439351)-50.3838885855, 149.111246092, 429.775736623
25given(0.378485616148, 0.920046423419, -0.101307537346), (0.923214895547, -0.383103425153, -0.0301002039281), (-0.0665048495192, -0.0821361332789, -0.994399698612)-33.8988229445, 95.6250107809, 416.049287968
26given(0.404282864456, 0.911614480631, 0.0742590345448), (0.912312478069, -0.396144400365, -0.103708998739), (-0.0651253243107, 0.109675214905, -0.991831658785)-74.2651382939, 114.316973471, 381.953861161

-
Components

-
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

-
Non-polymers , 5 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.: 12 / Source method: obtained synthetically / Formula: C9H16N3O14P3
#7: Chemical
ChemComp-MG / MAGNESIUM ION


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

-
Details

Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: E. coli aspartate transcarbamoylase in the presence of substrate analogs CP and succinate and nucleotide effector CTP
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)aminomethaneC4H11NO31
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 with 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: 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: 3.53 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 450000 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 101 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002421990
ELECTRON MICROSCOPYf_angle_d0.464529892
ELECTRON MICROSCOPYf_chiral_restr0.04093450
ELECTRON MICROSCOPYf_plane_restr0.00323870
ELECTRON MICROSCOPYf_dihedral_angle_d6.19783194
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2CCELECTRON MICROSCOPYNCS constraints9.43727910793E-12
ens_1d_3CCELECTRON MICROSCOPYNCS constraints5.19731233732E-11
ens_1d_4CCELECTRON MICROSCOPYNCS constraints5.67974779557E-13
ens_1d_5CCELECTRON MICROSCOPYNCS constraints6.10433041988E-13
ens_1d_6CCELECTRON MICROSCOPYNCS constraints1.26852293254E-11
ens_2d_2GGELECTRON MICROSCOPYNCS constraints6.91497821451E-13
ens_2d_3GGELECTRON MICROSCOPYNCS constraints1.90575154508E-12
ens_2d_4GGELECTRON MICROSCOPYNCS constraints2.65422598262E-13
ens_2d_5GGELECTRON MICROSCOPYNCS constraints3.96567747391E-13
ens_2d_6GGELECTRON MICROSCOPYNCS constraints1.76367630059E-13
ens_3d_2DDELECTRON MICROSCOPYNCS constraints3.43728239812E-12
ens_3d_3DDELECTRON MICROSCOPYNCS constraints1.84323490173E-12
ens_3d_4DDELECTRON MICROSCOPYNCS constraints8.11913035392E-14
ens_3d_5DDELECTRON MICROSCOPYNCS constraints2.19803593977E-13
ens_3d_6DDELECTRON MICROSCOPYNCS constraints7.32117953168E-13
ens_4d_2IIELECTRON MICROSCOPYNCS constraints3.93738454893E-13
ens_4d_3IIELECTRON MICROSCOPYNCS constraints1.09774812741E-13
ens_4d_4IIELECTRON MICROSCOPYNCS constraints1.5662879675E-13
ens_4d_5IIELECTRON MICROSCOPYNCS constraints8.98157558793E-14
ens_4d_6IIELECTRON MICROSCOPYNCS constraints1.0797072934E-13
ens_5d_2DDELECTRON MICROSCOPYNCS constraints2.36604142969E-13
ens_6d_2IIELECTRON MICROSCOPYNCS constraints1.9948241441E-13
ens_7d_2LLELECTRON MICROSCOPYNCS constraints1.49682395953E-10
ens_8d_2DDELECTRON MICROSCOPYNCS constraints1.22743599139E-13
ens_9d_2HHELECTRON MICROSCOPYNCS constraints1.50819233109E-13
ens_10d_2LLELECTRON MICROSCOPYNCS constraints9.02774110611E-11

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