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

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Basic information

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


aspartate carbamoyltransferase complex / pyrimidine nucleotide biosynthetic process / aspartate carbamoyltransferase / aspartate carbamoyltransferase activity / amino acid metabolic process / amino acid binding / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / transferase activity / metal ion binding / cytosol
Similarity search - Function
Aspartate transcarbamylase regulatory subunit / Aspartate carbamoyltransferase regulatory subunit, C-terminal / Aspartate carbamoyltransferase regulatory subunit, N-terminal / Aspartate carbamoyltransferase regulatory subunit, C-terminal domain superfamily / Aspartate carbamoyltransferase regulatory subunit, N-terminal domain superfamily / Aspartate carbamoyltransferase regulatory chain, allosteric domain / Aspartate carbamoyltransferase regulatory chain, metal binding domain / Aspartate carbamoyltransferase / Aspartate and ornithine carbamoyltransferases signature. / Aspartate/ornithine carbamoyltransferase ...Aspartate transcarbamylase regulatory subunit / Aspartate carbamoyltransferase regulatory subunit, C-terminal / Aspartate carbamoyltransferase regulatory subunit, N-terminal / Aspartate carbamoyltransferase regulatory subunit, C-terminal domain superfamily / Aspartate carbamoyltransferase regulatory subunit, N-terminal domain superfamily / Aspartate carbamoyltransferase regulatory chain, allosteric domain / Aspartate carbamoyltransferase regulatory chain, metal binding domain / Aspartate carbamoyltransferase / Aspartate and ornithine carbamoyltransferases signature. / Aspartate/ornithine carbamoyltransferase / Aspartate/ornithine carbamoyltransferase, Asp/Orn-binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding / Aspartate/ornithine carbamoyltransferase superfamily / Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / PHOSPHORIC ACID MONO(FORMAMIDE)ESTER / 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)317,06348
Polymers308,88412
Non-polymers8,17936
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 "K" and (resid 1 through 86 or resid 88 through 134 or resid 293 through 310 or resid 401))
d_2ens_1(chain "G" and (resid 1 through 86 or resid 88 through 134 or resid 293 through 310 or resid 401))
d_3ens_1(chain "C" and (resid 1 through 86 or resid 88 through 134 or resid 293 through 310 or resid 401))
d_4ens_1(chain "A" and (resid 1 through 86 or resid 88 through 134 or resid 293 through 310 or resid 401))
d_5ens_1(chain "F" and (resid 1 through 86 or resid 88 through 134 or resid 293 through 310 or resid 401))
d_6ens_1(chain "B" and (resid 1 through 86 or resid 88 through 134 or resid 293 through 310 or resid 401))
d_1ens_2(chain "B" and (resid 137 through 291 or resid 402))
d_2ens_2(chain "G" and (resid 137 through 291 or resid 402))
d_3ens_2(chain "K" and (resid 137 through 291 or resid 402))
d_4ens_2(chain "A" and (resid 137 through 291 or resid 402))
d_5ens_2(chain "F" and (resid 137 through 291 or resid 402))
d_6ens_2(chain "C" and (resid 137 through 291 or resid 402))
d_1ens_3(chain "D" and (resid 10 through 23 or resid 25...
d_2ens_3(chain "E" and (resid 10 through 23 or resid 25...
d_3ens_3(chain "J" and (resid 10 through 23 or resid 25...
d_4ens_3(chain "I" and (resid 10 through 23 or resid 25...
d_5ens_3(chain "H" and (resid 10 through 23 or resid 25...
d_6ens_3(chain "L" and (resid 10 through 23 or resid 25...
d_1ens_4(chain "H" and (resid 102 through 118 or resid 120...
d_2ens_4(chain "E" and (resid 102 through 118 or resid 120...
d_3ens_4(chain "J" and (resid 102 through 118 or resid 120...
d_4ens_4(chain "I" and (resid 102 through 118 or resid 120...
d_5ens_4(chain "D" and (resid 102 through 118 or resid 120...
d_6ens_4(chain "L" and (resid 102 through 118 or resid 120...

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_1ALAALAGLUGLUKK1 - 861 - 86
d_12ens_1LEULEUHISHISKK88 - 13488 - 134
d_13ens_1ILEILELEULEUKK293 - 310293 - 310
d_14ens_1CPCPCPCPKQA401
d_21ens_1ALAALAGLUGLUGG1 - 861 - 86
d_22ens_1LEULEUHISHISGG88 - 13488 - 134
d_23ens_1ILEILELEULEUGG293 - 310293 - 310
d_24ens_1CPCPCPCPGCA401
d_31ens_1ALAALAGLUGLUCC1 - 861 - 86
d_32ens_1LEULEUHISHISCC88 - 13488 - 134
d_33ens_1ILEILELEULEUCC293 - 310293 - 310
d_34ens_1CPCPCPCPCQ401
d_41ens_1ALAALAGLUGLUAA1 - 861 - 86
d_42ens_1LEULEUHISHISAA88 - 13488 - 134
d_43ens_1ILEILELEULEUAA293 - 310293 - 310
d_44ens_1CPCPCPCPAM401
d_51ens_1ALAALAGLUGLUFF1 - 861 - 86
d_52ens_1LEULEUHISHISFF88 - 13488 - 134
d_53ens_1ILEILELEULEUFF293 - 310293 - 310
d_54ens_1CPCPCPCPFAA401
d_61ens_1ALAALAGLUGLUBB1 - 861 - 86
d_62ens_1LEULEUHISHISBB88 - 13488 - 134
d_63ens_1ILEILELEULEUBB293 - 310293 - 310
d_64ens_1CPCPCPCPBO401
d_11ens_2GLNGLNASNASNBB137 - 291137 - 291
d_12ens_2SINSINSINSINBP402
d_21ens_2GLNGLNASNASNGG137 - 291137 - 291
d_22ens_2SINSINSINSINGDA402
d_31ens_2GLNGLNASNASNKK137 - 291137 - 291
d_32ens_2SINSINSINSINKRA402
d_41ens_2GLNGLNASNASNAA137 - 291137 - 291
d_42ens_2SINSINSINSINAN402
d_51ens_2GLNGLNASNASNFF137 - 291137 - 291
d_52ens_2SINSINSINSINFBA402
d_61ens_2GLNGLNASNASNCC137 - 291137 - 291
d_62ens_2SINSINSINSINCR402
d_11ens_3GLUGLUALAALADD10 - 2310 - 23
d_12ens_3ILEILETHRTHRDD25 - 3625 - 36
d_13ens_3THRTHRPROPRODD38 - 7938 - 79
d_14ens_3ALAALALYSLYSDD81 - 9481 - 94
d_15ens_3ATPATPATPATPDT202
d_16ens_3ATPATPATPATPDU203
d_21ens_3GLUGLUALAALAEE10 - 2310 - 23
d_22ens_3ILEILETHRTHREE25 - 3625 - 36
d_23ens_3THRTHRPROPROEE38 - 7938 - 79
d_24ens_3ALAALALYSLYSEE81 - 9481 - 94
d_25ens_3ATPATPATPATPEX202
d_26ens_3ATPATPATPATPEY203
d_31ens_3GLUGLUALAALAJJ10 - 2310 - 23
d_32ens_3ILEILETHRTHRJJ25 - 3625 - 36
d_33ens_3THRTHRPROPROJJ38 - 7938 - 79
d_34ens_3ALAALALYSLYSJJ81 - 9481 - 94
d_35ens_3ATPATPATPATPJNA202
d_36ens_3ATPATPATPATPJOA203
d_41ens_3GLUGLUALAALAII10 - 2310 - 23
d_42ens_3ILEILETHRTHRII25 - 3625 - 36
d_43ens_3THRTHRPROPROII38 - 7938 - 79
d_44ens_3ALAALALYSLYSII81 - 9481 - 94
d_45ens_3ATPATPATPATPIJA202
d_46ens_3ATPATPATPATPIKA203
d_51ens_3GLUGLUALAALAHH10 - 2310 - 23
d_52ens_3ILEILETHRTHRHH25 - 3625 - 36
d_53ens_3THRTHRPROPROHH38 - 7938 - 79
d_54ens_3ALAALALYSLYSHH81 - 9481 - 94
d_55ens_3ATPATPATPATPHFA202
d_56ens_3ATPATPATPATPHGA203
d_61ens_3GLUGLUALAALALL10 - 2310 - 23
d_62ens_3ILEILETHRTHRLL25 - 3625 - 36
d_63ens_3THRTHRPROPROLL38 - 7938 - 79
d_64ens_3ALAALALYSLYSLL81 - 9481 - 94
d_65ens_3ATPATPATPATPLTA202
d_66ens_3ATPATPATPATPLUA203
d_11ens_4ARGARGALAALAHH102 - 118102 - 118
d_12ens_4PROPROVALVALHH120 - 127120 - 127
d_13ens_4ARGARGASNASNHH130 - 153130 - 153
d_21ens_4ARGARGALAALAEE102 - 118102 - 118
d_22ens_4PROPROVALVALEE120 - 127120 - 127
d_23ens_4ARGARGASNASNEE130 - 153130 - 153
d_31ens_4ARGARGALAALAJJ102 - 118102 - 118
d_32ens_4PROPROVALVALJJ120 - 127120 - 127
d_33ens_4ARGARGASNASNJJ130 - 153130 - 153
d_41ens_4ARGARGALAALAII102 - 118102 - 118
d_42ens_4PROPROVALVALII120 - 127120 - 127
d_43ens_4ARGARGASNASNII130 - 153130 - 153
d_51ens_4ARGARGALAALADD102 - 118102 - 118
d_52ens_4PROPROVALVALDD120 - 127120 - 127
d_53ens_4ARGARGASNASNDD130 - 153130 - 153
d_61ens_4ARGARGALAALALL102 - 118102 - 118
d_62ens_4PROPROVALVALLL120 - 127120 - 127
d_63ens_4ARGARGASNASNLL130 - 153130 - 153

NCS ensembles :
ID
ens_1
ens_2
ens_3
ens_4

NCS oper:
IDCodeMatrixVector
1given(-0.496892182304, -0.866791037217, 0.0420886797748), (0.867812257554, -0.496295592466, 0.0243427717775), (-0.000211670132848, 0.0486208052047, 0.998817286843)358.044119052, 92.6995912017, -7.22317474682
2given(-0.501648243378, 0.865070342507, 0.00153050008821), (-0.864046407181, -0.501139014275, 0.0477859247983), (0.0421051796378, 0.0226493021308, 0.998856427601)98.4474999109, 357.158625257, -9.7225886095
3given(-0.94158814207, -0.336750565274, -0.00329051694977), (-0.336593443111, 0.941372290283, -0.0228706174177), (0.0107992948208, -0.0204271357326, -0.999733018039)349.932323212, 63.8167978358, 309.456362695
4given(0.175323137581, 0.983381137811, -0.0471522557809), (0.984235659381, -0.176205495601, -0.0152246550851), (-0.023280125239, -0.0437396972617, -0.998771682945)-18.9293728421, 30.7162312375, 318.154076532
5given(0.762385198324, -0.646854038079, -0.0186725144903), (-0.646500314859, -0.762599900812, 0.0218799947052), (-0.0283928206265, -0.00460919760548, -0.999586215909)137.089439472, 366.96005036, 313.033460544
6given(0.181086650054, 0.983175548134, -0.0239471652494), (0.982185447907, -0.182039768635, -0.0466183285302), (-0.0501933371272, -0.015078600282, -0.998625687994)-20.0696993669, 39.4539620089, 317.79327208
7given(0.762363039805, -0.646526301575, -0.0283960720972), (-0.646879287257, -0.762578745755, -0.0045655493245), (-0.0187024933248, 0.0218494369405, -0.99958632386)141.620053361, 369.956925699, 307.443065544
8given(-0.500110032036, 0.865390383365, 0.0314553689586), (-0.86504420457, -0.500922184732, 0.0278476028261), (0.0398557398258, -0.0132834190787, 0.999117145674)91.0496587201, 357.44060451, -3.88217980121
9given(-0.501547840804, -0.864313802442, 0.037568794149), (0.8646387881, -0.502253290619, -0.0118910965102), (0.0291466893259, 0.0265194828639, 0.999223292127)355.227003806, 100.218547991, -8.36970647645
10given(-0.942040121721, -0.335386576855, 0.00873230405852), (-0.3354979935, 0.941809867426, -0.0208631248166), (-0.00122695811295, -0.022583571132, -0.999744205729)347.924407787, 64.0819630994, 311.699607407
11given(-0.943910495055, -0.329753670438, -0.0171899434961), (-0.329836390318, 0.944035684181, 0.00214070446496), (0.0155220149147, 0.0076905023238, -0.999849950356)351.640528045, 58.8541652826, 306.028203327
12given(0.78697147962, -0.61612345149, 0.032676945828), (-0.616093737216, -0.787578855871, -0.0121676928064), (0.0332324724971, -0.0105564344646, -0.999391897337)123.927292204, 371.08837762, 306.367482183
13given(-0.445357039719, -0.894956259701, -0.0266533374013), (0.894944369316, -0.445855809254, 0.0169461849075), (-0.0270496395774, -0.0163061514858, 0.999501088755)364.68741324, 84.7641146002, 2.99436160912
14given(0.126487395451, 0.991553199838, 0.0286912997751), (0.991292808143, -0.127415544581, 0.0332242008696), (0.0365992802699, 0.0242390364894, -0.999036016265)-24.5880676521, 17.8698565975, 303.640831491
15given(-0.519119846041, 0.854700221758, 0.00145477624826), (-0.854530581887, -0.518981274284, -0.02087873471), (-0.0170900575555, -0.0120817163421, 0.999780957042)100.789077403, 367.208625369, 1.43115282822
16given(-0.502960131034, -0.863595488898, 0.0351274557229), (0.863505355484, -0.503829827301, -0.0226717042212), (0.0372774414414, 0.0189297828154, 0.999125645593)356.065098734, 102.355025257, -8.37254529836
17given(-0.49807271405, 0.86685165768, 0.0221760027196), (-0.866174164798, -0.498561685475, 0.0343301909796), (0.0408152882521, -0.00210934923914, 0.999164482401)92.0731630555, 356.199330059, -5.66229497327
18given(-0.944624050354, -0.328122261394, 0.0046027243749), (-0.328154537863, 0.944533366223, -0.0130889025739), (-5.26664359184E-5, -0.0138744970542, -0.999903743146)348.070675236, 61.2781182902, 310.336717451
19given(0.188843114601, 0.981563554216, -0.0295172339977), (0.980558356174, -0.190111505288, -0.048609934116), (-0.0533253054884, -0.0197637190886, -0.998381593982)-20.0389724583, 41.0511696406, 318.880467207
20given(0.753872881701, -0.656567595213, -0.0243858801617), (-0.656784162658, -0.754077694801, -0.00118062906262), (-0.0176136855135, 0.0169063041163, -0.999701923057)143.473209348, 369.62908326, 308.137721661

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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 , 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-ATP / ADENOSINE-5'-TRIPHOSPHATE


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

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: E. coli aspartate transcarbamoylase isolated at a neutral pH and complexed with CP, succinate, ATP, and Mg2+
Type: COMPLEX / Entity ID: #2, #1 / 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 type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2300 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 52.47 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21.1_5286 / Category: model refinement
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: 934000 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 63.33 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002122110
ELECTRON MICROSCOPYf_angle_d0.497430066
ELECTRON MICROSCOPYf_chiral_restr0.04063462
ELECTRON MICROSCOPYf_plane_restr0.00333912
ELECTRON MICROSCOPYf_dihedral_angle_d5.81733256
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2KKELECTRON MICROSCOPYNCS constraints1.39584122688E-12
ens_1d_3KKELECTRON MICROSCOPYNCS constraints1.05055965653E-11
ens_1d_4KKELECTRON MICROSCOPYNCS constraints3.48751321314E-13
ens_1d_5KKELECTRON MICROSCOPYNCS constraints2.90138729466E-13
ens_1d_6KKELECTRON MICROSCOPYNCS constraints5.68630707369E-13
ens_2d_2BBELECTRON MICROSCOPYNCS constraints2.50776642909E-13
ens_2d_3BBELECTRON MICROSCOPYNCS constraints3.11720943518E-13
ens_2d_4BBELECTRON MICROSCOPYNCS constraints2.82254765553E-13
ens_2d_5BBELECTRON MICROSCOPYNCS constraints8.21984366258E-13
ens_2d_6BBELECTRON MICROSCOPYNCS constraints4.75459707773E-13
ens_3d_2DDELECTRON MICROSCOPYNCS constraints5.30682626757E-13
ens_3d_3DDELECTRON MICROSCOPYNCS constraints2.12799008021E-13
ens_3d_4DDELECTRON MICROSCOPYNCS constraints5.58645709825E-13
ens_3d_5DDELECTRON MICROSCOPYNCS constraints2.19863919382E-13
ens_3d_6DDELECTRON MICROSCOPYNCS constraints1.8046797439E-13
ens_4d_2HHELECTRON MICROSCOPYNCS constraints2.2406139969E-13
ens_4d_3HHELECTRON MICROSCOPYNCS constraints6.98414424236E-13
ens_4d_4HHELECTRON MICROSCOPYNCS constraints2.53871109405E-13
ens_4d_5HHELECTRON MICROSCOPYNCS constraints1.53302785651E-13
ens_4d_6HHELECTRON MICROSCOPYNCS constraints5.54519522577E-12

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