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- EMDB-47959: Cryo-EM model of E. coli aspartate transcarbamoylase in the T-sta... -

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Basic information

Entry
Database: EMDB / ID: EMD-47959
TitleCryo-EM model of E. coli aspartate transcarbamoylase in the T-state complexed with CP, CTP, and Mg2+
Map data
Sample
  • Complex: E. coli aspartate transcarbamoylase in the T-state complexed with CP, CTP, and Mg2+
    • Protein or peptide: Aspartate carbamoyltransferase
    • Protein or peptide: Aspartate carbamoyltransferase regulatory chain
  • Ligand: ZINC ION
  • Ligand: CYTIDINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHORIC ACID MONO(FORMAMIDE)ESTER
KeywordsComplex / Allostery / ATCase / R-State / CTP / UTP / CP / Succinate / CYTOSOLIC PROTEIN
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
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
Aspartate carbamoyltransferase / Aspartate carbamoyltransferase regulatory chain
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.85 Å
AuthorsMiller RC / Ando N
Funding support United States, 4 items
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
CitationJournal: 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, 2024-
Header (metadata) releaseApr 1, 2026-
Map releaseApr 1, 2026-
UpdateApr 1, 2026-
Current statusApr 1, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47959.png

Downloads & links

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Map

FileDownload / File: emd_47959.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 360 pix.
= 384.84 Å		1.07 Å/pix.
x 360 pix.
= 384.84 Å		1.07 Å/pix.
x 360 pix.
= 384.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.069 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00289
Minimum - Maximum-0.010592669 - 0.0146392165
Average (Standard dev.)0.00000005414929 (±0.0004276859)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 384.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_47959_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_47959_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_47959_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : E. coli aspartate transcarbamoylase in the T-state complexed with...

EntireName: E. coli aspartate transcarbamoylase in the T-state complexed with CP, CTP, and Mg2+
Components
  • Complex: E. coli aspartate transcarbamoylase in the T-state complexed with CP, CTP, and Mg2+
    • Protein or peptide: Aspartate carbamoyltransferase
    • Protein or peptide: Aspartate carbamoyltransferase regulatory chain
  • Ligand: ZINC ION
  • Ligand: CYTIDINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHORIC ACID MONO(FORMAMIDE)ESTER

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Supramolecule #1: E. coli aspartate transcarbamoylase in the T-state complexed with...

SupramoleculeName: E. coli aspartate transcarbamoylase in the T-state complexed with CP, CTP, and Mg2+
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2, #1
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Aspartate carbamoyltransferase regulatory chain

MacromoleculeName: Aspartate carbamoyltransferase regulatory chain / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 15.945273 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
AIKRGTVIDH IPAQIGFKLL SLFKLTETDQ RITIGLNLPS GEMGRKDLIK IENTFLSEDQ VDQLALYAPQ ATVNRIDNYE VVGKSRPSL PERIDNVLVC PNSNCISHAE PVSSSFAVRK RANDIALKCK YCEKEFSHNV VLAN

UniProtKB: Aspartate carbamoyltransferase regulatory chain

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Macromolecule #2: Aspartate carbamoyltransferase

MacromoleculeName: Aspartate carbamoyltransferase / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO / EC number: aspartate carbamoyltransferase
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 34.337105 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: ANPLYQKHII SINDLSRDDL NLVLATAAKL KANPQPELLK HKVIASCFFE ASTRTRLSFE TSMHRLGASV VGFSDSANTS LGKKGETLA DTISVISTYV DAIVMRHPQE GAARLATEFS GNVPVLNAGD GSNQHPTQTL LDLFTIQETQ GRLDNLHVAM V GDLKYGRT ...String:
ANPLYQKHII SINDLSRDDL NLVLATAAKL KANPQPELLK HKVIASCFFE ASTRTRLSFE TSMHRLGASV VGFSDSANTS LGKKGETLA DTISVISTYV DAIVMRHPQE GAARLATEFS GNVPVLNAGD GSNQHPTQTL LDLFTIQETQ GRLDNLHVAM V GDLKYGRT VHSLTQALAK FDGNRFYFIA PDALAMPQYI LDMLDEKGIA WSLHSSIEEV MAEVDILYMT RVQKERLDPS EY ANVKAQF VLRASDLHNA KANMKVLHPL PRVDEIATDV DKTPHAWYFQ QAGNGIFARQ ALLALVLNRD LVL

UniProtKB: Aspartate carbamoyltransferase

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Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 6 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #4: CYTIDINE-5'-TRIPHOSPHATE

MacromoleculeName: CYTIDINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 12 / Formula: CTP
Molecular weightTheoretical: 483.156 Da
Chemical component information

ChemComp-CTP:
CYTIDINE-5'-TRIPHOSPHATE

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 6 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #6: PHOSPHORIC ACID MONO(FORMAMIDE)ESTER

MacromoleculeName: PHOSPHORIC ACID MONO(FORMAMIDE)ESTER / type: ligand / ID: 6 / Number of copies: 6 / Formula: CP
Molecular weightTheoretical: 141.02 Da
Chemical component information

ChemComp-CP:
PHOSPHORIC ACID MONO(FORMAMIDE)ESTER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
Component:
ConcentrationFormulaName
40.0 mMTris-HClTris Hydrochloride
15.0 mMMgCl2Magnesium chloride
1.0 mMTCEPtris(2-carboxyethyl)phosphine
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
Details: Grids were manually coated with graphene-oxide following glow-discharge as is described in the associated publication.
VitrificationCryogen name: ETHANE
DetailsE. coli aspartate transcarbamoylase was isolated in a neutral buffer and complexed with CP and nucleotide effector CTP in the presence of a physilogical concentration of Mg2+

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 51.75 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.85 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 85000
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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