[English] 日本語
Yorodumi
- PDB-9fs2: Mutant S1538A of the dihydroorotase domain of human CAD protein b... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9fs2
TitleMutant S1538A of the dihydroorotase domain of human CAD protein bound to substrate
ComponentsMultifunctional protein CAD
KeywordsHYDROLASE / Nucleotide metabolism / de novo pyrimidine synthesis / CAD disease / multienzymatic protein / zinc / carboxylated lysine
Function / homology
Function and homology information


aspartate binding / carbamoyl-phosphate synthase (glutamine-hydrolysing) / carbamoyl-phosphate synthase (ammonia) / carbamoyl-phosphate synthase (ammonia) activity / carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity / dihydroorotase / response to cortisol / citrulline biosynthetic process / aspartate carbamoyltransferase / glutaminase ...aspartate binding / carbamoyl-phosphate synthase (glutamine-hydrolysing) / carbamoyl-phosphate synthase (ammonia) / carbamoyl-phosphate synthase (ammonia) activity / carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity / dihydroorotase / response to cortisol / citrulline biosynthetic process / aspartate carbamoyltransferase / glutaminase / aspartate carbamoyltransferase activity / dihydroorotase activity / Pyrimidine biosynthesis / UDP biosynthetic process / glutaminase activity / glutamine metabolic process / UTP biosynthetic process / response to caffeine / response to starvation / response to amine / response to testosterone / 'de novo' UMP biosynthetic process / animal organ regeneration / 'de novo' pyrimidine nucleobase biosynthetic process / lactation / peptidyl-threonine phosphorylation / xenobiotic metabolic process / cellular response to epidermal growth factor stimulus / liver development / cell projection / female pregnancy / response to insulin / terminal bouton / nuclear matrix / heart development / protein autophosphorylation / protein kinase activity / neuronal cell body / enzyme binding / protein-containing complex / extracellular exosome / zinc ion binding / ATP binding / identical protein binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
Carbamoyl-phosphate synthase small subunit, N-terminal domain / Carbamoyl-phosphate synthetase, large subunit oligomerisation domain / Carbamoyl-phosphate synthase large subunit, CPSase domain / Carbamoyl-phosphate synthase, small subunit / Carbamoyl-phosphate synthase, large subunit / Carbamoyl-phosphate synthase small subunit, GATase1 domain / Carbamoyl-phosphate synthase small subunit, N-terminal domain superfamily / Carbamoyl-phosphate synthetase, large subunit oligomerisation domain superfamily / Carbamoyl-phosphate synthase small chain, CPSase domain / Carbamoyl-phosphate synthetase large chain, oligomerisation domain ...Carbamoyl-phosphate synthase small subunit, N-terminal domain / Carbamoyl-phosphate synthetase, large subunit oligomerisation domain / Carbamoyl-phosphate synthase large subunit, CPSase domain / Carbamoyl-phosphate synthase, small subunit / Carbamoyl-phosphate synthase, large subunit / Carbamoyl-phosphate synthase small subunit, GATase1 domain / Carbamoyl-phosphate synthase small subunit, N-terminal domain superfamily / Carbamoyl-phosphate synthetase, large subunit oligomerisation domain superfamily / Carbamoyl-phosphate synthase small chain, CPSase domain / Carbamoyl-phosphate synthetase large chain, oligomerisation domain / Carbamoyl-phosphate synthetase large chain, oligomerisation domain / Carbamoyl-phosphate synthase small chain, CPSase domain / Dihydroorotase signature 1. / Dihydroorotase signature 2. / Dihydroorotase, conserved site / Methylglyoxal synthase-like domain / Methylglyoxal synthase-like domain superfamily / MGS-like domain / MGS-like domain profile. / MGS-like 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 / Glutamine amidotransferase / Glutamine amidotransferase class-I / Glutamine amidotransferase type 1 domain profile. / Carbamoyl-phosphate synthase subdomain signature 1. / Carbamoyl-phosphate synthetase large subunit-like, ATP-binding domain / Carbamoyl-phosphate synthase L chain, ATP binding domain / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / Class I glutamine amidotransferase-like / Metal-dependent hydrolase / Carbamoyl-phosphate synthase subdomain signature 2.
Similarity search - Domain/homology
Chem-DOR / FORMIC ACID / N-CARBAMOYL-L-ASPARTATE / Multifunctional protein CAD
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.12 Å
Authorsdel Cano-Ochoa, F. / Ramon-Maiques, S.
Funding support Spain, 2items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN)PID2021-128468NB-I00 Spain
Other privateFundacion Ramon Areces
CitationJournal: J.Mol.Biol. / Year: 2024
Title: Disruption of CAD Oligomerization by Pathogenic Variants.
Authors: Del Cano-Ochoa, F. / Ramadane-Morchadi, L. / Eixeres, L. / Moreno-Morcillo, M. / Fernandez-Leiro, R. / Ramon-Maiques, S.
History
DepositionJun 20, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Multifunctional protein CAD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,78118
Polymers39,6781
Non-polymers1,10217
Water9,080504
1
A: Multifunctional protein CAD
hetero molecules

A: Multifunctional protein CAD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,56136
Polymers79,3572
Non-polymers2,20434
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area7940 Å2
ΔGint-337 kcal/mol
Surface area25070 Å2
Unit cell
Length a, b, c (Å)82.142, 158.579, 61.950
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-2400-

HOH

21A-2432-

HOH

31A-2462-

HOH

41A-2495-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Multifunctional protein CAD / Carbamoyl phosphate synthetase 2-aspartate transcarbamylase-dihydroorotase


Mass: 39678.430 Da / Num. of mol.: 1 / Mutation: S1538A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CAD / Plasmid: pOPIN-M-huDHO-S1538A / Cell (production host): Epithelial-like / Cell line (production host): HEK293S-GnTI / Organ (production host): Embryo / Production host: Homo sapiens (human) / Tissue (production host): Kidney
References: UniProt: P27708, carbamoyl-phosphate synthase (glutamine-hydrolysing), glutaminase, carbamoyl-phosphate synthase (ammonia), aspartate carbamoyltransferase, dihydroorotase

-
Non-polymers , 5 types, 521 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NCD / N-CARBAMOYL-L-ASPARTATE


Mass: 176.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H8N2O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-DOR / (4S)-2,6-DIOXOHEXAHYDROPYRIMIDINE-4-CARBOXYLIC ACID / DIHYDROOROTIC ACID


Mass: 158.112 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6N2O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: CH2O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 504 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.36 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7
Details: 100 mM HEPES pH 7, 2.5 M sodium formate, 2 mM carbamoyl aspartate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Apr 11, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.12→47.22 Å / Num. obs: 152076 / % possible obs: 98.8 % / Redundancy: 2 % / Biso Wilson estimate: 10.97 Å2 / CC1/2: 0.998 / Net I/σ(I): 6.26
Reflection shellResolution: 1.12→1.16 Å / Mean I/σ(I) obs: 0.68 / Num. unique obs: 13868 / CC1/2: 0.459

-
Processing

Software
NameVersionClassification
EDNAdata collection
autoPROCdata processing
Aimlessdata scaling
PHASERCCP4 v8.0phasing
REFMACCCP4 v8.0refinement
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.12→47.22 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.2177
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1688 7624 5.01 %
Rwork0.1468 144422 -
obs0.1479 152046 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.65 Å2
Refinement stepCycle: LAST / Resolution: 1.12→47.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2753 0 60 504 3317
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01363104
X-RAY DIFFRACTIONf_angle_d1.32834252
X-RAY DIFFRACTIONf_chiral_restr0.0995481
X-RAY DIFFRACTIONf_plane_restr0.0131565
X-RAY DIFFRACTIONf_dihedral_angle_d7.2077442
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.12-1.130.35672400.34544218X-RAY DIFFRACTION88
1.13-1.150.33082190.33034447X-RAY DIFFRACTION91.51
1.15-1.160.34982320.32744508X-RAY DIFFRACTION93.75
1.16-1.180.31852290.31164718X-RAY DIFFRACTION96.73
1.18-1.190.29132520.29874745X-RAY DIFFRACTION97.83
1.19-1.210.30372150.28384819X-RAY DIFFRACTION98.94
1.21-1.230.31022440.2764760X-RAY DIFFRACTION99.03
1.23-1.240.29612320.26844822X-RAY DIFFRACTION99.12
1.24-1.260.26752580.25054860X-RAY DIFFRACTION99.57
1.26-1.280.2562540.23534788X-RAY DIFFRACTION99.76
1.28-1.310.22532390.22134840X-RAY DIFFRACTION99.9
1.31-1.330.22752660.21864828X-RAY DIFFRACTION99.9
1.33-1.360.2222550.20984842X-RAY DIFFRACTION99.94
1.36-1.380.23692730.19544823X-RAY DIFFRACTION99.98
1.38-1.410.20242630.18124855X-RAY DIFFRACTION99.94
1.41-1.450.20182800.17524820X-RAY DIFFRACTION99.96
1.45-1.480.19262730.16034841X-RAY DIFFRACTION99.96
1.48-1.520.16792660.13414837X-RAY DIFFRACTION99.98
1.52-1.570.18242370.1234882X-RAY DIFFRACTION100
1.57-1.620.14882370.11544881X-RAY DIFFRACTION99.96
1.62-1.680.13622570.114889X-RAY DIFFRACTION99.98
1.68-1.740.14652510.10784877X-RAY DIFFRACTION100
1.74-1.820.14682500.10924894X-RAY DIFFRACTION100
1.82-1.920.13992760.10784840X-RAY DIFFRACTION100
1.92-2.040.11942370.1044931X-RAY DIFFRACTION100
2.04-2.20.11772860.10194887X-RAY DIFFRACTION99.98
2.2-2.420.13792730.10694918X-RAY DIFFRACTION100
2.42-2.770.142530.11774934X-RAY DIFFRACTION99.98
2.77-3.490.1392710.12484980X-RAY DIFFRACTION100
3.49-47.220.15173060.13185138X-RAY DIFFRACTION99.94

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more