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- PDB-9gn8: Crystal Structure of UFC1 E149D -

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Basic information

Entry
Database: PDB / ID: 9gn8
TitleCrystal Structure of UFC1 E149D
ComponentsUbiquitin-fold modifier-conjugating enzyme 1
KeywordsLIGASE / UFM1 conjugating enzyme activity / UBC core domain containing protein / Brain development / Infantile encephalopathy
Function / homology
Function and homology information


UFM1 conjugating enzyme activity / UFM1 transferase activity / protein K69-linked ufmylation / protein ufmylation / regulation of type II interferon production / reticulophagy / response to endoplasmic reticulum stress / brain development / extracellular exosome
Similarity search - Function
Ubiquitin-fold modifier-conjugating enzyme 1 / Ubiquitin-fold modifier-conjugating enzyme 1 / Ubiquitin-conjugating enzyme/RWD-like
Similarity search - Domain/homology
FORMIC ACID / Ubiquitin-fold modifier-conjugating enzyme 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsKumar, M. / Banerjee, S. / Isupov, M.N. / Wiener, R.
Funding support Israel, 1items
OrganizationGrant numberCountry
Israel Science Foundation491/2021 Israel
CitationJournal: Nat Commun / Year: 2025
Title: UFC1 reveals the multifactorial and plastic nature of oxyanion holes in E2 conjugating enzymes.
Authors: Kumar, M. / Banerjee, S. / Cohen-Kfir, E. / Mitelberg, M.B. / Tiwari, S. / Isupov, M.N. / Dessau, M. / Wiener, R.
History
DepositionAug 31, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 7, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Ubiquitin-fold modifier-conjugating enzyme 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8506
Polymers19,6271
Non-polymers2235
Water3,315184
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.398, 46.829, 80.201
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ubiquitin-fold modifier-conjugating enzyme 1 / Ufm1-conjugating enzyme 1


Mass: 19626.518 Da / Num. of mol.: 1 / Mutation: E149D
Source method: isolated from a genetically manipulated source
Details: Glutamate at 149th position is mutated to Aspartate
Source: (gene. exp.) Homo sapiens (human) / Gene: UFC1, CGI-126, HSPC155 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y3C8
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: CH2O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2% (v/v) Tacsimate Ph 7.0, 0.1M Hepes pH 7.5, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54187 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jul 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 1.397→40.47 Å / Num. obs: 33844 / % possible obs: 99.98 % / Redundancy: 2 % / Biso Wilson estimate: 18.535 Å2 / CC1/2: 1 / Rrim(I) all: 0.0388 / Net I/σ(I): 14.18
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 2 % / Mean I/σ(I) obs: 0.63 / Num. unique obs: 3301 / CC1/2: 0.398 / Rrim(I) all: 1.428 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
Coot0.9.6model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→38.873 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.912 / SU B: 6.449 / SU ML: 0.17 / Cross valid method: FREE R-VALUE / ESU R: 0.24 / ESU R Free: 0.202
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2573 610 5.166 %
Rwork0.1946 11199 -
all0.198 --
obs-11809 94.253 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 20.328 Å2
Baniso -1Baniso -2Baniso -3
1-0.942 Å20 Å20 Å2
2---0.368 Å20 Å2
3----0.573 Å2
Refinement stepCycle: LAST / Resolution: 1.96→38.873 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1384 0 14 184 1582
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0131534
X-RAY DIFFRACTIONr_bond_other_d0.0020.0151456
X-RAY DIFFRACTIONr_angle_refined_deg1.2711.6522091
X-RAY DIFFRACTIONr_angle_other_deg1.3141.5883366
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5855192
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.16121.19692
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.21815273
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.951514
X-RAY DIFFRACTIONr_chiral_restr0.0820.2191
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021753
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02383
X-RAY DIFFRACTIONr_nbd_refined0.1820.2286
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1950.21266
X-RAY DIFFRACTIONr_nbtor_refined0.1640.2677
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.2652
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2134
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0950.216
X-RAY DIFFRACTIONr_nbd_other0.2130.289
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.130.226
X-RAY DIFFRACTIONr_mcbond_it1.7081.95704
X-RAY DIFFRACTIONr_mcbond_other1.7071.954705
X-RAY DIFFRACTIONr_mcangle_it2.7892.908886
X-RAY DIFFRACTIONr_mcangle_other2.7872.918887
X-RAY DIFFRACTIONr_scbond_it1.8892.137830
X-RAY DIFFRACTIONr_scbond_other1.8712.12825
X-RAY DIFFRACTIONr_scangle_it3.0833.0741193
X-RAY DIFFRACTIONr_scangle_other3.0843.0771194
X-RAY DIFFRACTIONr_lrange_it5.58922.131801
X-RAY DIFFRACTIONr_lrange_other5.41521.4581753
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-2.0110.267190.321439X-RAY DIFFRACTION50.8324
2.011-2.0660.292410.318676X-RAY DIFFRACTION82.2248
2.066-2.1250.355490.274756X-RAY DIFFRACTION93.4959
2.125-2.1910.299400.263785X-RAY DIFFRACTION98.6842
2.191-2.2620.242440.24744X-RAY DIFFRACTION97.6456
2.262-2.3410.264430.24756X-RAY DIFFRACTION99.1315
2.341-2.430.303370.213707X-RAY DIFFRACTION99.7319
2.43-2.5280.273360.216686X-RAY DIFFRACTION99.7238
2.528-2.640.271420.208672X-RAY DIFFRACTION99.5816
2.64-2.7690.275360.167640X-RAY DIFFRACTION99.705
2.769-2.9180.211280.167613X-RAY DIFFRACTION99.226
2.918-3.0940.215230.162587X-RAY DIFFRACTION99.3485
3.094-3.3060.264300.155548X-RAY DIFFRACTION100
3.306-3.5690.263230.144521X-RAY DIFFRACTION100
3.569-3.9060.189270.144472X-RAY DIFFRACTION100
3.906-4.3620.253230.139442X-RAY DIFFRACTION99.7854
4.362-5.0270.214340.154376X-RAY DIFFRACTION100
5.027-6.1340.282160.188339X-RAY DIFFRACTION100
6.134-8.5760.261150.196268X-RAY DIFFRACTION99.6479
8.576-38.8730.30940.21172X-RAY DIFFRACTION96.1749

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