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- PDB-9gmm: Crystal Structure of UFC1 T106I -

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Basic information

Entry
Database: PDB / ID: 9gmm
TitleCrystal Structure of UFC1 T106I
ComponentsUbiquitin-fold modifier-conjugating enzyme 1
KeywordsLIGASE / UFM1 conjugation / UFMylation pathway component / 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
Ubiquitin-fold modifier-conjugating enzyme 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsKumar, M. / Banerjee, S. / 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 29, 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)19,7452
Polymers19,6531
Non-polymers921
Water3,081171
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-1 kcal/mol
Surface area9840 Å2
Unit cell
Length a, b, c (Å)41.653, 48.002, 82.580
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: 19652.598 Da / Num. of mol.: 1 / Mutation: T106I
Source method: isolated from a genetically manipulated source
Details: T106 is mutated to Isoleucine. This genetic mutation cause early onset of encephalopathy in infants
Source: (gene. exp.) Homo sapiens (human) / Gene: UFC1, CGI-126, HSPC155 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y3C8
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.1 Å3/Da / Density % sol: 41.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.5M Ammonium sulfate, 0.1M Bis-Tris Propane pH 7.0

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.91976 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91976 Å / Relative weight: 1
ReflectionResolution: 1.35→29.4 Å / Num. obs: 36233 / % possible obs: 97.43 % / Redundancy: 1.83 % / Biso Wilson estimate: 19.12 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.066 / Net I/σ(I): 7.8
Reflection shellResolution: 1.35→1.398 Å / Redundancy: 3 % / Mean I/σ(I) obs: 0.86 / Num. unique obs: 3493 / CC1/2: 0.467 / Rrim(I) all: 1.179 / % possible all: 96.09

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→29.399 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.973 / SU B: 1.217 / SU ML: 0.048 / Cross valid method: FREE R-VALUE / ESU R: 0.058 / ESU R Free: 0.058
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.201 1148 3.168 %
Rwork0.1822 35085 -
all0.183 --
obs-36233 97.218 %
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: 21.324 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å20 Å20 Å2
2--0.336 Å2-0 Å2
3----0.926 Å2
Refinement stepCycle: LAST / Resolution: 1.35→29.399 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1357 0 6 171 1534
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0131400
X-RAY DIFFRACTIONr_bond_other_d0.0010.0151318
X-RAY DIFFRACTIONr_angle_refined_deg1.8461.6441898
X-RAY DIFFRACTIONr_angle_other_deg1.5221.583037
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6865166
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.50521.86775
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.71415239
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8751510
X-RAY DIFFRACTIONr_chiral_restr0.1020.2176
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021553
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02324
X-RAY DIFFRACTIONr_nbd_refined0.2430.2262
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1950.21239
X-RAY DIFFRACTIONr_nbtor_refined0.1790.2681
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.2617
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.296
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3370.216
X-RAY DIFFRACTIONr_nbd_other0.330.239
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1170.220
X-RAY DIFFRACTIONr_mcbond_it1.7661.94667
X-RAY DIFFRACTIONr_mcbond_other1.7631.934666
X-RAY DIFFRACTIONr_mcangle_it2.6162.904832
X-RAY DIFFRACTIONr_mcangle_other2.6152.911833
X-RAY DIFFRACTIONr_scbond_it3.1322.31733
X-RAY DIFFRACTIONr_scbond_other3.132.311734
X-RAY DIFFRACTIONr_scangle_it4.6543.3111066
X-RAY DIFFRACTIONr_scangle_other4.6523.3131067
X-RAY DIFFRACTIONr_lrange_it6.00223.9391617
X-RAY DIFFRACTIONr_lrange_other5.83423.3281582
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.3830.375790.342418X-RAY DIFFRACTION92.6187
1.383-1.4210.348810.3122475X-RAY DIFFRACTION96.9651
1.421-1.4620.305790.2762427X-RAY DIFFRACTION98.0055
1.462-1.5070.245790.242393X-RAY DIFFRACTION98.2903
1.507-1.5560.234750.2242310X-RAY DIFFRACTION98.3505
1.556-1.6110.221730.2052213X-RAY DIFFRACTION97.2766
1.611-1.6710.231700.1972148X-RAY DIFFRACTION97.1954
1.671-1.7390.273680.1872079X-RAY DIFFRACTION98.1261
1.739-1.8160.247650.1752002X-RAY DIFFRACTION98.4755
1.816-1.9050.209630.1761912X-RAY DIFFRACTION98.4056
1.905-2.0070.224600.1771827X-RAY DIFFRACTION97.9242
2.007-2.1280.211560.181725X-RAY DIFFRACTION97.5356
2.128-2.2740.188540.1721648X-RAY DIFFRACTION98.5524
2.274-2.4550.198510.1671546X-RAY DIFFRACTION99.5636
2.455-2.6880.18460.1741416X-RAY DIFFRACTION98.9844
2.688-3.0020.183420.1761296X-RAY DIFFRACTION97.4508
3.002-3.460.175370.1731119X-RAY DIFFRACTION96.3333
3.46-4.2240.179310.148967X-RAY DIFFRACTION95.8694
4.224-5.9120.16250.162744X-RAY DIFFRACTION93.0993
5.912-29.3990.185140.211420X-RAY DIFFRACTION85.2652

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