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- PDB-9i9p: Crystal Structure of UFC1 W145H -

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Basic information

Entry
Database: PDB / ID: 9i9p
TitleCrystal Structure of UFC1 W145H
ComponentsUbiquitin-fold modifier-conjugating enzyme 1
KeywordsLIGASE / UFMylation / UFM1 conjugating enzyme / transthiolation activity / aminoacyltransferase activity / oxyanion hole impairing mutation
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: 2.022 Å
AuthorsManoj Kumar, P. / Banerjee, S. / Weiner, R.
Funding support Israel, 1items
OrganizationGrant numberCountry
Israel Science Foundation 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
DepositionFeb 6, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 7, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)19,8634
Polymers19,5821
Non-polymers2803
Water1,62190
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area430 Å2
ΔGint-5 kcal/mol
Surface area9310 Å2
Unit cell
Length a, b, c (Å)36.548, 46.512, 45.588
Angle α, β, γ (deg.)90.000, 97.742, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 19582.463 Da / Num. of mol.: 1 / Mutation: W145H
Source method: isolated from a genetically manipulated source
Details: Tryptophan at 145th position is mutated to Histidine
Source: (gene. exp.) Homo sapiens (human) / Gene: UFC1, CGI-126, HSPC155 / Production host: Escherichia coli (E. coli) / Strain (production host): T7 express strain / References: UniProt: Q9Y3C8
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 1.94 Å3/Da / Density % sol: 36.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M Lithium sulfate monohydrate, 0.1M HEPES pH 7.5, 25% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87313 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 20, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 2.022→32.405 Å / Num. obs: 9919 / % possible obs: 98.8 % / Redundancy: 3.5 % / Biso Wilson estimate: 15.8 Å2 / CC1/2: 0.925 / Rrim(I) all: 0.414 / Net I/σ(I): 2.6
Reflection shellResolution: 2.022→5.479 Å / Redundancy: 3.5 % / Rmerge(I) obs: 1.223 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 470 / CC1/2: 0.378 / Rpim(I) all: 0.754 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
autoPROCdata processing
autoPROCdata scaling
Coot0.9.6model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.022→32.405 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.849 / SU B: 8.241 / SU ML: 0.221 / Cross valid method: FREE R-VALUE / ESU R: 0.29 / ESU R Free: 0.211
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2672 487 4.927 %
Rwork0.2362 9397 -
all0.238 --
obs-9884 98.476 %
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: 17.466 Å2
Baniso -1Baniso -2Baniso -3
1--0.592 Å2-0 Å2-0.245 Å2
2---0.897 Å20 Å2
3---1.5 Å2
Refinement stepCycle: LAST / Resolution: 2.022→32.405 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1269 0 17 90 1376
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0131316
X-RAY DIFFRACTIONr_bond_other_d0.0020.0151238
X-RAY DIFFRACTIONr_angle_refined_deg1.4391.6451784
X-RAY DIFFRACTIONr_angle_other_deg1.2821.5822845
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5625155
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.34421.85770
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.20215215
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.045159
X-RAY DIFFRACTIONr_chiral_restr0.0670.2168
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021444
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02302
X-RAY DIFFRACTIONr_nbd_refined0.1960.2305
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2130.21203
X-RAY DIFFRACTIONr_nbtor_refined0.1720.2621
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.2553
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.272
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.420.213
X-RAY DIFFRACTIONr_nbd_other0.3220.259
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1480.210
X-RAY DIFFRACTIONr_mcbond_it0.8771.809629
X-RAY DIFFRACTIONr_mcbond_other0.8751.806628
X-RAY DIFFRACTIONr_mcangle_it1.4612.694781
X-RAY DIFFRACTIONr_mcangle_other1.462.697782
X-RAY DIFFRACTIONr_scbond_it0.7631.865687
X-RAY DIFFRACTIONr_scbond_other0.7621.857684
X-RAY DIFFRACTIONr_scangle_it1.262.7551003
X-RAY DIFFRACTIONr_scangle_other1.2612.743998
X-RAY DIFFRACTIONr_lrange_it4.2732.9725403
X-RAY DIFFRACTIONr_lrange_other4.17132.7815353
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.022-2.0740.293360.322672X-RAY DIFFRACTION96.7213
2.074-2.1310.266430.292651X-RAY DIFFRACTION97.7465
2.131-2.1920.3310.274656X-RAY DIFFRACTION99.1342
2.192-2.260.316280.285631X-RAY DIFFRACTION98.8006
2.26-2.3340.385300.259626X-RAY DIFFRACTION98.2036
2.334-2.4150.195240.243608X-RAY DIFFRACTION99.2151
2.415-2.5060.311260.254588X-RAY DIFFRACTION99.1922
2.506-2.6080.205350.238555X-RAY DIFFRACTION98.6622
2.608-2.7240.305350.233519X-RAY DIFFRACTION99.2831
2.724-2.8560.28210.231523X-RAY DIFFRACTION99.6337
2.856-3.010.246290.204485X-RAY DIFFRACTION99.0366
3.01-3.1920.23200.226454X-RAY DIFFRACTION99.5798
3.192-3.4110.251150.209452X-RAY DIFFRACTION97.6987
3.411-3.6820.202280.208399X-RAY DIFFRACTION99.0719
3.682-4.0310.29190.193374X-RAY DIFFRACTION98.9924
4.031-4.5020.171180.188346X-RAY DIFFRACTION99.1826
4.502-5.190.306140.207306X-RAY DIFFRACTION98.7654
5.19-6.3360.341120.256249X-RAY DIFFRACTION98.1203
6.336-8.8730.269190.282193X-RAY DIFFRACTION96.3636
8.873-32.4050.36940.246110X-RAY DIFFRACTION87.0229

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