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- PDB-7nvk: Crystal structure of UBA5 fragment fused to the N-terminus of UFC1 -

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Basic information

Entry
Database: PDB / ID: 7nvk
TitleCrystal structure of UBA5 fragment fused to the N-terminus of UFC1
ComponentsUbiquitin-like modifier-activating enzyme 5,Ubiquitin-fold modifier-conjugating enzyme 1
KeywordsLIGASE / Ubiquitin like fold modifier enzyme 5 (UBA5) / E1 / Ubiquitin fold modifier 1 (UFM1) / Ubiquitin fold modifier conjugating enzyme 1 (UFC1) / UFMYLATION
Function / homology
Function and homology information


UFM1 conjugating enzyme activity / UFM1 activating enzyme activity / UFM1 transferase activity / protein ufmylation / protein K69-linked ufmylation / megakaryocyte differentiation / regulation of intracellular estrogen receptor signaling pathway / reticulophagy / neuromuscular process / localization ...UFM1 conjugating enzyme activity / UFM1 activating enzyme activity / UFM1 transferase activity / protein ufmylation / protein K69-linked ufmylation / megakaryocyte differentiation / regulation of intracellular estrogen receptor signaling pathway / reticulophagy / neuromuscular process / localization / response to endoplasmic reticulum stress / erythrocyte differentiation / brain development / Antigen processing: Ubiquitination & Proteasome degradation / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / Golgi apparatus / protein homodimerization activity / extracellular exosome / zinc ion binding / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ubiquitin-fold modifier-conjugating enzyme 1 / Ubiquitin-fold modifier-conjugating enzyme 1 / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / ThiF/MoeB/HesA family / Ubiquitin-activating enzyme / THIF-type NAD/FAD binding fold / ThiF family / Ubiquitin-conjugating enzyme/RWD-like
Similarity search - Domain/homology
Ubiquitin-like modifier-activating enzyme 5 / Ubiquitin-fold modifier-conjugating enzyme 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.651 Å
AuthorsManoj Kumar, P. / Padala, P. / Isupov, M.N. / Wiener, R.
Funding support Israel, 1items
OrganizationGrant numberCountry
Israel Science Foundation1383/17 Israel
CitationJournal: Nat Commun / Year: 2021
Title: Structural basis for UFM1 transfer from UBA5 to UFC1.
Authors: Kumar, M. / Padala, P. / Fahoum, J. / Hassouna, F. / Tsaban, T. / Zoltsman, G. / Banerjee, S. / Cohen-Kfir, E. / Dessau, M. / Rosenzweig, R. / Isupov, M.N. / Schueler-Furman, O. / Wiener, R.
History
DepositionMar 15, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 29, 2021Provider: repository / Type: Initial release
Revision 1.1May 11, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: Ubiquitin-like modifier-activating enzyme 5,Ubiquitin-fold modifier-conjugating enzyme 1


Theoretical massNumber of molelcules
Total (without water)25,9181
Polymers25,9181
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.630, 84.630, 60.770
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64

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Components

#1: Protein Ubiquitin-like modifier-activating enzyme 5,Ubiquitin-fold modifier-conjugating enzyme 1 / Ubiquitin-activating enzyme 5 / ThiFP1 / UFM1-activating enzyme / Ubiquitin-activating enzyme E1 ...Ubiquitin-activating enzyme 5 / ThiFP1 / UFM1-activating enzyme / Ubiquitin-activating enzyme E1 domain-containing protein 1 / Ufm1-conjugating enzyme 1


Mass: 25917.533 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBA5, UBE1DC1, UFC1, CGI-126, HSPC155 / Plasmid: pET32A / Production host: Escherichia coli (E. coli) / References: UniProt: Q9GZZ9, UniProt: Q9Y3C8

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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: 2.51 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2% (v/v) Tacsimate pH 7.0, 20% PEG 3350, 0.1M HEPES pH 7.5, 6mM zinc sulfate

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.65→46.78 Å / Num. obs: 7314 / % possible obs: 100 % / Redundancy: 20.4 % / Biso Wilson estimate: 127.1 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.112 / Net I/σ(I): 13.1
Reflection shellResolution: 2.65→2.78 Å / Redundancy: 21.4 % / Num. unique obs: 953 / CC1/2: 0.292 / Rrim(I) all: 0.6 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XSCALEdata scaling
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Z6O

2z6o


Resolution: 2.651→46.78 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.968 / SU B: 23.987 / SU ML: 0.466 / Cross valid method: NONE / ESU R: 0.723 / ESU R Free: 0.33
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2638 373 5.112 %Random selection
Rwork0.2165 6923 --
all0.219 ---
obs-7296 99.986 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 157.069 Å2
Baniso -1Baniso -2Baniso -3
1--2.318 Å2-1.159 Å2-0 Å2
2---2.318 Å2-0 Å2
3---7.519 Å2
Refinement stepCycle: LAST / Resolution: 2.651→46.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1488 0 0 0 1488
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0121524
X-RAY DIFFRACTIONr_angle_refined_deg1.4541.642065
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8445182
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.88122.56182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.97615275
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2221510
X-RAY DIFFRACTIONr_chiral_restr0.1090.2193
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021160
X-RAY DIFFRACTIONr_nbd_refined0.2680.2749
X-RAY DIFFRACTIONr_nbtor_refined0.3270.21011
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2020.251
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.220.259
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2930.24
X-RAY DIFFRACTIONr_mcbond_it22.25530.794731
X-RAY DIFFRACTIONr_mcangle_it30.38757.365912
X-RAY DIFFRACTIONr_scbond_it23.01131.576792
X-RAY DIFFRACTIONr_scangle_it30.94658.2871152
X-RAY DIFFRACTIONr_lrange_it39.925293.1886285
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.651-2.7190.544290.436493X-RAY DIFFRACTION100
2.719-2.7940.637210.427516X-RAY DIFFRACTION100
2.794-2.8750.456220.405474X-RAY DIFFRACTION100
2.875-2.9630.457300.391470X-RAY DIFFRACTION100
2.963-3.060.535390.372438X-RAY DIFFRACTION100
3.06-3.1670.386220.277434X-RAY DIFFRACTION100
3.167-3.2870.359240.273423X-RAY DIFFRACTION100
3.287-3.4210.376100.288417X-RAY DIFFRACTION100
3.421-3.5720.323290.251390X-RAY DIFFRACTION100
3.572-3.7460.358170.264379X-RAY DIFFRACTION100
3.746-3.9480.373250.235341X-RAY DIFFRACTION100
3.948-4.1870.326220.223349X-RAY DIFFRACTION100
4.187-4.4750.307140.207318X-RAY DIFFRACTION100
4.475-4.8320.341150.198292X-RAY DIFFRACTION100
4.832-5.2910.345100.206294X-RAY DIFFRACTION100
5.291-5.9120.44840.205251X-RAY DIFFRACTION100
5.912-6.8190.224130.207218X-RAY DIFFRACTION100
6.819-8.3330.18180.187195X-RAY DIFFRACTION100
8.333-11.710.189140.121143X-RAY DIFFRACTION100
11.71-46.780.07850.23888X-RAY DIFFRACTION98.9362

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