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- PDB-5hkh: Crystal structure of Ufm1 in complex with UBA5 -

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Basic information

Entry
Database: PDB / ID: 5hkh
TitleCrystal structure of Ufm1 in complex with UBA5
Components
  • ASP-ASN-GLU-TRP-GLY-ILE-GLU-LEU-VAL
  • Ubiquitin-fold modifier 1
KeywordsSIGNALING PROTEIN
Function / homology
Function and homology information


UFM1 activating enzyme activity / protein ufmylation / protein K69-linked ufmylation / megakaryocyte differentiation / regulation of intracellular estrogen receptor signaling pathway / reticulophagy / neuromuscular process / negative regulation of protein import into nucleus / localization / response to endoplasmic reticulum stress ...UFM1 activating enzyme activity / protein ufmylation / protein K69-linked ufmylation / megakaryocyte differentiation / regulation of intracellular estrogen receptor signaling pathway / reticulophagy / neuromuscular process / negative regulation of protein import into nucleus / localization / response to endoplasmic reticulum stress / erythrocyte differentiation / brain development / Antigen processing: Ubiquitination & Proteasome degradation / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / negative regulation of apoptotic process / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / zinc ion binding / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ubiquitin-fold modifier 1 / Ubiquitin fold modifier 1 protein / 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 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin-like domain superfamily ...Ubiquitin-fold modifier 1 / Ubiquitin fold modifier 1 protein / 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 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-fold modifier 1 / Ubiquitin-like modifier-activating enzyme 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsHuber, J. / Doetsch, V. / Rogov, V.V. / Akutsu, M.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Structural and Functional Analysis of a Novel Interaction Motif within UFM1-activating Enzyme 5 (UBA5) Required for Binding to Ubiquitin-like Proteins and Ufmylation.
Authors: Habisov, S. / Huber, J. / Ichimura, Y. / Akutsu, M. / Rogova, N. / Loehr, F. / McEwan, D.G. / Johansen, T. / Dikic, I. / Doetsch, V. / Komatsu, M. / Rogov, V.V. / Kirkin, V.
History
DepositionJan 14, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2016Group: Database references
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin-fold modifier 1
B: ASP-ASN-GLU-TRP-GLY-ILE-GLU-LEU-VAL
C: Ubiquitin-fold modifier 1


Theoretical massNumber of molelcules
Total (without water)19,4653
Polymers19,4653
Non-polymers00
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-10 kcal/mol
Surface area9740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.656, 82.656, 62.027
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-108-

HOH

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Components

#1: Protein Ubiquitin-fold modifier 1


Mass: 9195.574 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UFM1, C13orf20, BM-002 / Production host: Escherichia coli (E. coli) / References: UniProt: P61960
#2: Protein/peptide ASP-ASN-GLU-TRP-GLY-ILE-GLU-LEU-VAL


Mass: 1074.141 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9GZZ9*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O

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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: 3.14 Å3/Da / Density % sol: 60.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium acetate, 0.01 M magnesium acetate, 30% polyethylene glycol 8000, 0.05 M sodium cacodylate, pH 8.0

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.072 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 2.55→46.88 Å / Num. obs: 8280 / % possible obs: 100 % / Redundancy: 19.4 % / Net I/σ(I): 41.5

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Processing

Software
NameVersionClassification
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WXS

1wxs


Resolution: 2.55→46.877 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.08
RfactorNum. reflection% reflection
Rfree0.2476 810 9.81 %
Rwork0.1931 --
obs0.1984 8261 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 85.39 Å2 / Biso mean: 47.31 Å2 / Biso min: 28.33 Å2
Refinement stepCycle: final / Resolution: 2.55→46.877 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1317 0 0 25 1342
Biso mean---47.14 -
Num. residues----174
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011344
X-RAY DIFFRACTIONf_angle_d1.2581828
X-RAY DIFFRACTIONf_chiral_restr0.076219
X-RAY DIFFRACTIONf_plane_restr0.006234
X-RAY DIFFRACTIONf_dihedral_angle_d14.445492
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.5502-2.70990.30511260.241612401366
2.7099-2.91910.33641300.24112001330
2.9191-3.21280.27791430.227712191362
3.2128-3.67760.27291510.211712241375
3.6776-4.63270.20321120.164312681380
4.6327-46.88460.23071480.181513001448

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