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- PDB-5l95: Crystal structure of human UBA5 in complex with UFM1 and AMP -

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Basic information

Entry
Database: PDB / ID: 5l95
TitleCrystal structure of human UBA5 in complex with UFM1 and AMP
Components
  • Ubiquitin-fold modifier 1
  • Ubiquitin-like modifier-activating enzyme 5
KeywordsCELL CYCLE / Ubiquitin like protein E1 / UBL
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 / ThiF/MoeB/HesA family / Ubiquitin-activating enzyme / THIF-type NAD/FAD binding fold / ThiF family / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / 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 / ThiF/MoeB/HesA family / Ubiquitin-activating enzyme / THIF-type NAD/FAD binding fold / ThiF family / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin-like domain superfamily / NAD(P)-binding Rossmann-like Domain / Roll / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / Ubiquitin-fold modifier 1 / Ubiquitin-like modifier-activating enzyme 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsOweis, W. / Padala, P. / Wiener, R.
Funding support Israel, 1items
OrganizationGrant numberCountry
BSF Israel
CitationJournal: Cell Rep / Year: 2016
Title: Trans-Binding Mechanism of Ubiquitin-like Protein Activation Revealed by a UBA5-UFM1 Complex.
Authors: Oweis, W. / Padala, P. / Hassouna, F. / Cohen-Kfir, E. / Gibbs, D.R. / Todd, E.A. / Berndsen, C.E. / Wiener, R.
History
DepositionJun 9, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2016Group: Database references
Revision 1.2Jan 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-like modifier-activating enzyme 5
B: Ubiquitin-like modifier-activating enzyme 5
C: Ubiquitin-fold modifier 1
D: Ubiquitin-fold modifier 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,6497
Polymers79,1714
Non-polymers4783
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11060 Å2
ΔGint-60 kcal/mol
Surface area27100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.875, 139.875, 99.742
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Ubiquitin-like modifier-activating enzyme 5 / 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


Mass: 30994.381 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBA5, UBE1DC1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9GZZ9
#2: Protein Ubiquitin-fold modifier 1


Mass: 8590.877 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
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 3.92 Å3/Da / Density % sol: 68.65 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.1M HEPES pH7.5, 10% PEG 6000 and 5% 2-Methyl-2,4-pentanediol (MPD)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.1→77 Å / Num. obs: 65695 / % possible obs: 99.8 % / Redundancy: 8.7 % / Rmerge(I) obs: 0.155 / Net I/σ(I): 8.5
Reflection shellHighest resolution: 2.1 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10_2142: ???)refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IAA

5iaa


Resolution: 2.1→76.999 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.77
RfactorNum. reflection% reflection
Rfree0.2218 3326 5.07 %
Rwork0.1983 --
obs0.1995 65664 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→76.999 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5040 0 25 193 5258
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065160
X-RAY DIFFRACTIONf_angle_d0.8847002
X-RAY DIFFRACTIONf_dihedral_angle_d13.7753093
X-RAY DIFFRACTIONf_chiral_restr0.053809
X-RAY DIFFRACTIONf_plane_restr0.006908
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.130.30831550.3112556X-RAY DIFFRACTION99
2.13-2.16180.32791490.31242541X-RAY DIFFRACTION100
2.1618-2.19560.34361220.29542571X-RAY DIFFRACTION99
2.1956-2.23160.31781620.28432575X-RAY DIFFRACTION99
2.2316-2.27010.37091590.31262502X-RAY DIFFRACTION99
2.2701-2.31140.29431100.25962610X-RAY DIFFRACTION100
2.3114-2.35580.25681290.24562596X-RAY DIFFRACTION100
2.3558-2.40390.28451290.24312571X-RAY DIFFRACTION100
2.4039-2.45620.23441230.23612602X-RAY DIFFRACTION100
2.4562-2.51330.25691490.21822547X-RAY DIFFRACTION100
2.5133-2.57620.2091270.21892595X-RAY DIFFRACTION100
2.5762-2.64590.21681530.20392596X-RAY DIFFRACTION100
2.6459-2.72370.20121260.19962586X-RAY DIFFRACTION100
2.7237-2.81160.21021280.1882585X-RAY DIFFRACTION100
2.8116-2.91210.20061480.19092609X-RAY DIFFRACTION100
2.9121-3.02870.2131250.18382587X-RAY DIFFRACTION99
3.0287-3.16660.18561250.17672617X-RAY DIFFRACTION100
3.1666-3.33350.17191400.16572607X-RAY DIFFRACTION100
3.3335-3.54240.19581520.17262577X-RAY DIFFRACTION100
3.5424-3.81590.20171470.17112628X-RAY DIFFRACTION100
3.8159-4.19990.1811450.16462614X-RAY DIFFRACTION100
4.1999-4.80750.18541290.15322652X-RAY DIFFRACTION100
4.8075-6.05660.21041460.19322659X-RAY DIFFRACTION100
6.0566-77.05080.22921480.18652755X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.56440.15490.2821.5198-0.49112.0580.0752-0.1151-0.03140.15230.00920.136-0.2093-0.05620.0490.1534-0.06950.01040.1340.00070.17153.8654-42.245615.8417
21.93350.9304-0.29721.9410.22771.7619-0.0459-0.01360.28390.18090.04170.47130.1444-0.3538-0.11490.2071-0.12710.03140.26340.02970.277728.7106-58.39529.1767
30.3446-0.18340.20310.6765-0.18660.8934-0.19360.04360.0295-0.32370.27130.179-0.2235-0.23080.03750.373-0.124-0.02810.2809-0.00590.285851.7109-31.3142-7.6828
40.54740.0662-0.24150.48950.3220.631-0.19590.0419-0.22350.1060.1968-0.09880.42760.22260.01930.4053-0.11430.02140.3667-0.00640.277343.6643-74.2674-4.2265
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 68:346)
2X-RAY DIFFRACTION2(chain B and resseq 68:346)
3X-RAY DIFFRACTION3(chain C and resseq 4:83)
4X-RAY DIFFRACTION4(chain D and resseq 4:83)

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