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- PDB-5iaa: Crystal structure of human UBA5 in complex with UFM1 -

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Basic information

Entry
Database: PDB / ID: 5iaa
TitleCrystal structure of human UBA5 in complex with UFM1
Components
  • Ubiquitin-fold modifier 1
  • Ubiquitin-like modifier-activating enzyme 5
KeywordsCELL CYCLE / Ubiquitin like protein and E1
Function / homology
Function and homology information


UFM1 activating enzyme activity / protein K69-linked ufmylation / protein ufmylation / megakaryocyte differentiation / regulation of type II interferon production / regulation of intracellular estrogen receptor signaling pathway / reticulophagy / neuromuscular process / negative regulation of protein import into nucleus / response to endoplasmic reticulum stress ...UFM1 activating enzyme activity / protein K69-linked ufmylation / protein ufmylation / megakaryocyte differentiation / regulation of type II interferon production / regulation of intracellular estrogen receptor signaling pathway / reticulophagy / neuromuscular process / negative regulation of protein import into nucleus / 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 / endoplasmic reticulum / Golgi apparatus / 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 / THIF-type NAD/FAD binding fold / ThiF family / Ubiquitin-activating enzyme / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / NAD(P)-binding Rossmann-like Domain ...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 / THIF-type NAD/FAD binding fold / ThiF family / Ubiquitin-activating enzyme / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / NAD(P)-binding Rossmann-like Domain / Ubiquitin-like domain superfamily / Roll / Rossmann fold / 3-Layer(aba) Sandwich / 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: 1.85 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
DepositionFeb 21, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 28, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)82,4056
Polymers82,2744
Non-polymers1312
Water2,630146
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10450 Å2
ΔGint-61 kcal/mol
Surface area27240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.081, 138.081, 99.178
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11TYRTYRVALVALAA68 - 34612 - 290
21TYRTYRVALVALBB68 - 34612 - 290
12VALVALGLYGLYCC4 - 834 - 83
22VALVALGLYGLYDD4 - 834 - 83

NCS ensembles :
ID
1
2

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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: 32198.885 Da / Num. of mol.: 2 / Fragment: UNP residues 57-346
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: 8938.331 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-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 146 / 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: 3.32 Å3/Da / Density % sol: 62.92 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 8% Tascimate, pH 7.0 and 16% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.3 / Wavelength: 0.896 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.896 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.871
11-h,-k,l20.129
ReflectionResolution: 1.85→76.3 Å / Num. obs: 93040 / % possible obs: 100 % / Redundancy: 18.5 % / Rmerge(I) obs: 0.174 / Net I/σ(I): 11.6
Reflection shellHighest resolution: 1.85 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WXS and 3H8V

1wxs

3h8v


Resolution: 1.85→69.04 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.987 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.021 / ESU R Free: 0.02 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20605 4641 5 %RANDOM
Rwork0.18741 ---
obs0.18834 88360 99.99 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.487 Å2
Baniso -1Baniso -2Baniso -3
1-29.33 Å20 Å20 Å2
2--29.33 Å20 Å2
3----58.66 Å2
Refinement stepCycle: LAST / Resolution: 1.85→69.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5070 0 2 146 5218
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0195180
X-RAY DIFFRACTIONr_bond_other_d0.0070.024986
X-RAY DIFFRACTIONr_angle_refined_deg1.7661.9637023
X-RAY DIFFRACTIONr_angle_other_deg1.3933.00111462
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4895650
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.96725.088226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.92515865
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4281522
X-RAY DIFFRACTIONr_chiral_restr0.1020.2812
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0215866
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021142
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5991.1962630
X-RAY DIFFRACTIONr_mcbond_other1.5991.1962629
X-RAY DIFFRACTIONr_mcangle_it2.4071.7723270
X-RAY DIFFRACTIONr_mcangle_other2.4071.7723271
X-RAY DIFFRACTIONr_scbond_it2.5131.4292549
X-RAY DIFFRACTIONr_scbond_other2.5131.4292549
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3662.0663753
X-RAY DIFFRACTIONr_long_range_B_refined6.73710.2735699
X-RAY DIFFRACTIONr_long_range_B_other6.73310.0725663
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A274180.1
12B274180.1
21C90460.09
22D90460.09
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 323 -
Rwork0.353 6486 -
obs--99.99 %
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)
10.5728-0.04190.01791.53-0.13472.25260.0141-0.0372-0.01940.0448-0.02680.0751-0.0422-0.09810.01270.13120.0650.00460.04030.00410.4924-75.71525.324-0.496
20.9326-0.0937-0.2111.7191-0.22032.01090.0267-0.0367-0.0493-0.0303-0.06820.11630.1631-0.04820.04150.22130.0624-0.01720.02950.00260.4936-74.773-3.931-6.923
31.4196-0.81190.04021.2492-1.62973.51350.3370.17950.0429-0.3132-0.11830.15120.0535-0.1439-0.21870.43280.2069-0.01940.1674-0.03840.5834-86.09329.354-24.202
41.7218-0.2388-1.44591.91710.64562.79-0.0268-0.0296-0.0147-0.07930.1938-0.2137-0.00810.432-0.1670.17250.0669-0.01990.1534-0.00120.5301-53.2960.586-20.582
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A68 - 346
2X-RAY DIFFRACTION2B68 - 346
3X-RAY DIFFRACTION3C4 - 83
4X-RAY DIFFRACTION4D4 - 83

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