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- PDB-7nw1: Crystal structure of UFC1 in complex with UBA5 -

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Basic information

Entry
Database: PDB / ID: 7nw1
TitleCrystal structure of UFC1 in complex with UBA5
Components
  • Ubiquitin-fold modifier-conjugating enzyme 1
  • Ubiquitin-like modifier-activating enzyme 5
KeywordsLIGASE / Ubiquitin like fold modifier enzyme 5 (UBA5) / E1 / Ubiquitin fold modifier 1 (UFM1) / Ubiquitin fold modifier conjugating enzyme2 (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
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / 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: 1.95 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 16, 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 / struct_ncs_dom_lim
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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
AAA: Ubiquitin-fold modifier-conjugating enzyme 1
BBB: Ubiquitin-fold modifier-conjugating enzyme 1
CCC: Ubiquitin-like modifier-activating enzyme 5
FFF: Ubiquitin-like modifier-activating enzyme 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,19523
Polymers42,6894
Non-polymers1,50619
Water91951
1
AAA: Ubiquitin-fold modifier-conjugating enzyme 1
FFF: Ubiquitin-like modifier-activating enzyme 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,72619
Polymers21,3452
Non-polymers1,38117
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4510 Å2
ΔGint13 kcal/mol
Surface area10380 Å2
MethodPISA
2
BBB: Ubiquitin-fold modifier-conjugating enzyme 1
CCC: Ubiquitin-like modifier-activating enzyme 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4694
Polymers21,3452
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-6 kcal/mol
Surface area10220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.204, 67.421, 133.984
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11Chains AAA BBB
22Chains CCC FFF

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASPASPCYSCYSAAAA3 - 1654 - 166
121ASPASPCYSCYSBBBB3 - 1654 - 166
212GLYGLYMETMETCCCC170 - 1833 - 16
222GLYGLYMETMETFFFD170 - 1833 - 16

NCS ensembles :
IDDetails
1local
2local

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Components

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Protein / Protein/peptide , 2 types, 4 molecules AAABBBCCCFFF

#1: Protein Ubiquitin-fold modifier-conjugating enzyme 1 / Ufm1-conjugating enzyme 1 / UFC1


Mass: 19543.447 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UFC1, CGI-126, HSPC155 / Plasmid: pET32A / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y3C8
#2: Protein/peptide 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 / UBA5


Mass: 1801.069 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBA5, UBE1DC1 / Plasmid: pET32A / Production host: Escherichia coli (E. coli) / References: UniProt: Q9GZZ9

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Non-polymers , 5 types, 70 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.13 Å3/Da / Density % sol: 42.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 35 mM citric acid, 65 mM bis-tris propane, 19% PEG3350, 100 mM lithium chloride

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 1.95→33.71 Å / Num. obs: 15162 / % possible obs: 46.5 % / Redundancy: 8.3 % / Biso Wilson estimate: 49.5 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.132 / Net I/σ(I): 11.7
Reflection shellResolution: 1.95→2.05 Å / Redundancy: 6.8 % / Num. unique obs: 152 / CC1/2: 0.478 / Rrim(I) all: 1.87 / % possible all: 3

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Processing

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

2z6o


Resolution: 1.95→23.761 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.902 / Cross valid method: NONE / ESU R: 0.662 / ESU R Free: 0.33
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2801 814 5.389 %Random selection
Rwork0.2146 14291 --
all0.219 ---
obs0.2185 15105 47.144 %-
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: 59.743 Å2
Baniso -1Baniso -2Baniso -3
1-0.059 Å20 Å20 Å2
2--0.502 Å2-0 Å2
3----0.562 Å2
Refinement stepCycle: LAST / Resolution: 1.95→23.761 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2902 0 98 51 3051
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0123053
X-RAY DIFFRACTIONr_angle_refined_deg1.5551.6494085
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3085350
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.0622.346162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.33215544
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.261520
X-RAY DIFFRACTIONr_chiral_restr0.1120.2370
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022276
X-RAY DIFFRACTIONr_nbd_refined0.2120.21339
X-RAY DIFFRACTIONr_nbtor_refined0.3110.22022
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.292
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2250.228
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1170.22
X-RAY DIFFRACTIONr_mcbond_it4.7025.7181412
X-RAY DIFFRACTIONr_mcangle_it7.1978.5471758
X-RAY DIFFRACTIONr_scbond_it6.0596.1251641
X-RAY DIFFRACTIONr_scangle_it9.1758.9982327
X-RAY DIFFRACTIONr_lrange_it12.70875.0694513
X-RAY DIFFRACTIONr_ncsr_local_group_10.1070.055188
X-RAY DIFFRACTIONr_ncsr_local_group_20.1170.05360
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.949-1.9990.58130.385480.39523210.3130.7192.19730.379
1.999-2.0540.41160.365980.36822610.7130.7524.59970.342
2.054-2.1130.383160.3611630.36321940.7320.7528.15860.343
2.113-2.1770.382150.2952650.29921340.6610.77513.12090.273
2.177-2.2480.429150.2953550.320840.8010.80417.75430.284
2.248-2.3260.334240.2864230.28919930.8420.82922.42850.262
2.326-2.4130.337280.2945660.29619490.8570.8330.47720.265
2.413-2.5110.25450.2646550.26418630.8850.87437.57380.235
2.511-2.6210.351490.2467930.25318060.8570.8946.62240.205
2.621-2.7470.241460.2449130.24417320.9240.89855.36950.194
2.747-2.8940.203510.2489970.24516270.9170.90764.4130.206
2.894-3.0660.283640.2411760.24315830.90.9178.33230.198
3.066-3.2740.299640.24113040.24414760.9070.91692.68290.196
3.274-3.5310.318630.22712940.23113790.9060.93398.40460.194
3.531-3.860.273530.20212190.20512800.9430.95499.3750.183
3.86-4.3010.274750.19711000.20211820.9410.95799.40780.186
4.301-4.9390.24670.1769630.1810350.9530.96699.51690.169
4.939-5.9850.298610.2018330.2089080.9380.95398.45810.196
5.985-8.2080.244390.2246870.2257300.9530.94599.45210.231
8.208-23.7610.311300.1664390.1764810.9590.9797.50520.203

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