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- PDB-7ovc: Structure of the human UFC1 protein in complex with the UBA5 C-te... -

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Basic information

Entry
Database: PDB / ID: 7ovc
TitleStructure of the human UFC1 protein in complex with the UBA5 C-terminal UFC1-binding motif.
Components
  • Ubiquitin-fold modifier-conjugating enzyme 1
  • Ubiquitin-like modifier-activating enzyme 5
KeywordsLIGASE / UFM1 / UBA5 / UFC1 / ufmylation / complex structure
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)
MethodSOLUTION NMR / molecular dynamics
AuthorsWesch, W. / Loehr, F. / Rogova, N. / Doetsch, V. / Rogov, V.V.
Funding support Germany, European Union, 3items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB1173 Germany
European Union (EU)875510European Union
The Structural Genomic Consortium (SGC)
CitationJournal: Int J Mol Sci / Year: 2021
Title: A Concerted Action of UBA5 C-Terminal Unstructured Regions Is Important for Transfer of Activated UFM1 to UFC1.
Authors: Wesch, N. / Lohr, F. / Rogova, N. / Dotsch, V. / Rogov, V.V.
History
DepositionJun 14, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin-fold modifier-conjugating enzyme 1
B: Ubiquitin-like modifier-activating enzyme 5


Theoretical massNumber of molelcules
Total (without water)22,5212
Polymers22,5212
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area2100 Å2
ΔGint-19 kcal/mol
Surface area11850 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

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


Mass: 19486.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UFC1, CGI-126, HSPC155 / Plasmid: pET39_Ub19 / Production host: Escherichia coli (E. coli) / Strain (production host): NEB T7 express / 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


Mass: 3034.459 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBA5, UBE1DC1 / Plasmid: pET39_Ub19 / Production host: Escherichia coli (E. coli) / Strain (production host): NEB T7 Express / References: UniProt: Q9GZZ9

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D [15N,1H]-TROSY-(H)C(CC)(CO)NH-TOCSY
121isotropic13D [15N,1H]-TROSY-H(C)(CC)(CO)NH-TOCSY
131isotropic43D BEST-[15N,1H]-TROSY-HN(CA)CB
141isotropic43D F1-13C/15N-filtered NOESY-[13C,1H]-HSQC
151isotropic43D F1-13C/15N-filtered NOESY-[15N,1H]-SOFAST-HMQC
161isotropic43D F1-13C/15N-filtered NOESY-[13C,1H]-SOFAST-HMQC (aro)
171isotropic43D NOESY-[13C,1H]-SOFAST-HMQC (aro)
181isotropic43D NOESY-[13C,1H]-HSQC (aliphatic region)
191isotropic43D NOESY-BEST-[15N,1H]-TROSY
1102isotropic43D BEST-[15N,1H]-TROSY-HNCA
1112isotropic43D BEST-[15N,1H]-TROSY-HN(CA)CB
1122isotropic43D F1-13C/15N-filtered NOESY-[13C,1H]-HSQC
1132isotropic13D [15N,1H]-TROSY-(H)C(CC)(CO)NH-TOCSY
1142isotropic33D NOESY [13C,1H]-HSQC
1152isotropic53D [15N,1H]-TROSY-H(CC)(CO)NH-TOCSY
1162isotropic23D NOESY-[15N,1H]-SOFAST-HMQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11.0 mM [U-100% 13C; U-100% 15N] Ubiquitin-fold modifier-conjugating enzyme 1, 1.0 mM Ubiquitin-like modifier-activating enzyme 5, 50 mM TRIS, 100 mM sodium chloride, 2 mM TCEP, 5 mM AEBSF protease inhibitor, 0.15 mM DSS, 95% H2O/5% D2O13C,15N-UFC1_NL-UBA5-R395% H2O/5% D2O
solution21.2 mM Ubiquitin-fold modifier-conjugating enzyme 1, 0.3 mM [U-100% 13C; U-100% 15N] Ubiquitin-like modifier-activating enzyme 5, 50 mM TRIS, 100 mM sodium chloride, 2 mM TCEP, 5 mM AEBSF protease inhibitor, 0.15 mM DSS, 95% H2O/5% D2O13C,15N-UBA5-R3_NL-UFC195% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMUbiquitin-fold modifier-conjugating enzyme 1[U-100% 13C; U-100% 15N]1
1.0 mMUbiquitin-like modifier-activating enzyme 5natural abundance1
50 mMTRISnatural abundance1
100 mMsodium chloridenatural abundance1
2 mMTCEPnatural abundance1
5 mMAEBSF protease inhibitornatural abundance1
0.15 mMDSSnatural abundance1
1.2 mMUbiquitin-fold modifier-conjugating enzyme 1natural abundance2
0.3 mMUbiquitin-like modifier-activating enzyme 5[U-100% 13C; U-100% 15N]2
50 mMTRISnatural abundance2
100 mMsodium chloridenatural abundance2
2 mMTCEPnatural abundance2
5 mMAEBSF protease inhibitornatural abundance2
0.15 mMDSSnatural abundance2
Sample conditionsIonic strength: 100 mM / Ionic strength err: 0.2 / Label: Condition_1 / pH: 7.5 / PH err: 0.05 / Pressure: AMBIENT atm / Pressure err: 0.01 / Temperature: 298 K / Temperature err: 0.2

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIBrukerAVANCE II6005
Bruker AVANCE III HDBrukerAVANCE III HD7001
Bruker AVANCE III HDBrukerAVANCE III HD8002
Bruker AVANCE NEOBrukerAVANCE NEO9003
Bruker AVANCE IIIBrukerAVANCE III9504

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.6.2Bruker Biospincollection
Sparky3.114Goddardchemical shift assignment
CYANA3.98Guntert, Mumenthaler and Wuthrichstructure calculation
OPALp1.4Koradi, R., Billeter, M. and Guentert, Prefinement
Sparky3.114Goddardpeak picking
RefinementMethod: molecular dynamics / Software ordinal: 4
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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