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- PDB-6sap: Structure of the PUB domain from Ubiquitin Regulatory X domain pr... -

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Basic information

Entry
Database: PDB / ID: 6sap
TitleStructure of the PUB domain from Ubiquitin Regulatory X domain protein 1 (UBXD1)
ComponentsUBX domain-containing protein 6
KeywordsPROTEIN BINDING / UBXD1 / PUB domain / p97 / protein interaction / NMR solution structure
Function / homology
Function and homology information


endosome to lysosome transport via multivesicular body sorting pathway / ERAD pathway / macroautophagy / late endosome membrane / early endosome membrane / endosome / lysosomal membrane / centrosome / protein-containing complex / extracellular exosome ...endosome to lysosome transport via multivesicular body sorting pathway / ERAD pathway / macroautophagy / late endosome membrane / early endosome membrane / endosome / lysosomal membrane / centrosome / protein-containing complex / extracellular exosome / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
UBXN6, PUB domain / Domain present in ubiquitin-regulatory proteins / PUB-like domain superfamily / PUB domain / PUB domain / UBX domain / UBX domain / UBX domain profile. / domain in protein kinases, N-glycanases and other nuclear proteins / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
UBX domain-containing protein 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
AuthorsBeuck, C. / Bayer, P. / Blueggel, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationCRC 1093 Germany
CitationJournal: Biomolecules / Year: 2019
Title: Structure of the PUB Domain from Ubiquitin Regulatory X Domain Protein 1 (UBXD1) and Its Interaction with the p97 AAA+ ATPase.
Authors: Blueggel, M. / van den Boom, J. / Meyer, H. / Bayer, P. / Beuck, C.
History
DepositionJul 17, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 25, 2019Provider: 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: UBX domain-containing protein 6


Theoretical massNumber of molelcules
Total (without water)13,8231
Polymers13,8231
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, in addition 15N relaxation rates T1 & T2 by NMR
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7890 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein UBX domain-containing protein 6 / UBX domain-containing protein 1


Mass: 13822.567 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The first 4 residues represent a cloning artifact. / Source: (gene. exp.) Homo sapiens (human) / Gene: UBXN6, UBXD1, UBXDC2 / Plasmid: pET28a
Details (production host): encodes for His6-Tag with Thrombin cleavage site
Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 / References: UniProt: Q9BZV1

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
122isotropic12D 1H-13C HSQC aliphatic
131isotropic13D CBCA(CO)NH
141isotropic13D HN(CA)CB
151isotropic13D HNCO
161isotropic13D HN(CA)CO
171isotropic13D H(CCO)NH
181isotropic13D C(CO)NH
191isotropic13D 1H-15N TOCSY
1103isotropic13D 1H-15N NOESY
1112isotropic13D (H)CCH-COSY aliphatic
1122isotropic13D (H)CCH-TOCSY aliphatic
1131isotropic13D (H)CCH-TOCSY
1141isotropic13D 1H-13C NOESY aliphatic
1151isotropic13D 1H-13C NOESY aromatic
1161isotropic12D Histidin H(C)N-SOFAST-HMQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution1900 uM [U-98% 13C; U-98% 15N] UBXD1 PUB domain, 16 mM potassium phosphate, 34 mM sodium phosphate, 90 % H2O, 10 % [U-99% 2H] D2O, 0.1 mM DSS, 90% H2O/10% D2O13C_15N_H2O90% H2O/10% D2O
solution2500 uM [U-98% 13C; U-98% 15N] UBXD1 PUB domain, 16 mM potassium phosphate, 34 mM sodium phosphate, 100 % [U-99% 2H] D2O, 0.1 mM DSS, 100% D2O13C_15N_D2O100% D2O
solution3700 uM [U-98% 15N] UBXD1 PUB domain, 16 mM potassium phosphate, 34 mM sodium phosphate, 90 % H2O, 10 % [U-99% 2H] D2O, 90% H2O/10% D2O15N_H2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
900 uMUBXD1 PUB domain[U-98% 13C; U-98% 15N]1
16 mMpotassium phosphatenatural abundance1
34 mMsodium phosphatenatural abundance1
90 %H2Onatural abundance1
10 %D2O[U-99% 2H]1
0.1 mMDSSnatural abundance1
500 uMUBXD1 PUB domain[U-98% 13C; U-98% 15N]2
16 mMpotassium phosphatenatural abundance2
34 mMsodium phosphatenatural abundance2
100 %D2O[U-99% 2H]2
0.1 mMDSSnatural abundance2
700 uMUBXD1 PUB domain[U-98% 15N]3
16 mMpotassium phosphatenatural abundance3
34 mMsodium phosphatenatural abundance3
90 %H2Onatural abundance3
10 %D2O[U-99% 2H]3
Sample conditionsIonic strength: 50 mM / Label: conditions_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE II / Manufacturer: Bruker / Model: AVANCE II / Field strength: 700 MHz / Details: TCI cryoprobe

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.5Bruker Biospincollection
TopSpinBruker Biospinprocessing
CARA1.6Keller and Wuthrichchemical shift assignment
UNIO10Herrmannpeak picking
CYANA3.98.9Guntert, Mumenthaler and Wuthrichstructure calculation
YASARA11.12.31Kriegerrefinement
RefinementMethod: molecular dynamics / Software ordinal: 6
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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