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- PDB-2mx2: UBX-L domain of VCIP135 -

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Basic information

Entry
Database: PDB / ID: 2mx2
TitleUBX-L domain of VCIP135
ComponentsDeubiquitinating protein VCIP135
KeywordsHYDROLASE / UBX domain / mitosis / Golgi
Function / homology
Function and homology information


Ovarian tumor domain proteases / endoplasmic reticulum membrane fusion / protein K11-linked deubiquitination / Golgi reassembly / protein K48-linked deubiquitination / Golgi stack / regulation of protein localization to chromatin / protein deubiquitination / Golgi organization / cysteine-type peptidase activity ...Ovarian tumor domain proteases / endoplasmic reticulum membrane fusion / protein K11-linked deubiquitination / Golgi reassembly / protein K48-linked deubiquitination / Golgi stack / regulation of protein localization to chromatin / protein deubiquitination / Golgi organization / cysteine-type peptidase activity / mitotic cell cycle / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / protein ubiquitination / synapse / DNA damage response / endoplasmic reticulum / nucleus
Similarity search - Function
Deubiquitinating protein VCPIP1 / OTU-like cysteine protease / OTU domain / OTU domain profile. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Deubiquitinating protein VCPIP1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / simulated annealing
Model detailsfewest violations, model1
AuthorsIwazu, T. / Murayama, S. / Igarashi, R. / Hrioaki, H. / Shirakawa, M. / Tochio, H.
CitationJournal: To be Published
Title: Structure and interaction mode of the UBX-L domain of VCIP135 determined by solution NMR spectroscopy
Authors: Iwazu, T. / Murayama, S. / Igarashi, R. / Hrioaki, H. / Shirakawa, M. / Tochio, H.
History
DepositionDec 7, 2014Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jul 13, 2016Provider: repository / Type: Initial release
Revision 2.0May 1, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_poly_seq_scheme / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_mon_prot_cis / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site.label_seq_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity_name_com.name / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_seq_type / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _struct_mon_prot_cis.label_seq_id / _struct_mon_prot_cis.pdbx_label_seq_id_2 / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Deubiquitinating protein VCIP135


Theoretical massNumber of molelcules
Total (without water)9,8161
Polymers9,8161
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein Deubiquitinating protein VCIP135 / Valosin-containing protein p97/p47 complex-interacting protein 1 / Valosin-containing protein ...Valosin-containing protein p97/p47 complex-interacting protein 1 / Valosin-containing protein p97/p47 complex-interacting protein p135 / VCP/p47 complex-interacting 135-kDa protein / Deubiquitinating protein VCPIP1


Mass: 9816.275 Da / Num. of mol.: 1 / Fragment: UBX-L domain, UNP residues 772-852
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Vcpip1, Vcip135 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8CF97, ubiquitinyl hydrolase 1

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D HN(CA)CB
1413D HNCA
1513D HN(CO)CA
1613D (H)CCH-TOCSY
1713D 1H-15N NOESY
1813D 1H-13C NOESY
1913D (H)CCH-COSY
11012D 1H-13C HSQC
11112D 1H-13C HSQC aliphatic

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Sample preparation

DetailsContents: 1.86 mM [U-13C; U-15N] VCIP135 UBX-1, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 1.86 mM / Component: VCIP135 UBX-1 / Isotopic labeling: [U-13C; U-15N]
Sample conditionsIonic strength: 50 / pH: 7.4 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX7001
Bruker DPXBrukerDPX6002

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
CNSBRUNGER, ADAMS, CLORE, GROS, NILGES AND READrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1

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