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- PDB-5ij4: Solution structure of AN1-type zinc finger domain from Cuz1 (Cdc4... -

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Basic information

Entry
Database: PDB / ID: 5ij4
TitleSolution structure of AN1-type zinc finger domain from Cuz1 (Cdc48 associated ubiquitin-like/zinc-finger protein-1)
ComponentsCDC48-associated ubiquitin-like/zinc finger protein 1
KeywordsMETAL BINDING PROTEIN
Function / homology
Function and homology information


cellular response to arsenic-containing substance / cellular response to arsenite ion / stress granule disassembly / proteasome binding / proteasome-mediated ubiquitin-dependent protein catabolic process / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
Zinc finger, AN1-type / AN1-like Zinc finger / AN1-like Zinc finger / Zinc finger AN1-type profile. / AN1-like Zinc finger
Similarity search - Domain/homology
CDC48-associated ubiquitin-like/zinc finger protein 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
AuthorsSun, Z.-Y.J. / Hanna, J. / Wagner, G. / Bhanu, M.K. / Allan, M. / Arthanari, H.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/Office of the Director5DP5-OD019800 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)PO1-GM047467 United States
National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB)PO1-EB002026 United States
CitationJournal: Plos One / Year: 2016
Title: Solution Structure of the Cuz1 AN1 Zinc Finger Domain: An Exposed LDFLP Motif Defines a Subfamily of AN1 Proteins.
Authors: Sun, Z.J. / Bhanu, M.K. / Allan, M.G. / Arthanari, H. / Wagner, G. / Hanna, J.
History
DepositionMar 1, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Structure summary / Category: entity / pdbx_audit_support
Item: _entity.pdbx_number_of_molecules / _pdbx_audit_support.funding_organization
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_spectrometer.model
Revision 1.3May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CDC48-associated ubiquitin-like/zinc finger protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,1353
Polymers6,0041
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide CDC48-associated ubiquitin-like/zinc finger protein 1 / CDC48-associated UBL/Zn-finger protein 1


Mass: 6003.831 Da / Num. of mol.: 1 / Fragment: residues 11-59
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: CUZ1, YNL155W, N1751 / Plasmid: pJH190
Details (production host): 6xHIS-Cuz1-AN1-ZnF (residues 11-59) in pET45b
Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: P53899
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D 1H-15N NOESY
122isotropic13D 1H-13C NOESY
132isotropic13D HNCA
142isotropic13D HN(CO)CA
152isotropic13D HNCO
162isotropic13D HN(CA)CO
172isotropic13D HN(CA)CB
182isotropic13D HN(COCA)CB
192isotropic13D C(CO)NH
1102isotropic13D H(CCO)NH
1112isotropic13D (H)CCH-TOCSY
1123isotropic22D NOESY
1133isotropic22D TOCSY
1142isotropic12D 1H-15N HSQC
1152isotropic12D 1H-13C HSQC
1162isotropic12D 1H-13C HSQC aromatic

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11.0 mM [U-100% 15N] cuz1, 5 mM Tris, 50 mM NaCl, 0.2 mM ZnCl2, 1 mM DTT, 90% H2O/10% D2O15N-cuz190% H2O/10% D2O
solution20.7 mM [U-100% 13C; U-100% 15N] cuz1, 5 mM Tris, 50 mM NaCl, 0.2 mM ZnCl2, 1 mM DTT, 90% H2O/10% D2O15N/13C-cuz190% H2O/10% D2O
solution30.85 mM cuz1, 5 mM [U-2H] Tris, 50 mM NaCl, 0.2 mM ZnCl2, 1 mM [U-2H] DTT, 100% D2Ounlabeled cuz1100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMcuz1[U-100% 15N]1
5 mMTrisnatural abundance1
50 mMNaClnatural abundance1
0.2 mMZnCl2natural abundance1
1 mMDTTnatural abundance1
0.7 mMcuz1[U-100% 13C; U-100% 15N]2
5 mMTrisnatural abundance2
50 mMNaClnatural abundance2
0.2 mMZnCl2natural abundance2
1 mMDTTnatural abundance2
0.85 mMcuz1natural abundance3
5 mMTris[U-2H]3
50 mMNaClnatural abundance3
0.2 mMZnCl2natural abundance3
1 mMDTT[U-2H]3
Sample conditionsIonic strength: 50 mM / Label: regular / pH: 7.5 / Pressure: 1 atm / Temperature: 25 C

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Agilent DD2AgilentDD26001
Bruker AVANCE IIIBrukerAVANCE III7502

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichpeak picking
hmsISTHyberts, S.G and Wagner, Gprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: simulated annealing with torsion angle dynamics
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 15

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