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- PDB-2kzy: Solution NMR structure of the ZNF216 A20 zinc finger -

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Basic information

Entry
Database: PDB / ID: 2kzy
TitleSolution NMR structure of the ZNF216 A20 zinc finger
ComponentsZfand5 protein (Zinc finger protein 216 (Predicted), isoform CRA_a)
KeywordsMETAL BINDING PROTEIN / A20 domain / ZNF216 / Atrogene / zinc finger
Function / homology
Function and homology information


respiratory system process / smooth muscle tissue development / fibroblast migration / vasculature development / skeletal system morphogenesis / face development / platelet-derived growth factor receptor signaling pathway / in utero embryonic development / DNA binding / zinc ion binding / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #4770 / Zinc finger, AN1-type / AN1-like Zinc finger / AN1-like Zinc finger / Zinc finger AN1-type profile. / AN1-like Zinc finger / Zinc finger, A20-type / A20-like zinc finger / Zinc finger A20-type profile. / A20-like zinc fingers ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #4770 / Zinc finger, AN1-type / AN1-like Zinc finger / AN1-like Zinc finger / Zinc finger AN1-type profile. / AN1-like Zinc finger / Zinc finger, A20-type / A20-like zinc finger / Zinc finger A20-type profile. / A20-like zinc fingers / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
AN1-type zinc finger protein 5
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
Model detailslowest energy, model 1
AuthorsGarner, T.P. / Long, J.E. / Searle, M.S. / Layfield, R.
CitationJournal: To be Published
Title: Co-localisation of ubiquitin receptors ZNF216 and p62 in a ubiquitin-mediated ternary complex
Authors: Garner, T.P. / Strachan, J. / Long, J.E. / Layfield, R. / Searle, M.S.
History
DepositionJun 28, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Zfand5 protein (Zinc finger protein 216 (Predicted), isoform CRA_a)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,6042
Polymers6,5381
Non-polymers651
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 #1lowest energy

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Components

#1: Protein Zfand5 protein (Zinc finger protein 216 (Predicted), isoform CRA_a) / ZNF216-A20


Mass: 6538.265 Da / Num. of mol.: 1 / Fragment: A20
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Zfand5 / Production host: Escherichia coli (E. coli) / Strain (production host): c41 (DE3) / References: UniProt: B5DF11
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: NMR structure of ZNF216 residues 1 to 60 containing an A20 type zinc finger from residues 14 to 45, the termini are disordered.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1212D 1H-1H TOCSY
1322D 1H-15N HSQC
1423D 1H-15N NOESY
1523D 1H-15N TOCSY
1633D CBCA(CO)NH
1733D HN(CA)CB
1833D HNCO
1933D HN(CA)CO
11033D 1H-13C NOESY
11133D (H)CCH-TOCSY
11242D 1H-15N HSQC IPAP

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM ZNF216-A20-1, 50 uM Zinc-2, 0.1 mM DSS-3, 5 mM TRIS-4, 50 mM sodium chloride-5, 90% H2O/10% D2O90% H2O/10% D2O
21.2 mM [U-100% 15N] ZNF216-A20-6, 50 uM Zinc-7, 0.1 mM DSS-8, 5 mM TRIS-9, 50 mM sodium chloride-10, 90% H2O/10% D2O90% H2O/10% D2O
30.8 mM [U-100% 13C; U-100% 15N] ZNF216-A20-11, 50 uM Zinc-12, 0.1 mM DSS-13, 5 mM TRIS-14, 50 mM sodium chloride-15, 90% H2O/10% D2O90% H2O/10% D2O
41.2 mM [U-100% 15N] ZNF216-A20-16, 50 uM Zinc-17, 0.1 mM DSS-18, 5 mM TRIS-19, 50 mM sodium chloride-20, 7 % Polyacrylamide gel-21, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMZNF216-A20-11
50 uMZinc-21
0.1 mMDSS-31
5 mMTRIS-41
50 mMsodium chloride-51
1.2 mMZNF216-A20-6[U-100% 15N]2
50 uMZinc-72
0.1 mMDSS-82
5 mMTRIS-92
50 mMsodium chloride-102
0.8 mMZNF216-A20-11[U-100% 13C; U-100% 15N]3
50 uMZinc-123
0.1 mMDSS-133
5 mMTRIS-143
50 mMsodium chloride-153
1.2 mMZNF216-A20-16[U-100% 15N]4
50 uMZinc-174
0.1 mMDSS-184
5 mMTRIS-194
50 mMsodium chloride-204
7 %Polyacrylamide gel-214
Sample conditionsIonic strength: 0.1 / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospinprocessing
CcpNMR1.1.15CCPNchemical shift assignment
CcpNMR1.1.15CCPNchemical shift calculation
CcpNMR1.1.15CCPNpeak picking
CcpNMR1.1.15CCPNdata analysis
X-PLOR NIH2.14Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH2.14Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
Details: using NOE, dihedral and RDC restraints using XPLOR-NIH, incorperating soft restraints (NOE, dihedral and RDC) using XPLOR-NIH
NMR constraintsNOE constraints total: 724 / NOE intraresidue total count: 299 / NOE long range total count: 132 / NOE medium range total count: 110 / NOE sequential total count: 183 / Protein chi angle constraints total count: 12 / Protein other angle constraints total count: 61 / Protein phi angle constraints total count: 57 / Protein psi angle constraints total count: 48
NMR representativeSelection criteria: lowest energy
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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