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- PDB-2nab: Nizp1-C2HR zinc finger structure -

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Basic information

Entry
Database: PDB / ID: 2nab
TitleNizp1-C2HR zinc finger structure
ComponentsZinc finger protein 496
KeywordsTRANSCRIPTION / Nizp1 / C2HR / zinc finger / NSD1
Function / homology
Function and homology information


Generic Transcription Pathway / : / nuclear body / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / DNA binding / nucleus / metal ion binding
Similarity search - Function
Zinc finger protein 496 / SCAN domain / SCAN domain superfamily / SCAN domain / SCAN box profile. / leucine rich region / Krueppel-associated box (KRAB) profile. / KRAB box / Krueppel-associated box / KRAB domain superfamily ...Zinc finger protein 496 / SCAN domain / SCAN domain superfamily / SCAN domain / SCAN box profile. / leucine rich region / Krueppel-associated box (KRAB) profile. / KRAB box / Krueppel-associated box / KRAB domain superfamily / Classic Zinc Finger / Zinc finger, C2H2 type / Double Stranded RNA Binding Domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Zinc finger protein 496
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsBerardi, A. / Quilici, G. / Spiliotopoulos, D. / Corral-Rodriguez, M. / Martin, F. / Degano, M. / Tonon, G. / Musco, G.
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: Structural basis for PHDVC5HCHNSD1-C2HRNizp1 interaction: implications for Sotos syndrome.
Authors: Berardi, A. / Quilici, G. / Spiliotopoulos, D. / Corral-Rodriguez, M.A. / Martin-Garcia, F. / Degano, M. / Tonon, G. / Ghitti, M. / Musco, G.
History
DepositionDec 22, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1May 4, 2016Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_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
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Zinc finger protein 496
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,0502
Polymers4,9851
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)15 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Zinc finger protein 496 / NSD1-interacting zinc finger protein 1 / Zinc finger protein with KRAB and SCAN domains 17


Mass: 4984.836 Da / Num. of mol.: 1 / Fragment: UNP residue 397-434
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Znf496, Nizp11, Zfp496, Zkscan17 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SXI5
#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
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1232D 1H-1H TOCSY
1342D 1H-1H TOCSY
1432D 1H-1H NOESY
1542D 1H-1H NOESY
1613D HNCA
1713D CBCA(CO)NH
1813D HNCO

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8 mM [U-99% 13C; U-99% 15N] sodium phosphate, 90% H2O/10% D2O90% H2O/10% D2O
20.8 mM [U-99% 15N] sodium phosphate, 90% H2O/10% D2O90% H2O/10% D2O
30.8 mM sodium phosphate, 90% H2O/10% D2O90% H2O/10% D2O
40.8 mM sodium phosphate, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMsodium phosphate-1[U-99% 13C; U-99% 15N]1
0.8 mMsodium phosphate-2[U-99% 15N]2
0.8 mMsodium phosphate-33
0.8 mMsodium phosphate-44
Sample conditionsIonic strength: 0.150 / pH: 6.3 / Pressure: ambient / Temperature: 295 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
NameDeveloperClassification
ARIALinge, O'Donoghue and Nilgesstructure solution
ARIArefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 569 / NOE intraresidue total count: 191 / NOE long range total count: 100 / NOE medium range total count: 31 / NOE sequential total count: 156 / Protein phi angle constraints total count: 20 / Protein psi angle constraints total count: 20
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 15

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