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- PDB-5n14: NMR structure calculation of a composite Cys2His2 type zinc finge... -

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Basic information

Entry
Database: PDB / ID: 5n14
TitleNMR structure calculation of a composite Cys2His2 type zinc finger protein containing a non-peptide (or oligourea) helical domain
ComponentsProtein (chimeric oligourea-peptide zinc finger)
KeywordsTRANSCRIPTION/DNA / ZINC FINGER / CHIMERIC / OULIGOUREAS / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


glomerular mesangial cell proliferation / positive regulation of glomerular metanephric mesangial cell proliferation / cellular response to interleukin-8 / regulation of progesterone biosynthetic process / regulation of protein sumoylation / cellular response to heparin / cellular response to mycophenolic acid / circadian temperature homeostasis / positive regulation of post-translational protein modification / positive regulation of hormone biosynthetic process ...glomerular mesangial cell proliferation / positive regulation of glomerular metanephric mesangial cell proliferation / cellular response to interleukin-8 / regulation of progesterone biosynthetic process / regulation of protein sumoylation / cellular response to heparin / cellular response to mycophenolic acid / circadian temperature homeostasis / positive regulation of post-translational protein modification / positive regulation of hormone biosynthetic process / double-stranded methylated DNA binding / hemi-methylated DNA-binding / positive regulation of gene expression via chromosomal CpG island demethylation / NGF-stimulated transcription / interleukin-1-mediated signaling pathway / histone acetyltransferase binding / skeletal muscle cell differentiation / locomotor rhythm / T cell differentiation / estrous cycle / BMP signaling pathway / regulation of neuron apoptotic process / response to glucose / positive regulation of chemokine production / positive regulation of interleukin-1 beta production / Regulation of PTEN gene transcription / response to ischemia / promoter-specific chromatin binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / circadian regulation of gene expression / response to insulin / negative regulation of canonical Wnt signaling pathway / cellular response to gamma radiation / positive regulation of miRNA transcription / sequence-specific double-stranded DNA binding / Interferon alpha/beta signaling / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / transcription cis-regulatory region binding / response to hypoxia / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / positive regulation of gene expression / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Early growth response protein 1, C-terminal / Early growth response, N-terminal / Domain of unknown function (DUF3432) / Early growth response N-terminal domain / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type
Similarity search - Domain/homology
Early growth response protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsVenkateshaiah M, V.K. / Salgado, G.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyFoldart France
CitationJournal: To Be Published
Title: NMR structure calculation of a composite Cys2His2 type zinc finger protein containing a non-peptide (or oligourea) helical domain.
Authors: Venkateshaiah Machohally, V.K. / Salgado, G. / Lombardo, C. / Mergny, J.L. / Guichard, G.
History
DepositionFeb 5, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 2.0May 22, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations
Category: atom_site / pdbx_audit_support ...atom_site / pdbx_audit_support / pdbx_distant_solvent_atoms / pdbx_nmr_software / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _pdbx_audit_support.funding_organization / _pdbx_distant_solvent_atoms.PDB_model_num / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance / _pdbx_nmr_software.name / _struct_conn.pdbx_dist_value
Revision 3.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer / struct_conn / struct_conn_type
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein (chimeric oligourea-peptide zinc finger)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,3202
Polymers3,2551
Non-polymers651
Water3,585199
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3180 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: Protein/peptide Protein (chimeric oligourea-peptide zinc finger)


Mass: 3254.846 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P18146*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / Source method: isolated from a natural source / Formula: H2O

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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
121isotropic12D 1H-13C HSQC
131isotropic12D 1H-1H TOCSY
141isotropic12D 1H-1H NOESY
171isotropic12D 1H-1H COSY
161isotropic22D 1H-1H TOCSY
151isotropic22D 1H-15N HSQC
181isotropic22D 1H-13C HSQC
191anisotropic22D 1H-1H NOESY

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Sample preparation

DetailsType: solution / Contents: 3.2 mM CL112, 90% H2O/10% D2O
Details: 3.2 mM CL112, pH 6.5 was adjusted using HCl and NaOH. To fold the CL112 Zn(ClO4)2 was added to supply the zinc ions to form metal coordination. Temperature 298K.
Label: CL112 / Solvent system: 90% H2O/10% D2O
SampleConc.: 3.2 mM / Component: CL112 / Isotopic labeling: natural abundance
Sample conditionsIonic strength: 0.1 M / Label: Condition_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCE IIIBrukerAVANCE III9501Equipped with CryoProbe
Bruker AVANCE IIIBrukerAVANCE III8002Equipped with CryoProbe

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Processing

NMR software
NameVersionDeveloperClassification
Sparky12Goddardchemical shift assignment
Amber12Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanstructure calculation
UCSF ChimeraPettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrinrefinement
TopSpinBruker Biospinprocessing
RefinementMethod: simulated annealing / Software ordinal: 5
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

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