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- PDB-1srk: Solution structure of the third zinc finger domain of FOG-1 -

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Basic information

Entry
Database: PDB / ID: 1srk
TitleSolution structure of the third zinc finger domain of FOG-1
ComponentsZinc finger protein ZFPM1
KeywordsTRANSCRIPTION / classical zinc finger
Function / homology
Function and homology information


tricuspid valve formation / negative regulation of mast cell differentiation / regulation of chemokine production / regulation of definitive erythrocyte differentiation / definitive erythrocyte differentiation / negative regulation of interleukin-4 production / mitral valve formation / atrial septum morphogenesis / primitive erythrocyte differentiation / megakaryocyte differentiation ...tricuspid valve formation / negative regulation of mast cell differentiation / regulation of chemokine production / regulation of definitive erythrocyte differentiation / definitive erythrocyte differentiation / negative regulation of interleukin-4 production / mitral valve formation / atrial septum morphogenesis / primitive erythrocyte differentiation / megakaryocyte differentiation / granulocyte differentiation / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Factors involved in megakaryocyte development and platelet production / cardiac muscle tissue morphogenesis / atrioventricular valve morphogenesis / embryonic hemopoiesis / platelet formation / megakaryocyte development / ventricular septum morphogenesis / outflow tract morphogenesis / homeostasis of number of cells / transcription repressor complex / erythrocyte differentiation / negative regulation of protein binding / transcription corepressor activity / positive regulation of type II interferon production / heart development / RNA polymerase II-specific DNA-binding transcription factor binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus / metal ion binding
Similarity search - Function
: / Zinc finger protein ZFPM1-like, PR domain / Zinc finger CCHC FOG-type / FOG family / Zinc finger CCHC FOG-type profile. / Zinc-finger of C2H2 type / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily ...: / Zinc finger protein ZFPM1-like, PR domain / Zinc finger CCHC FOG-type / FOG family / Zinc finger CCHC FOG-type profile. / Zinc-finger of C2H2 type / 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
Zinc finger protein ZFPM1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing, molecular dynamics, torsion angle dynamics
AuthorsSimpson, R.J.Y. / Lee, S.H.Y. / Bartle, N. / Matthews, J.M. / Mackay, J.P. / Crossley, M.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: A Classic Zinc Finger from Friend of GATA Mediates an Interaction with the Coiled-coil of Transforming Acidic Coiled-coil 3.
Authors: Simpson, R.J.Y. / Lee, S.H.Y. / Bartle, N. / Sum, E.Y. / Visvader, J.E. / Matthews, J.M. / Mackay, J.P. / Crossley, M.
History
DepositionMar 22, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / 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_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_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Zinc finger protein ZFPM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,8802
Polymers3,8141
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 1000structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Zinc finger protein ZFPM1 / Zinc finger protein multitype 1 / Friend of GATA protein 1 / Friend of GATA-1 / FOG-1


Mass: 3814.467 Da / Num. of mol.: 1 / Fragment: residues 328-360 / Mutation: E330K, L336R, E349A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: ZFPM1, FOG1, FOG / Plasmid: pGEX-2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: O35615
#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
1112D NOESY
1212D TOCSY
131DQF-COSY
242HNHA
NMR detailsText: Structure was determined using standard 2D homonuclear NMR spectroscopy

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Sample preparation

Details
Solution-IDContentsSolvent system
10.27 mM FOG-F3, 2mM TCEP, 1 mM ZnSO4, 95% H2O, 5% D2O95% H2O/5% D2O
20.245 mM 15N-FOG-F3, 2mM TCEP, 1 mM ZnSO4, 95% H2O, 5% D2O95% H2O/5% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10 mM 5.6 ambient 275 K
20 mM 5.6 ambient 275 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukerprocessing
XEASY1.3.13Bartels et aldata analysis
DYANA1.5Guntert et alrefinement
ARIA1.2Linge et alstructure solution
RefinementMethod: simulated annealing, molecular dynamics, torsion angle dynamics
Software ordinal: 1
Details: final structures were based on 859 unambiguous NOE-derived distance constraints, 20 ambiguous constraints and 31 dihedral angle restraints
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1000 / Conformers submitted total number: 20

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