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- PDB-2mpl: Solution structure of the PR domain of FOG-1 -

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Basic information

Entry
Database: PDB / ID: 2mpl
TitleSolution structure of the PR domain of FOG-1
ComponentsZinc finger protein ZFPM1
KeywordsTRANSCRIPTION / PR domain / FOG-1 / GATA-1 / zinc-finger protein
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 / torsion angle dynamics, simulated annealing
Model detailslowest energy, model1
AuthorsMackay, J.P. / Clifton, M.K. / Westman, B.J. / Blobel, G.A.
CitationJournal: Plos One / Year: 2014
Title: The Identification and Structure of an N-Terminal PR Domain Show that FOG1 Is a Member of the PRDM Family of Proteins.
Authors: Clifton, M.K. / Westman, B.J. / Thong, S.Y. / O'Connell, M.R. / Webster, M.W. / Shepherd, N.E. / Quinlan, K.G. / Crossley, M. / Blobel, G.A. / Mackay, J.P.
History
DepositionMay 26, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
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_software.name / _pdbx_nmr_spectrometer.model
Revision 1.2May 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 ZFPM1


Theoretical massNumber of molelcules
Total (without water)14,0611
Polymers14,0611
Non-polymers00
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 / 500structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 14060.939 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Fog, Fog1, Zfpm1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O35615

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1212D 1H-1H NOESY
1333D CBCA(CO)NH
1433D HNCO
1533D HN(CA)CB
1633D HBHA(CO)NH
1733D HN(CO)CA
1833D HNCA
1933D (H)CCH-TOCSY
11033D HNHA
11133D 1H-15N NOESY
11233D 1H-15N TOCSY
11333D (H)CCH-COSY
11433D HNHB

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5-1 mM FOG-1 PR, 20 mM sodium phosphate, 0.01 mM DSS, 95% H2O/5% D2O95% H2O/5% D2O
20.5-1 mM [U-100% 15N] FOG-1 PR, 20 mM sodium phosphate, 0.01 mM DSS, 95% H2O/5% D2O95% H2O/5% D2O
30.5-1 mM [U-100% 13C; U-100% 15N] FOG-1 PR, 20 mM sodium phosphate, 0.01 mM DSS, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMFOG-1 PR-10.5-11
20 mMsodium phosphate-21
0.01 mMDSS-31
mMFOG-1 PR-4[U-100% 15N]0.5-12
20 mMsodium phosphate-52
0.01 mMDSS-62
mMFOG-1 PR-7[U-100% 13C; U-100% 15N]0.5-13
20 mMsodium phosphate-83
0.01 mMDSS-93
Sample conditionsIonic strength: 0.06 / 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
TopSpin3Bruker Biospinprocessing
Sparky3Goddardchemical shift assignment
Sparky3Goddardpeak picking
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
Details: Initial structure calculations including automated NOE assignment carried out in CYANA. Calculations carried out with iterative manual assignment until no restraint violations remained., ...Details: Initial structure calculations including automated NOE assignment carried out in CYANA. Calculations carried out with iterative manual assignment until no restraint violations remained., RECOORD protocol carried out using unambiguous restraint list derived from CYANA calculations. 500 structures calculated using simulated annealing and the top 40 subject to water refinement. Top 20 from these were used to represent the final structure.
NMR constraintsNOE constraints total: 1244 / NOE intraresidue total count: 289 / NOE long range total count: 451 / NOE medium range total count: 124 / NOE sequential total count: 366 / Protein phi angle constraints total count: 89 / Protein psi angle constraints total count: 89
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 20

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