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- PDB-2m9w: Solution NMR Structure of Transcription Factor GATA-4 from Homo s... -

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Basic information

Entry
Database: PDB / ID: 2m9w
TitleSolution NMR Structure of Transcription Factor GATA-4 from Homo sapiens, Northeast Structural Genomics Consortium (NESG) Target HR4783B
ComponentsTranscription factor GATA-4
KeywordsTRANSCRIPTION / Structural Genomics / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) / PSI-Biology / Protein Structure Initiative
Function / homology
Function and homology information


: / atrial septum secundum morphogenesis / DNA-binding transcription factor binding => GO:0140297 / transdifferentiation / RNA polymerase II-specific DNA-binding transcription factor binding => GO:0061629 / atrioventricular valve formation / embryonic heart tube anterior/posterior pattern specification / positive regulation of cardioblast differentiation / intestinal epithelial cell differentiation / cardiac right ventricle morphogenesis ...: / atrial septum secundum morphogenesis / DNA-binding transcription factor binding => GO:0140297 / transdifferentiation / RNA polymerase II-specific DNA-binding transcription factor binding => GO:0061629 / atrioventricular valve formation / embryonic heart tube anterior/posterior pattern specification / positive regulation of cardioblast differentiation / intestinal epithelial cell differentiation / cardiac right ventricle morphogenesis / co-SMAD binding / cell growth involved in cardiac muscle cell development / atrial septum morphogenesis / cardiac muscle tissue regeneration / endocardial cushion development / cardiac ventricle morphogenesis / Physiological factors / response to xenobiotic stimulus => GO:0009410 / atrial septum primum morphogenesis / embryonic foregut morphogenesis / chromatin => GO:0000785 / YAP1- and WWTR1 (TAZ)-stimulated gene expression / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / endoderm development / positive regulation of BMP signaling pathway / regulation of cardiac muscle cell contraction / response to vitamin A / aortic valve morphogenesis / negative regulation of cardiac muscle cell apoptotic process / ventricular septum development / NFAT protein binding / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / heart looping / negative regulation of apoptotic signaling pathway / transcription factor binding / positive regulation of vascular endothelial growth factor production / cell fate commitment / response to mechanical stimulus / negative regulation of autophagy / cellular response to glucose stimulus / RNA polymerase II transcription regulatory region sequence-specific DNA binding / wound healing / RNA polymerase II transcription regulator complex / male gonad development / positive regulation of angiogenesis / blood coagulation / sequence-specific double-stranded DNA binding / cell-cell signaling / Factors involved in megakaryocyte development and platelet production / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / positive regulation of ERK1 and ERK2 cascade / nuclear body / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of DNA-templated transcription / protein kinase binding / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
GATA-type transcription activator, N-terminal / Transcription factor GATA-4/5/6 / GATA-type transcription activator, N-terminal / Transcription factor GATA / GATA-type zinc finger domain. / GATA-type zinc finger domain profile. / zinc finger binding to DNA consensus sequence [AT]GATA[AG] / GATA zinc finger / Zinc finger, GATA-type / Erythroid Transcription Factor GATA-1, subunit A ...GATA-type transcription activator, N-terminal / Transcription factor GATA-4/5/6 / GATA-type transcription activator, N-terminal / Transcription factor GATA / GATA-type zinc finger domain. / GATA-type zinc finger domain profile. / zinc finger binding to DNA consensus sequence [AT]GATA[AG] / GATA zinc finger / Zinc finger, GATA-type / Erythroid Transcription Factor GATA-1, subunit A / Erythroid Transcription Factor GATA-1; Chain A / Zinc finger, NHR/GATA-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Transcription factor GATA-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsXu, X. / Eletsky, A. / Lee, D. / Kohn, E. / Janjua, H. / Xiao, R. / Acton, T.B. / Everett, J.K. / Montelione, G.T. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR Structure of a Transcription Factor GATA-4 from Homo sapiens, Northeast Structural Genomics Consortium (NESG) Target HR4783B
Authors: Xu, X. / Eletsky, A. / Lee, D. / Kohn, E. / Janjua, H. / Xiao, R. / Acton, T. / Everett, J.K. / Montelione, G.T. / Szyperski, T.
History
DepositionJun 20, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 10, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 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_software / 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_software.name / _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
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: Transcription factor GATA-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,1392
Polymers7,0731
Non-polymers651
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Transcription factor GATA-4 / GATA-binding factor 4


Mass: 7073.291 Da / Num. of mol.: 1 / Fragment: GATA-type 2 zinc finger residues 262-321
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GATA4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pMgK / References: UniProt: P43694
#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 1H-15N HSQC
1212D CT 1H-13C HSQC ali
1313D HNCO
1413D CBCA(CO)NH
1513D HN(CA)CB
1612D CT 1H-13C HSQC aro
1713D simutaneous 13C-aromatic,13C-aliphatic,15N edited 1H-1H NOESY
1813D CCH-TOCSY
1913D HBHA(CO)NH
11012D 1H-15N HSQC His
11112D 1H-15N HSQC wide
11213D (H)CCH-COSY ali
11322D 1H-13C HSQC methyl

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Sample preparation

Details
Solution-IDContentsSolvent system
10.378 mM [U-100% 13C; U-100% 15N] HR4783B.009, 100 mM sodium chloride, 5 mM DTT, 10 mM Tris-HCl, 50 uM DSS, 0.02 % sodium azide, 50 uM ZINC ION, 90% H2O/10% D2O90% H2O/10% D2O
20.156 mM [U-5% 13C; U-100% 15N] HR4783B.009, 100 mM sodium chloride, 5 mM DTT, 10 mM Tris-HCl, 50 uM DSS, 0.02 % sodium azide, 50 uM ZINC ION, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.378 mMHR4783B.009-1[U-100% 13C; U-100% 15N]1
100 mMsodium chloride-21
5 mMDTT-31
10 mMTris-HCl-41
50 uMDSS-51
0.02 %sodium azide-61
50 uMZINC ION-71
0.156 mMHR4783B.009-8[U-5% 13C; U-100% 15N]2
100 mMsodium chloride-92
5 mMDTT-102
10 mMTris-HCl-112
50 uMDSS-122
0.02 %sodium azide-132
50 uMZINC ION-142
Sample conditionspH: 7.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 750 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
CYANA3Guntert, Mumenthaler and Wuthrichgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
AutoStructure2.1Huang, Tejero, Powers and Montelionedata analysis
AutoStructure2.1Huang, Tejero, Powers and Montelionerefinement
AutoAssign2.3.1Zimmerman, Moseley, Kulikowski and Montelionedata analysis
AutoAssign2.3.1Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
XEASYBartels et al.data analysis
XEASYBartels et al.peak picking
XEASYBartels et al.chemical shift assignment
VnmrJ2.3.1Variancollection
TALOS+Shen, Cornilescu, Delaglio and Baxgeometry optimization
PSVS1.4Bhattacharya, Montelionestructure validation
PROSAGuntertdata analysis
CSIWishart and Sykesdata analysis
CARA1.8.4Keller and Wuthrichdata analysis
CARA1.8.4Keller and Wuthrichpeak picking
CARA1.8.4Keller and Wuthrichchemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Structure determination was performed by runnning CYANA and ASDP in parallel using NOE-based constraints and phi and psi dihedral angle constraints from Talos+. Consensus peak assignments ...Details: Structure determination was performed by runnning CYANA and ASDP in parallel using NOE-based constraints and phi and psi dihedral angle constraints from Talos+. Consensus peak assignments were selected and used in iterative refinement with CYANA. The 20 conformers out of 100 with the lowest target function were further refined by simulated annealing in explicit water bath using the program CNS with PARAM19 force field.
NMR constraintsProtein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 10 / Protein psi angle constraints total count: 10
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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