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- PDB-2lmd: Minimal Constraints Solution NMR Structure of Prospero Homeobox p... -

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Basic information

Entry
Database: PDB / ID: 2lmd
TitleMinimal Constraints Solution NMR Structure of Prospero Homeobox protein 1 from Homo sapiens, Northeast Structural Genomics Consortium Target HR4660B
ComponentsProspero homeobox protein 1
KeywordsTRANSCRIPTION / Structural Genomics / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM / NESG / PSI-Biology / Protein Structure Initiative
Function / homology
Function and homology information


hepatocyte cell migration / branching involved in pancreas morphogenesis / positive regulation of cell cycle checkpoint / positive regulation of forebrain neuron differentiation / : / otic placode formation / negative regulation of bile acid biosynthetic process / olfactory placode formation / endocardium formation / lens placode formation involved in camera-type eye formation ...hepatocyte cell migration / branching involved in pancreas morphogenesis / positive regulation of cell cycle checkpoint / positive regulation of forebrain neuron differentiation / : / otic placode formation / negative regulation of bile acid biosynthetic process / olfactory placode formation / endocardium formation / lens placode formation involved in camera-type eye formation / dorsal spinal cord development / ventricular cardiac myofibril assembly / retina morphogenesis in camera-type eye / atrial cardiac muscle tissue morphogenesis / aorta smooth muscle tissue morphogenesis / lymphatic endothelial cell differentiation / embryonic retina morphogenesis in camera-type eye / positive regulation of sarcomere organization / cerebellar granule cell differentiation / positive regulation of heart growth / venous blood vessel morphogenesis / hepatocyte proliferation / lymphangiogenesis / acinar cell differentiation / lens fiber cell morphogenesis / chromatin => GO:0000785 / neuronal stem cell population maintenance / dentate gyrus development / cell fate determination / hepatocyte differentiation / positive regulation of neural precursor cell proliferation / pancreas development / neural tube development / lens development in camera-type eye / ventricular cardiac muscle tissue morphogenesis / DNA binding domain binding / negative regulation of viral genome replication / ventricular septum morphogenesis / LBD domain binding / skeletal muscle thin filament assembly / positive regulation of cyclin-dependent protein serine/threonine kinase activity / positive regulation of cell cycle / positive regulation of endothelial cell proliferation / positive regulation of endothelial cell migration / response to nutrient levels / liver development / kidney development / nuclear receptor binding / lung development / regulation of circadian rhythm / negative regulation of DNA-binding transcription factor activity / brain development / DNA-binding transcription repressor activity, RNA polymerase II-specific / circadian rhythm / sequence-specific double-stranded DNA binding / regulation of gene expression / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus / cytoplasm
Similarity search - Function
Prospero homeobox protein 1 / Homeo-prospero domain / Homeo-prospero domain / Homeo-prospero domain superfamily / Prospero homeodomain family / Homeo-prospero domain / Homeo-Prospero domain profile. / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Prospero homeobox protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
Model detailslowest energy, model 1
AuthorsRossi, P. / Lange, O.A. / Lee, H. / Maglaqui, M. / Janjua, H. / Ciccosanti, C. / Zhao, L. / Acton, T.B. / Xiao, R. / Everett, J.K. ...Rossi, P. / Lange, O.A. / Lee, H. / Maglaqui, M. / Janjua, H. / Ciccosanti, C. / Zhao, L. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Determination of solution structures of proteins up to 40 kDa using CS-Rosetta with sparse NMR data from deuterated samples.
Authors: Lange, O.F. / Rossi, P. / Sgourakis, N.G. / Song, Y. / Lee, H.W. / Aramini, J.M. / Ertekin, A. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Baker, D.
History
DepositionNov 29, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 21, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2012Group: Database references
Revision 1.2Jul 18, 2012Group: Database references
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Prospero homeobox protein 1


Theoretical massNumber of molelcules
Total (without water)20,7241
Polymers20,7241
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Prospero homeobox protein 1 / Homeobox prospero-like protein PROX1 / PROX-1


Mass: 20723.791 Da / Num. of mol.: 1 / Fragment: UNP residues 575-737
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PROX1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pMgK / References: UniProt: Q92786

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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 1H-13C HSQC
1323D HNCO
1423D CBCA(CO)NH
1523D HN(CA)CB
1613D 1H-13C arom NOESY
1713D 1H-15N NOESY
1823D 1H-13C-13C HSQC NOESY HSQC
1913D 1H-13C NOESY
11023D 1H-13C NOESY
11132D 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.96 mM [U-100% 13C; U-100% 15N] HR4660B, 200 mM sodium chloride, 10 mM DTT, 5 mM Calcium Chloride, 0.02 % sodium azide, 20 mM MES, 95% H2O/5% D2O95% H2O/5% D2O
20.2 mM [U-13C; U-15N; U-2H] HR4660B, 200 mM sodium chloride, 10 mM DTT, 5 mM Calcium Chloride, 0.02 % sodium azide, 20 mM MES, 95% H2O/5% D2O95% H2O/5% D2O
30.86 mM [5% 13C; U-100% 15N] HR4660B, 200 mM sodium chloride, 10 mM DTT, 5 mM Calcium Chloride, 0.02 % sodium azide, 20 mM MES, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.96 mMHR4660B-1[U-100% 13C; U-100% 15N]1
200 mMsodium chloride-21
10 mMDTT-31
5 mMCalcium Chloride-41
0.02 %sodium azide-51
20 mMMES-61
0.2 mMHR4660B-7[U-13C; U-15N; U-2H]2
200 mMsodium chloride-82
10 mMDTT-92
5 mMCalcium Chloride-102
0.02 %sodium azide-112
20 mMMES-122
0.86 mMHR4660B-13[5% 13C; U-100% 15N]3
200 mMsodium chloride-143
10 mMDTT-153
5 mMCalcium Chloride-163
0.02 %sodium azide-173
20 mMMES-183
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
CYANA3Guntert, Mumenthaler and Wuthrichgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TopSpinBruker Biospincollection
PINEBahrami, Markley, Assadi, and Eghbalniachemical shift assignment
SparkyGoddarddata analysis
TALOS+Shen, Cornilescu, Delaglio and Baxgeometry optimization
PALESPALES (Zweckstetter, Bax)geometry optimization
PSVSBhattacharya and Montelionedata analysis
RefinementMethod: molecular dynamics / Software ordinal: 1
Details: MD steps: 200 HEAT-1000 HOT 100 COOL, PARAM 19 timestep 0.004 ns heat, 0.004 ns hot, 0.001 ns cool, 0.3 weight rdc
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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