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- PDB-2miq: Solution NMR Structure of PHD Type 1 Zinc Finger Domain 1 of Lysi... -

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Entry
Database: PDB / ID: 2miq
TitleSolution NMR Structure of PHD Type 1 Zinc Finger Domain 1 of Lysine-specific Demethylase Lid from Drosophila melanogaster, Northeast Structural Genomics Consortium (NESG) Target FR824J
ComponentsLysine-specific demethylase lid
KeywordsOXIDOREDUCTASE / Zinc finger / PSI-Biology / Structural Genomics / Northeast Structural Genomics Consortium / NESG / Chaperone-Enabled Studies of Epigenetic Regulation Enzymes / CEBS
Function / homology
Function and homology information


TFAP2 (AP-2) family regulates transcription of cell cycle factors / histone H4R3 demethylase activity / male germ-line stem cell population maintenance / synaptonemal complex organization / oocyte karyosome formation / larval somatic muscle development / [histone H3]-trimethyl-L-lysine4 demethylase / histone H3K4me/H3K4me2/H3K4me3 demethylase activity / negative regulation of stem cell differentiation / enzyme inhibitor activity ...TFAP2 (AP-2) family regulates transcription of cell cycle factors / histone H4R3 demethylase activity / male germ-line stem cell population maintenance / synaptonemal complex organization / oocyte karyosome formation / larval somatic muscle development / [histone H3]-trimethyl-L-lysine4 demethylase / histone H3K4me/H3K4me2/H3K4me3 demethylase activity / negative regulation of stem cell differentiation / enzyme inhibitor activity / Sin3-type complex / locomotor rhythm / histone reader activity / circadian regulation of gene expression / chromatin organization / chromatin remodeling / chromatin / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / metal ion binding / nucleus
Similarity search - Function
: / : / Lysine-specific demethylase 5, C-terminal helical domain / Lysine-specific demethylase-like domain / PLU-1-like protein / Zinc finger, C5HC2-type / C5HC2 zinc finger / ARID/BRIGHT DNA binding domain / ARID DNA-binding domain / ARID DNA-binding domain superfamily ...: / : / Lysine-specific demethylase 5, C-terminal helical domain / Lysine-specific demethylase-like domain / PLU-1-like protein / Zinc finger, C5HC2-type / C5HC2 zinc finger / ARID/BRIGHT DNA binding domain / ARID DNA-binding domain / ARID DNA-binding domain superfamily / ARID/BRIGHT DNA binding domain / ARID domain profile. / BRIGHT, ARID (A/T-rich interaction domain) domain / JmjN domain / jmjN domain / JmjN domain profile. / Small domain found in the jumonji family of transcription factors / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Lysine-specific demethylase 5
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsXu, X. / Eletsky, A. / Shastry, R. / Maglaqui, M. / Janjua, H. / Xiao, R. / Everett, J.K. / Sukumaran, D.K. / Montelione, G.T. / Szyperski, T. ...Xu, X. / Eletsky, A. / Shastry, R. / Maglaqui, M. / Janjua, H. / Xiao, R. / Everett, J.K. / Sukumaran, D.K. / Montelione, G.T. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG) / Chaperone-Enabled Studies of Epigenetic Regulation Enzymes (CEBS)
CitationJournal: To be Published
Title: Solution NMR Structure of PHD Type 1 Zinc Finger Domain 1 from Lysine-specific Demethylase Lid from Drosophila melanogaster, Northeast Structural Genomics Consortium (NESG) Target FR824J
Authors: Xu, X. / Eletsky, A. / Shastry, R. / Maglaqui, M. / Janjua, H. / Xiao, R. / Everett, J.K. / Sukumaran, D. / Montelione, G.T. / Szyperski, T.
History
DepositionDec 17, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2014Group: Structure summary
Revision 1.2Apr 23, 2014Group: Database references / Structure summary
Revision 1.3Jun 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_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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysine-specific demethylase lid
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,2323
Polymers10,1021
Non-polymers1312
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 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Lysine-specific demethylase lid / Histone demethylase lid / Jumonji/ARID domain-containing protein lid / Protein little imaginal ...Histone demethylase lid / Jumonji/ARID domain-containing protein lid / Protein little imaginal disks / Retinoblastoma-binding protein 2 homolog


Mass: 10101.601 Da / Num. of mol.: 1 / Fragment: PHD-type 1 zinc finger residues 414-504
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CG9088, lid / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pMgK
References: UniProt: Q9VMJ7, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / 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
1122D 1H-15N HSQC
1223D HNCO
1323D CBCA(CO)NH
1423D HN(CA)CB
1523D HBHA(CO)NH
1623D simutaneous 13C-aromatic,13C-aliphatic,15N edited 1H-1H NOESY
1722D 1H-13C ct HSQC aliphatic
1822D 1H-13C ct HSQC aromatic
1923D HN(CA)CO
11023D (H)CCH-COSY-ali
11123D (H)CCH-COSY aro
11223D (H)CCH-TOCSY ali
11312D gNfHSQC His
11412D 1H-15N HSQC
11512D 1H-13C ct-HSQC(28ms)
11612D 1H-13C ct- HSQC(42ms)
11712D 1H-13C ct-HSQC(56ms)
11812D J-modulation 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.321 mM 10% 13C and 100% 15N labeled protein, 90% H2O/10% D2O90% H2O/10% D2O
20.321 mM 13C and 15N labeled protein, 90% H2O/10% D2O90% H2O/10% D2O
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA7501
Varian INOVAVarianINOVA6002

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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
CNSBrunger, Adams, Clore, Gros, Nilges and Readprocessing
CNSBrunger, Adams, Clore, Gros, Nilges and Readdata analysis
PROSAGuntertrefinement
PROSAGuntertstructure solution
PROSAGuntertgeometry optimization
PROSAGuntertprocessing
PROSAGuntertdata analysis
CARAKeller and Wuthrichrefinement
CARAKeller and Wuthrichstructure solution
CARAKeller and Wuthrichgeometry optimization
CARAKeller and Wuthrichprocessing
CARAKeller and Wuthrichdata analysis
CSIDavid Wishart,Leigh Willard,Tim Jellard,Brian Sykesrefinement
CSIDavid Wishart,Leigh Willard,Tim Jellard,Brian Sykessstructure solution
CSIDavid Wishart,Leigh Willard,Tim Jellard,Brian Sykesgeometry optimization
CSIDavid Wishart,Leigh Willard,Tim Jellard,Brian Sykesprocessing
CSIDavid Wishart,Leigh Willard,Tim Jellard,Brian Sykesdata analysis
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
AutoAssign2.1Zimmerman, Moseley, Kulikowski and Montelionedata analysis
AutoAssign2.1Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
XEASYBartels et al.data analysis
VnmrJVariancollection
TALOS+Shen, Cornilescu, Delaglio and Baxgeometry optimization
PSVSBhattacharya, Montelionestructure validation
MOLMOLKoradi, Billeter and Wuthrichdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Structure determination was performed by running 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 running 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 Ensemble Information
NMR constraintsNOE constraints total: 490 / NOE intraresidue total count: 151 / NOE long range total count: 114 / NOE medium range total count: 59 / NOE sequential total count: 157 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 12 / Protein psi angle constraints total count: 12
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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