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- PDB-2ma5: Solution NMR structure of PHD type Zinc finger domain of Lysine-s... -

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Basic information

Entry
Database: PDB / ID: 2ma5
TitleSolution NMR structure of PHD type Zinc finger domain of Lysine-specific demethylase 5B (PLU-1/JARID1B) from Homo sapiens, Northeast Structural Genomics Consortium (NESG) Target HR7375C
ComponentsLysine-specific demethylase 5B
KeywordsOXIDOREDUCTASE / Structural Genomics / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM / NESG / PSI-Biology / Protein Structure Initiative / Zinc binding protein / PHD
Function / homology
Function and homology information


regulation of estradiol secretion / mammary duct terminal end bud growth / uterus morphogenesis / TFAP2 (AP-2) family regulates transcription of cell cycle factors / positive regulation of mammary gland epithelial cell proliferation / [histone H3]-trimethyl-L-lysine4 demethylase / histone H3K4me/H3K4me2/H3K4me3 demethylase activity / lens fiber cell differentiation / histone H3K4 demethylase activity / cellular response to fibroblast growth factor stimulus ...regulation of estradiol secretion / mammary duct terminal end bud growth / uterus morphogenesis / TFAP2 (AP-2) family regulates transcription of cell cycle factors / positive regulation of mammary gland epithelial cell proliferation / [histone H3]-trimethyl-L-lysine4 demethylase / histone H3K4me/H3K4me2/H3K4me3 demethylase activity / lens fiber cell differentiation / histone H3K4 demethylase activity / cellular response to fibroblast growth factor stimulus / branching involved in mammary gland duct morphogenesis / single fertilization / histone demethylase activity / response to fungicide / cellular response to leukemia inhibitory factor / post-embryonic development / Chromatin modifications during the maternal to zygotic transition (MZT) / HDMs demethylate histones / transcription corepressor activity / rhythmic process / sequence-specific double-stranded DNA binding / histone binding / nucleic acid binding / chromatin remodeling / negative regulation of DNA-templated transcription / chromatin / positive regulation of gene expression / regulation of DNA-templated transcription / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol
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 ...: / : / : / : / 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 5B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, null
Model detailslowest energy, model1
AuthorsHassan, F. / Ramelot, T.A. / Yang, Y. / Cort, J.R. / Janjua, H. / Kohan, E. / Lee, D. / Xiao, R. / Acton, T.B. / Everett, J.K. ...Hassan, F. / Ramelot, T.A. / Yang, Y. / Cort, J.R. / Janjua, H. / Kohan, E. / Lee, D. / Xiao, R. / Acton, T.B. / Everett, J.K. / Montelione, G.T. / Kennedy, M.A. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR structure of PHD type Zinc finger domain of Lysine-specific demethylase 5B (PLU-1/JARID1B) from Homo sapiens, Northeast Structural Genomics Consortium (NESG) Target HR7375C
Authors: Hassan, F. / Ramelot, T.A. / Yang, Y. / Cort, J.R. / Janjua, H. / Kohan, E. / Lee, D. / Xiao, R. / Acton, T.B. / Everett, J.K. / Montelione, G.T. / Kennedy, M.A.
History
DepositionJun 28, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 14, 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_nmr_spectrometer / 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_nmr_spectrometer.model / _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

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Assembly

Deposited unit
A: Lysine-specific demethylase 5B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,9713
Polymers6,8401
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Lysine-specific demethylase 5B / Cancer/testis antigen 31 / CT31 / Histone demethylase JARID1B / Jumonji/ARID domain-containing ...Cancer/testis antigen 31 / CT31 / Histone demethylase JARID1B / Jumonji/ARID domain-containing protein 1B / PLU-1 / Retinoblastoma-binding protein 2 homolog 1 / RBP2-H1


Mass: 6839.722 Da / Num. of mol.: 1 / Fragment: UNP residues 1487-1544
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: AVI tag cut with TEV protease / Gene: JARID1B, KDM5B, PLU1, RBBP2H1 / Plasmid: pET15Avi6HT_NESG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pMgK
References: UniProt: Q9UGL1, 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
1112D 1H-15N HSQC
1212D 1H-13C HSQC aliphatic
1313D 1H-15N NOESY NUS
1413D 1H-13C NOESY aliphatic NUS
1513D 1H-13C NOESY aromatic NUS
1632D 1H-15N HSQC
1732D 1H-13C HSQC aliphatic
1832D 1H-15N HSQC HIS
1911D 1H-15N HSQC T1 array
11011D 1H-15N HSQC T2 array
11112D 1H-15N HSQC NH2 only
11212D 1H-13C HSQC aromatic ct
11312D 1H-13C HSQC aromatic noct
11413D HN(CA)CB
11513D CBCA(CO)NH
11613D HN(CO)CA
11713D HNCO
11813D HBHA(CO)NH
11913D C(CO)NH
12013D H(CCO)NH
12113D (H)CCH-TOCSY
12213D CCH-TOCSY
12342D 1H-15N HSQC
12423D 1H-15N NOESY
12523D 1H-13C NOESY aliphatic
12623D 1H-13C NOESY aromatic

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Sample preparation

Details
Solution-IDContentsSolvent system
11.04 mM [U-100% 13C; U-100% 15N] HR7375C.005, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 10 % D2O, 50 uM DSS, 90% H2O/10% D2O90% H2O/10% D2O
21.04 mM [U-100% 13C; U-100% 15N] HR7375C.006, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 10 % D2O, 50 uM DSS, 90% H2O/10% D2O90% H2O/10% D2O
30.33 mM [U-100% 15N] 5% 13C fractionally labeled HR7375C.007, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 10 % D2O, 50 uM DSS, 90% H2O/10% D2O90% H2O/10% D2O
41.04 mM [U-100% 13C; U-100% 15N] HR7375C.005, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 100 % D2O, 50 uM DSS, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.04 mMHR7375C.005-1[U-100% 13C; U-100% 15N]1
0.02 %NaN3-21
10 mMDTT-31
5 mMCaCL2-41
100 mMNaCL-51
1 %Proteinase Inhibitors-61
20 mMMES pH 6.5-71
10 %D2O-81
50 uMDSS-91
1.04 mMHR7375C.006-10[U-100% 13C; U-100% 15N]2
0.02 %NaN3-112
10 mMDTT-122
5 mMCaCL2-132
100 mMNaCL-142
1 %Proteinase Inhibitors-152
20 mMMES pH 6.5-162
10 %D2O-172
50 uMDSS-182
0.33 mMHR7375C.007-19[U-100% 15N] 5% 13C fractionally labeled3
0.02 %NaN3-203
10 mMDTT-213
5 mMCaCL2-223
100 mMNaCL-233
1 %Proteinase Inhibitors-243
20 mMMES pH 6.5-253
10 %D2O-263
50 uMDSS-273
1.04 mMHR7375C.005-28[U-100% 13C; U-100% 15N]4
0.02 %NaN3-294
10 mMDTT-304
5 mMCaCL2-314
100 mMNaCL-324
1 %Proteinase Inhibitors-334
20 mMMES pH 6.5-344
100 %D2O-354
50 uMDSS-364
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker Avance IIBrukerAVANCE II8501
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA7503

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readrefinemen,structure solution,geometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichrefinement,geometry optimization,structure solution
AutoStructure2.1Huang, Tejero, Powers and Montelionedata analysis,refinement
NMRPipeNMRPipe-2008//nmrbin.linux9Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TopSpin2.4Bruker Biospincollection
VnmrJVariancollection
PINEBahrami, Markley, Assadi, and Eghbalniachemical shift assignment
Sparky3.113Goddarddata analysis
TALOS+Version 1.2009.0721.18Shen, Cornilescu, Delaglio and Baxgeometry optimization
PSVS1.4Bhattacharya, Montelionestructure validation
FMCGUIfmcgui2.1_linuxAlex Lemak, Cheryl Arrowmithrefinement
CNSrefinement
RefinementMethod: simulated annealing, null / Software ordinal: 1 / Details: CNS water refinement of Cyana structures, null
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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