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- PDB-2kgi: Solution structure of JARID1A C-terminal PHD finger in complex wi... -

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Basic information

Entry
Database: PDB / ID: 2kgi
TitleSolution structure of JARID1A C-terminal PHD finger in complex with H3(1-9)K4me3
Components
  • H3(1-9)K4me3
  • Histone demethylase JARID1A
KeywordsMETAL BINDING PROTEIN / PHD finger / JARID1A / histone modification / leukemia / Alternative splicing / Chromatin regulator / Developmental protein / Dioxygenase / Iron / Metal-binding / Nucleus / Oxidoreductase / Phosphoprotein / Polymorphism / Transcription / Transcription regulation / Zinc / Zinc-finger
Function / homology
Function and homology information


facultative heterochromatin formation / [histone H3]-trimethyl-L-lysine4 demethylase / histone H3K4me/H3K4me2/H3K4me3 demethylase activity / regulation of DNA-binding transcription factor activity / enzyme inhibitor activity / histone demethylase activity / Chromatin modifications during the maternal to zygotic transition (MZT) / circadian regulation of gene expression / HDMs demethylate histones / chromatin DNA binding ...facultative heterochromatin formation / [histone H3]-trimethyl-L-lysine4 demethylase / histone H3K4me/H3K4me2/H3K4me3 demethylase activity / regulation of DNA-binding transcription factor activity / enzyme inhibitor activity / histone demethylase activity / Chromatin modifications during the maternal to zygotic transition (MZT) / circadian regulation of gene expression / HDMs demethylate histones / chromatin DNA binding / histone binding / transcription coactivator activity / transcription cis-regulatory region binding / chromatin remodeling / regulation of DNA-templated transcription / chromatin / nucleolus / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
: / : / : / : / Lysine-specific demethylase-like domain / : / PLU-1-like protein / Lysine-specific demethylase 5, C-terminal helical domain / Zinc finger, C5HC2-type / C5HC2 zinc finger ...: / : / : / : / Lysine-specific demethylase-like domain / : / PLU-1-like protein / Lysine-specific demethylase 5, C-terminal helical domain / Zinc finger, C5HC2-type / C5HC2 zinc finger / 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 / ARID/BRIGHT DNA binding 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 5A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsSong, J. / Wang, Z. / Patel, D.J.
CitationJournal: Nature / Year: 2009
Title: Haematopoietic malignancies caused by dysregulation of a chromatin-binding PHD finger.
Authors: Wang, G.G. / Song, J. / Wang, Z. / Dormann, H.L. / Casadio, F. / Li, H. / Luo, J.L. / Patel, D.J. / Allis, C.D.
History
DepositionMar 12, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 5, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: 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_assembly / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone demethylase JARID1A
B: H3(1-9)K4me3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,0394
Polymers6,9082
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Histone demethylase JARID1A / Jumonji/ARID domain-containing protein 1A / Retinoblastoma-binding protein 2 / RBBP-2


Mass: 5802.490 Da / Num. of mol.: 1 / Fragment: PHD-TYPE C-terminal ZINC FINGER
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: JARID1A, RBBP2, RBP2 / Plasmid: pRSFDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2(DE3)
References: UniProt: P29375, 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: Protein/peptide H3(1-9)K4me3


Mass: 1105.334 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: 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
1111H,15N-HSQC
1211H,13C-HSQC
131HN(CA)CB
141HBHA(CO)NH
151CBCA(CO)NH
1612D 1H-1H NOESY
171HCCHTOCSY
18115N-EDITED 1H,1H-NOESY
19113C-EDITED 1H,1H-NOESY
210115N IPAP HSQC
111113C,15N-FILTERED, 13C-EDITED 1H,1H-NOESY
112113C,15N-FILTERED, 2D 1H,1H-NOESY
213215N IPAP HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.2-0.5 MM [U-100% 13C; U-100% 15N] JARID1A PHD FINGER 3, 0.2-0.5 MM H3(1-9)K4ME3, 5 MM DTT, 1 MM ZINC CHLORIDE, 20 MM SODIUM PHOSPHATE, 90% H2O/10% D2O90% H2O/10% D2O
20.2-0.5 MM [U-100% 15N] JARID1A PHD FINGER 3, 0.2-0.5 MM H3(1-9)K4ME3, 5 MM DTT, 1 MM ZINC CHLORIDE, 10 MM MOPS, 12 MG/ML BACTERIOPHAGE PF1, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMJARID1A PHD finger 3[U-100% 13C; U-100% 15N]0.2-0.51
mMH3(1-9)K4Me30.2-0.51
0.5 mMDTT1
1 mMZINC ION1
20 mMsodium phosphate1
mMJARID1A PHD finger 3[U-100% 15N]0.2-0.52
mMH3(1-9)K4Me30.2-0.52
5 mMDTT2
1 mMZINC ION2
10 mMMOPS2
12 mg/mLbacteriophage Pf12
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
120 mM SODIUM PHOSPHATE 71 atm293.2 K
2200 mM NACL 71 atm298.2 K

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.18Schwieters, C. et al.refinement
CYANA2.1Guntert, P. et al.structure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: the structure was first calculated using CYANA and then refined using XPLOR-NIH
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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