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- PDB-2jtf: Solution Structure of the PHF20L1 MBT domain -

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Basic information

Entry
Database: PDB / ID: 2jtf
TitleSolution Structure of the PHF20L1 MBT domain
ComponentsPHD finger protein 20-like 1
KeywordsPROTEIN BINDING / Histone binding / MBT domain
Function / homology
Function and homology information


methylation-dependent protein binding / NSL complex / Formation of WDR5-containing histone-modifying complexes / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of protein catabolic process / regulation of transcription by RNA polymerase II / nucleoplasm / metal ion binding
Similarity search - Function
: / PHD finger protein 20-like protein 1 / PHD finger protein 20-like / Agenet domain, plant type / Tudor-like domain present in plant sequences. / PhD finger domain / mbt repeat / Lysine-specific demethylase 4, Tudor domain / Jumonji domain-containing protein 2A Tudor domain / Tudor domain ...: / PHD finger protein 20-like protein 1 / PHD finger protein 20-like / Agenet domain, plant type / Tudor-like domain present in plant sequences. / PhD finger domain / mbt repeat / Lysine-specific demethylase 4, Tudor domain / Jumonji domain-containing protein 2A Tudor domain / Tudor domain / Tudor domain / SH3 type barrels. - #140 / Zinc finger, PHD-type, conserved site / Zinc finger PHD-type signature. / Zinc finger, FYVE/PHD-type / SH3 type barrels. / Zinc finger, RING/FYVE/PHD-type / Roll / Mainly Beta
Similarity search - Domain/homology
PHD finger protein 20-like protein 1 / PHD finger protein 20-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, simulated annealing
AuthorsBrockmann, C. / Iberg, A.N. / Rehbein, K. / Diehl, A. / Bedford, M.T. / Oschkinat, H.
CitationJournal: To be Published
Title: Structural Analysis of Histone H4K20 Methyllysine Recognition by the MBT Domain of PHF20L1
Authors: Brockmann, C. / Iberg, A.N. / Rehbein, K. / Diehl, A. / Bedford, M.T. / Oschkinat, H.
History
DepositionJul 30, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / 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 / _struct_ref_seq_dif.details
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHD finger protein 20-like 1


Theoretical massNumber of molelcules
Total (without water)10,0551
Polymers10,0551
Non-polymers00
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 / 200structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein PHD finger protein 20-like 1 /


Mass: 10055.441 Da / Num. of mol.: 1 / Fragment: residues 1-74
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PHF20L1 / Plasmid: pGEX6-P1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96BT0, UniProt: A8MW92*PLUS

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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
1313D CBCA(CO)NH
1413D HN(CA)CB
1513D 1H-15N NOESY
1623D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.89 mM [U-100% 13C; U-100% 15N] PHF20L1, 20 mM potassium phosphate, 50 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
20.89 mM [U-100% 13C; U-100% 15N] PHF20L1, 20 mM potassium phosphate, 50 mM sodium chloride, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.89 mMPHF20L1[U-100% 13C; U-100% 15N]1
20 mMpotassium phosphate1
50 mMsodium chloride1
0.89 mMPHF20L1[U-100% 13C; U-100% 15N]2
20 mMpotassium phosphate2
50 mMsodium chloride2
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 300 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DMXBrukerDMX7502

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.6Brukercollection
SparkyGoddardchemical shift assignment
Analysis1.0.12Vranken, Boucher, Stevens, Fogh, Pajon, Llinas, Ulrich, Markley, Ionides and Lauechemical shift assignment
X-PLOR NIH2.13Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH2.13Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing, simulated annealing / Software ordinal: 1 / Details: in explicit water
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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