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- PDB-2naa: NSD1-PHD_5-C5HCH tandem domain structure -

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Basic information

Entry
Database: PDB / ID: 2naa
TitleNSD1-PHD_5-C5HCH tandem domain structure
ComponentsHistone-lysine N-methyltransferase, H3 lysine-36 and H4 lysine-20 specific
KeywordsTRANSCRIPTION / NSD1 / PHD5C5HCH / PHD finger / tandem
Function / homology
Function and homology information


[histone H3]-lysine36 N-dimethyltransferase / histone H4K20 methyltransferase activity / regulation of peptidyl-serine phosphorylation / histone H3K36 dimethyltransferase activity / PKMTs methylate histone lysines / histone H3K36 methyltransferase activity / nuclear retinoic acid receptor binding / gastrulation with mouth forming second / nuclear thyroid hormone receptor binding / histone methyltransferase complex ...[histone H3]-lysine36 N-dimethyltransferase / histone H4K20 methyltransferase activity / regulation of peptidyl-serine phosphorylation / histone H3K36 dimethyltransferase activity / PKMTs methylate histone lysines / histone H3K36 methyltransferase activity / nuclear retinoic acid receptor binding / gastrulation with mouth forming second / nuclear thyroid hormone receptor binding / histone methyltransferase complex / nuclear androgen receptor binding / histone methyltransferase activity / nuclear retinoid X receptor binding / nuclear estrogen receptor binding / transcription coregulator activity / transcription corepressor activity / methylation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin binding / regulation of DNA-templated transcription / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / zinc ion binding / nucleus
Similarity search - Function
: / : / : / : / : / : / : / NSD, Cys-His rich domain / NSD Cys-His rich domain / AWS domain ...: / : / : / : / : / : / : / NSD, Cys-His rich domain / NSD Cys-His rich domain / AWS domain / AWS domain / AWS domain profile. / associated with SET domains / Cysteine-rich motif following a subset of SET domains / Post-SET domain / Post-SET domain profile. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / Zinc/RING finger domain, C3HC4 (zinc finger) / SET domain / SET domain profile. / SET domain / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / Herpes Virus-1 / 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, RING-type / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Histone-lysine N-methyltransferase, H3 lysine-36 specific
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsBerardi, A. / Quilici, G. / Spiliotopoulos, D. / Musco, G.
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: Structural basis for PHDVC5HCHNSD1-C2HRNizp1 interaction: implications for Sotos syndrome.
Authors: Berardi, A. / Quilici, G. / Spiliotopoulos, D. / Corral-Rodriguez, M.A. / Martin-Garcia, F. / Degano, M. / Tonon, G. / Ghitti, M. / Musco, G.
History
DepositionDec 22, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1May 4, 2016Group: Database references
Revision 1.2Jun 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_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_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone-lysine N-methyltransferase, H3 lysine-36 and H4 lysine-20 specific
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,7425
Polymers10,4801
Non-polymers2624
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 40structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Histone-lysine N-methyltransferase, H3 lysine-36 and H4 lysine-20 specific / H3-K36-HMTase / H4-K20-HMTase / Nuclear receptor-binding SET domain-containing protein 1 / NR- ...H3-K36-HMTase / H4-K20-HMTase / Nuclear receptor-binding SET domain-containing protein 1 / NR-binding SET domain-containing protein


Mass: 10480.036 Da / Num. of mol.: 1 / Fragment: UNP residues 2014-2104
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nsd1 / Production host: Escherichia coli (E. coli)
References: UniProt: O88491, histone-lysine N-methyltransferase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / 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
1132D 1H-15N HSQC
1252D 1H-13C HSQC
1312D 1H-1H TOCSY
1442D 1H-1H TOCSY
1512D 1H-1H NOESY
1642D 1H-1H NOESY
1723D CBCA(CO)NH
1823D C(CO)NH
1923D HNCO
11023D HNCA
11123D H(CCO)NH
11253D (H)CCH-TOCSY
11333D HNHA
11423D HN(CA)CB
11533D 1H-15N NOESY
11653D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.3 mM protein_1, 90% H2O/10% D2O90% H2O/10% D2O
20.3 mM [U-99% 13C; U-99% 15N] protein_1, 90% H2O/10% D2O90% H2O/10% D2O
30.3 mM [U-99% 15N] protein_1, 90% H2O/10% D2O90% H2O/10% D2O
40.3 mM protein_1, 100% D2O100% D2O
50.3 mM [U-99% 13C; U-99% 15N] protein_1, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.3 mMentity_1-11
0.3 mMentity_1-2[U-99% 13C; U-99% 15N]2
0.3 mMentity_1-3[U-99% 15N]3
0.3 mMentity_1-44
0.3 mMentity_1-5[U-99% 13C; U-99% 15N]5
Sample conditionsIonic strength: 0.150 / pH: 6.3 / Pressure: ambient / Temperature: 295 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE9002

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Processing

NMR software
NameVersionDeveloperClassification
ARIA2.3Linge, O'Donoghue and Nilgesstructure solution
ARIArefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1344 / NOE intraresidue total count: 631 / NOE long range total count: 303 / NOE medium range total count: 137 / NOE sequential total count: 273 / Hydrogen bond constraints total count: 7 / Protein phi angle constraints total count: 57 / Protein psi angle constraints total count: 57
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 40 / Conformers submitted total number: 15

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